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Evolution of vertebrate sex chromosomes and dosage compensation

November 2015
Nature Reviews Genetics 17(1)

November 2015
17(1)

DOI:10.1038/nrg.2015.2

Authors:

La Trobe University

Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.

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Sex chromosomes wonderfully illustrate what I call ‘dumb

design’: systems that make no functional sense but that

can be understood in terms of evolution. Sex chromo-

some differentiation imposes problems of pairing and

meiosis, exposing one sex to “the perils of hemizygosity”

(REF.1), and creates differences of gene dosage between

males and females.

The acquisition of a new sex-determining gene defines

a pair of proto-sex chromosomes that differentiates as

the sex-specific partner degenerates2,3. Genes that are

lost from this sex-specific chromosome are present on

the partner chromosome in a single copy in one sex

and in two copies in the other sex. This imbalance is

expected to cause problems in equilibrating gene prod-

ucts between the sexes and in interactions with genes

on other chromosomes (autosomes).

Sex chromosomes evolved independently in many

animal groups and are defined by different genes

that acquired either a male-determining or a female-

determining function. In different lineages different

mechanisms compensate, to a greater or lesser extent,

for the 2:1 gene dosage difference created between the

sexes4. These mechanisms are best known in mammals,

in which one entire Xchromosome is epigenetically

silenced in the somatic cells of females. However, in

other vertebrates, whole-X chromosome inactivation is the

exception; in monotreme mammals, birds, reptiles and

fish, dosage compensation seems to be gene-specific

and partial at best.

This leaves us to debate the point of gene dosage

compensation. Do dosage differences matter all that

much5,6? If so, does this apply to all genes, or to only a

few dosage-sensitive genes? How and why did mammals

evolve a complex whole-chromosome inactivation sys-

tem? Is X chromosome inactivation in eutherian (pla-

cental) mammals an elaboration of a ‘leaky’ ancestral

mammalian silencing mechanism? Do different systems

generally work in the same way or do they at least share

molecular mechanisms?

In this Review, I discuss how sex chromosomes arose

and differentiated in vertebrates, and outline the con-

sequences of this differentiation for gene expression. I

discuss new data on the expression of genes borne on

sex chromosomes in mammals and other vertebrates,

and the mechanisms that are thought to modify gene

expression in different taxa. I conclude that, although

these mechanisms evolved independently and produce

very different outcomes, they share elements of ancient

silencing mechanisms.

Sex chromosome evolution

Sex chromosome systems are one of two basic types:

XX females and XY males, as in humans and other

mammals, or ZW females and ZZ males, as in birds

and snakes. In XY systems the dosage difference for

X-borne genes is 2:1 in favour of females, and in ZW

systems the dosage difference for Z-borne genes is 2:1

in favour ofmales.

Trobe Institute of Molecular

Science, La Trobe University,

Bundoora, Victoria 3186,

Australia, and the Australian

National University and

University of Canberra,

Canberra, Australian Capital

Territory 2000, Australia.

Correspondence to

j.graves@latrobe.edu.au

doi:10.1038/nrg.2015.2

Published online 30 Nov 2015

Sex chromosomes

Chromosomes that are

different in male and female

individuals and defined by a

gene that determines sex.

Mammals have XX females and

XY males (the heterogametic

sex, producing two kinds of

sperm); birds have ZZ males

and ZW females (the

heterogametic sex, producing

two kinds of eggs).

Sex-determining gene

A gene that turns on the

pathway that directs

the undifferentiated gonad to

form either a testis or an ovary.

Evolution of vertebrate sex

chromosomes and

dosage compensation

Jennifer A.Marshall Graves

Abstract | Differentiated sex chromosomes in mammals and other vertebrates evolved

independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes

share the problems of the unequal expression of the genes borne on sex chromosomes, both

between the sexes and with respect to autosomes. Dosage compensation of genes on sex

chromosomes is surprisingly variable — and can even be absent — in different vertebrate groups.

Systems that compensate for different gene dosages include a wide range of global, regional and

gene‑by‑gene processes that differ in their extent and their molecular mechanisms. However,

many elements of these control systems are similar across distant phylogenetic divisions and

show parallels to other gene silencing systems. These dosage systems cannot be identical by

descent but were probably constructed from elements of ancient silencing mechanisms that are

ubiquitous among vertebrates and shared throughout eukaryotes.

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Proto-sex chromosomes

The first stage of sex

chromosome differentiation

from an autosome.

Autosomes

All of the chromosomes that

are not sex chromosomes.

Xchromosome inactivation

Mechanism to epigenetically

silence one Xchromosome in

the somatic cells of female

mammals.

Dosage compensation

Mechanism to equalize the

expression of genes on sex

chromosomes between males

and females, and with respect

to autosomes.

Comparative mapping

Mapping orthologous genes in

different species.

Pseudoautosomal region

(PAR). Pairing region shared

by X and Y, or Z and W

chromosomes. PAR genes

show an autosomal pattern

of inheritance. The boundary

between the PAR and the

X- and Y- specific (or Z- and

W-specific) regions is called the

pseudoautosomal boundary.

Synteny

Genes are in synteny when

they are on the same

chromosome (literally, the

“same thread”).

The raw material of sex chromosomes. Vertebrate sex

chromosomes, as for all sex chromosomes, evolved

from autosome pairs. Comparative mapping across widely

divergent species has revealed the independent origins

of these proto-sex chromosomes. For example, genes on

the human XY chromosome pair are autosomal in birds7,

reptiles8 and even monotreme mammals9. The short arm

of the human Xchromosome is autosomal even in marsu-

pials, and its existence as a separate evolutionary block in

birds shows that it was added to the X and Ychromosomes

only in the ancestor of placental mammals10. Similarly,

genes on the bird ZW chromosome pair are autosomal in

mammals, snakes and most other reptiles (FIG.1). In some

groups, such as fish related to the medaka (genus Oryzias),

closely related species with similar karyotypes have

quite different sex chromosomes11,12. Thus, sex chromo-

somes in different lineages evolved independently from

different regions of the conserved vertebrategenome.

Although the ‘raw material’ was different, the course of

sex chromosome differentiation was remarkably parallel

in different vertebrates. First, genes around the sex-

determining locus were selected for a sex-specific func-

tion and recombination was suppressed to keep this

package of sex-specific genes together. The absence of

recombination resulted in the rapid degradation of the

sex-specific chromosome. The size of the region of the sex

chromosomes that still pairs at meiosis and recombines

(the pseudoautosomal region (PAR)) varies depend-

ing on the age of the sex chromosomes and the rate of

degradation. This variation is exemplified in vertebrates

with different degrees of sex chromosome differentiation.

For example, birds present a range of W degradation:

from extreme degradation in chickens to imperceptible

degradation in ratite birds such as the emu. Similarly,

the snake group includes vipers with highly differenti-

ated Z and W chromosomes and pythons with Z and W

chromosomes that seem to be identical (FIG.2). Although

mammals lack such a range of Ychromosome degrada-

tion, the PAR is shorter in mice and longer in cattle than

in humans, and two rodent groups contain species that

have completely eliminated the Ychromosome13,14.

Origins of sex-determining genes. The evolution of

non-homologous sex chromosome systems was trig-

gered by the acquisition or evolution of different sex-

determining genes, the ancestors of which can be inferred

from homologues in other vertebrates that lie on the

autosome that shares the same gene complement (shared

synteny). For example, the human sex-determining

gene SRY evolved from the highly conserved SOX3 (SRY -

box 3) gene on the Xchromosome15. SOX3 is autoso-

mal in other vertebrates that lack SRY16,17. Likewise,

DMRT1 (doublesex Mab3-related transcription factor 1;

related to the sexual differentiation genes doublesex in

Drosophila spp. and mab3 in Caenorhabditis elegans), is

located on the Z chromosome and is essential for male

development in birds18 but is autosomal, albeit involved

in sex determination, in other vertebrates19,20.

Nature Reviews | Genetics

DMRT1

AMH

SOX3

SRY

DMRT1

SOX3 SRY

Ancestral vertebrate

X Y X Y X Y X Y X Y X Y X Y

TSD

310 MYA

190 MYA

166 MYA

290 MYA

100 MYA

450 MYA

Reptiles Mammals

Fish

Therian

Prototherian

1234Micro

5. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Z W Z W Z W

Crocodiles Birds Monotremes Marsupials PlacentalsSnakesSole

SOX3

DMRT1

AMH

Figure 1 | Non-homologous vertebrate sex chromosomes and vertebrate phylogeny. The phylogeny of higher

vertebrates is shown, with divergence dates at nodes25. The karyotype of the ancestral mammal was inferred from

extremely conserved genomes of mammals, birds and reptiles. The five coloured genome regions became sex

chromosomes in different lineages and contain sex‑determining genes. AMH, anti‑Mullerian hormone; DMRT1, doublesex

Mab3‑related transcription factor 1; Micro, microchromosomes; MYA, million years ago; SOX3, SRY‑like HMG‑box

containing gene 3; SRY, sex determining region Y; TSD, temperature sex determination.

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Epigenetic

Epigenetic changes are

somatically heritable changes,

not in the DNA sequence,

but in the level to which the

gene is expressed.

RNA-seq

Next-generation sequencing

to quantify transcripts of

every gene in a particular

tissue and/or stage.

Fluorescence in situ

hybridization

(FISH). Hybridization of DNA

or RNA sequences trapped

on a substrate (for example, a

microscope slide) with probe

sequences specific for a

particular gene.

LINE elements

Long Interspersed Elements.

A group of repetitive

retrotransposed elements

widespread throughout

eukaryote genomes.

Although they evolved independently, some genes,

for example, SOX3 and DMRT1, are sex-determining in

several distantly related taxa, and the regions in which

they are embedded have independently become sex

chromosomes. Evidently, some genes are good at deter-

mining sex and are pressed into service again and again

by evolution21,22.

Diverse dosage compensation mechanisms

All differentiated sex chromosomes share the same prob-

lem: degradation of the sex-specific Y or W chromo-

somes has left many genes on their partner chromosome

(X or Z, respectively) represented by two doses in one sex

and a single dose in the other. Clinical observations over

many decades show that monosomy for even small auto-

somes is fatal in humans, and trisomy can result in severe

phenotypes, so it is not surprising to find systems that

exist to compensate for sex differences in genedosage.

Gene dosage compensation systems are surpris-

ingly different across vertebrate lineages23,24, in both

their extent and their molecular mechanisms. We can

distinguish between chromosome-wide (‘global’) com-

pensation in mammals and several varieties of regional

compensation, as well as systems in which compensation

seems to act on individual genes — or not act atall.

Much information on gene dosage compensation

has come from comparisons between different ver-

tebrate groups, so it is important to understand how

mammals, birds and reptiles, and amphibians and fish

are related (FIG.1). There are three groups of mammals:

placental (eutherian) mammals diverged from marsu-

pials (metatherian mammals) around 166 million years

ago (MYA), and therians (marsupials and placentals)

diverged from prototherians (the egg-laying mono-

tremes) around 190 MYA25. We can deduce the ages of

sex chromosomes and dosage compensation systems

from this phylogeny. For example, the mammalian XY

system and Xchromosome inactivation are shared by

placental and marsupial mammals but are not pres-

ent in monotremes or birds, so they must have arisen

190–166MYA2.

Placental mammals. In eutherians, the epigenetic silenc-

ing of one entire Xchromosome in the somatic cells of

females mostly compensates for the 2:1 dosage difference

between females and males. As a whole-chromosome

phenomenon, Xchromosome inactivation became a

paradigm for the epigenetic change that is associated

with gene silencing on a chromosome-widescale.

The inactivation of X-borne genes in mice and

humans has been exhaustively studied during the

50years since Mary Lyon put forward her hypothesis

that one of the Xchromosomes becomes randomly and

heritably inactivated early in embryogenesis in mice26–28.

In the past 3years, RNA-seq comparisons of the full tran-

scriptome of different species have confirmed that, for

most genes on the Xchromosome of primates and mice,

the female/male ratio of gene expression in different tis-

sues is nearly 1.0 (REF.29) (FIG.3), and this is also the case

for other mammals30. RNA fluorescence in situ hybridization

(RNA-FISH), which detects primary transcripts on

individual cells, shows that every cell is 1 X-active for

most genes in humans, mice and elephants31. In line

with Lyon’s original hypothesis, Xchromosome inacti-

vation is random, and clonal expansion of the two var-

iants produces a mosaic phenotype across the animal’s

body. From the point of initiation, inactivation spreads

rapidly throughout the Xchromosome and is perhaps

propagated by a high density of LINE elements32.

Xchromosome inactivation was shown to result from

transcriptional inhibition33, which is brought on by many

molecular changes, including DNA methylation34,35, bind-

ing with specialized histones such as macroH2A36 and

binding with core histones modified by the attachment

of various chemical groups37. These post-translational

histone modifications probably act by altering the binding

of DNA to other proteins, as well as through a direct

effect on the negatively charged histones. The methyl-

ated DNA and the variant and modified histones con-

struct a chromatin silencing domain that prevents the

binding of RNA polymerase II to promoters38.

This silencing domain was dramatically revealed by

Hi-C studies of the interactions between sequences on dif-

ferent parts of the human Xchromosome. Sequencing

regions of juxtaposed DNA that were held together with

formamide showed that the chromatin of the active

Xchromosome is arranged in many short-range domains

(similar to those found in autosomes) but that the inac-

tive Xchromosome contains two massive domains39,40

Nature Reviews | Genetics

X Y W Z

Marine turtles

Carinate birds

Boid snakes

MDF FDF

Crocodiles

Ratite birds

Many ﬁsh

Vipers

Autosome pair

Acquisition of (a)

sex-determining gene(s)

Proto-sex chromosomes

Degradation of Y or W

chromosome

Loss of recombination

Complete diﬀerentiation

of Y or W chromosome

Loss of Y or W chromosome

Humans

Mice

Kangaroos

Frogs

Many ﬁsh

Spiny rats

Mole voles

Figure 2 | Differentiation of sex chromosomes from an original autosome as the

sex-specific element (Y or W chromosome) degenerates, with examples of animal

species that exhibit different extents of sex chromosome differentiation. An

autosome pair first acquires a sex‑determining allele on one member of the pair (a male

determining factor (MDF) or a female determining factor (FDF)). Degeneration of the

neighbouring region occurs as sex‑specific alleles accrue and crossing over is

suppressed. Dashes between the chromosomes represent exchange between X and Y

or between Z and W chromosomes.

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Histone modifications

The post-translational covalent

attachment of a chemical

group such as acetyl, methyl

and ubiquitin groups, to

the protruding tail of one

of the core histones (H2, H3,

H4) around which DNA is

wound. Nomenclature (for

example, H3K27me3) refers to

the amino acid (for example, K)

at a specific position (for

example, 27) that is modified

by the addition of chemical

groups (for example, three

methyl groups (me3)).

Hi-C

Method for detecting

interactions between different

sequences by binding DNA

with formaldehyde, cutting

on either side of the bound

sequences and ligating

and sequencing the chimeric

DNA. This method can be

made allele-specific using SNPs

that differentiate active and

inactive Xchromosome DNA.

Homologous

Homology between genes or

chromosomes is described

as orthology (genes or

chromosomes in different

species that derived from the

same gene or chromosome) or

paralogy (genes in the same

species that have diverged

from a common ancestor, for

example, diverged genes on

the X and Ychromosomes).

within which large loops are anchored at repetitive

sequences that bind the ‘insulator sequence’ CTCF41.

The two domains are separated by a ‘hinge’ composed

of a repetitive element transcribed into a long non-cod-

ing RNA (ncRNA); the same element separates two large

domains on the mouse inactive Xchromosome39.

These molecular changes are initiated by coating the

Xchromosome that is to be inactivated with another

long ncRNA produced by the X-borne XIST gene

(X-inactive specific transcript). XIST is transcribed only

from its locus on the inactive Xchromosome42. XIST

expression is also subject to complex regulation that

involves DNA methylation and histone modification27,

and this regulation seems to be different in humans,

mice and rabbits30,43–45. Coating of the Xchromosome

with the XIST long ncRNA seems to recruit elements of

the chromatin silencing domain46, including variant and

modified histones and several non-histone proteins47.

Although Xchromosome inactivation is random in

cells of the embryo, paternal Xchromosome inactivation

occurs in the extra-embryonic membranes of rodents

and bovids48,49, and even to some extent in mouse

somatic tissues50. In the extra-embryonic membranes of

the mouse, a maternal imprint on XIST, which involves

modified histones51, silences this locus in the embryo,

permitting the maternal Xchromosome to stay active

while the paternal allele is expressed and inactivates the

paternal Xchromosome.

In humans (but not in mice) many genes on the short

arm of the inactive Xchromosome escape silencing

either completely or partially52,53, reflecting the recent

addition of this region to both the X and the Ychromo-

somes9. A few of these escaper genes have active copies

on the Ychromosome, but for most genes dosage differ-

ences do not seem to matter. Escape is also common on

the Xchromosomes of other placental mammals such as

cows and elephants54, but only a few loci on the mouse

Xchromosome escape inactivation55.

Marsupials. The marsupial Xchromosome is homologous

to two-thirds of the human Xchromosome9 but lacks

LINE accumulation56. Xchromosome inactivation

occurs in marsupials but differs from that in placental

mammals in that it is always paternal and conspicu-

ously tissue-specific, gene-specific and partial57. These

differences have seemed less important since escaper

genes were discovered on the human Xchromosome52

and paternal Xchromosome inactivation was described

in the extra-embryonic membranes of rodents and

bovids48,49 and in mouse somatic tissues50.

Inactive genes in marsupials, as in humans and mice,

are silenced at the transcriptional level58–60. The partial

expression of escaper genes on the kangaroo Xchromo-

some was shown by RNA-FISH to be due to transcrip-

tion in only a small proportion of cells rather than due

to a low level of transcription in each cell61, as was also

observed for escaper genes on the human and elephant

Xchromosomes31.

However, RNA-seq studies of gene expression on the

opossum Xchromosome in several tissues from males

and females showed the dosage of gene expression to be

close to 1.0 (REF.29), which suggests that compensation

is nearly complete in this species (FIG.3). The expression

of maternal and paternal X alleles in the opossum brain

and placenta59 confirms that maternal alleles are always

active, whereas most paternally derived alleles are com-

pletely or partially inactivated; the rate of escape was

14%, similar to that in humans. The rate of escape is

much higher (30%) in cultured kangaroo fibroblasts62

but tissue differences make comparisons difficult.

The molecular mechanism of Xchromosome inac-

tivation differs between placental and marsupial mam-

mals. No DNA methylation was found at the promoter

sites of inactive paternal alleles or of active maternal

alleles in the opossum59, confirming early studies that

revealed no methylation differences in the Xchromo-

some in marsupials63. Furthermore, no evidence of LINE

accumulation was observed56. Marsupials and placental

mammals share some histone modifications that are

associated with Xchromosome inactivation, including

acetylation (an activation mark) and methylation (gener-

ally an inactivation mark)58,59,64–67. Several histone modi-

fications are absent from escaper genes68, which suggests

that histone modifications are involved in gene-by-gene

silencing. However, several inactivation marks that are

present on the inactive Xchromosome in humans and

mice are absent in marsupials (for example, H4K20me1)

or are restricted to specific cell cycle phases (such as

H3K27me3 and H3K9me3)64.

Marsupials have no XIST gene69–71; instead, the

homologous region that contains genes that flank XIST

in eutherians contains one of the protein-coding genes

present in birds and frogs but that has been lost in pla-

cental mammals72,73. However, an unrelated gene, RSX

(RNA on the silent X), has been discovered at another

Figure 3 | Dosage compensation of genes on X or Z

chromosomes in mammals, birds, reptiles and fish.

a | The frequency of genes with varying male (m)/female (f)

ratios of expression is expressed logarithmically (a zero

ratio, which denotes equal expression, is represented

by a dashed vertical line). Blue lines denote the

male/female ratio for genes on autosomes (for snakes,

macrochromosomes 1–5 are plotted separately), and red

lines denote the male/female ratio for sex chromosomes

(X for mammals, and Z for birds, snakes and fish). Dosage

compensation is almost complete for the mammalian

Xchromosome, partial for the bird, rattlesnake and sole

Z chromosome, and absent for the undifferentiated

boa Z chromosome. b | Patterns of dosage compensation of

genes arrayed along the Z chromosomes in birds, reptiles

and fish, expressed logarithmically (the horizontal zero line

denotes equal expression), except for birds (for which

dosage compensation is expressed as a linear ratio with 1

denoting equal expression). The dosage valley in the

chicken Z chromosome (which contains the Male

HyperMethylated (MHM) region) and the small

dosage‑compensated region on the sole Z chromosome

(which has a marked increase in methylated cytosines)

are marked with boxes. Part a adapted from

REFS29,88,102,and from REF.105, Nature Publishing Group.

Part b adapted from REFS92,102, and with permission from

REF.10 6, Cold Spring Harbor Laboratory Press.

▶

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locus on the marsupial Xchromosome that seems

to fulfil the same function as XIST74. RSX is active on

the paternal but not the maternal Xchromosome and

produces a ncRNA that coats the Xchromosome

and recruits variant and modified histones to form a

silencing domain. However, no differences in DNA meth-

ylation are observed at the promoters of genes on the

active and inactive Xchromosomes. Transcription of RSX

seems to be controlled by the binding of the promoter

with the activating mark H3K4me3, but not by the inac-

tivating mark H3K27me3, unlike mouse XIST. Curiously,

differential DNA methylation distinguishes active and

inactive RSX alleles, as is the case for XIST in the mouse59.

In this way, the maternal RSX allele is silenced and the

paternal allele is expressed early in embryogenesis, which

marks the paternal Xchromosome for inactivation50,66.

It will be interesting to determine whether RSX ncRNA

interacts with the same proteins as XISTncRNA.

Monotremes. The platypus has not one but five pairs of

sex chromosomes75. Females have five pairs of Xchromo-

somes, and males have five X and five Ychromosomes, all

of which are genetically different9,76,77. During male meio-

sis, X and Ychromosomes pair at the ends to form a chain

of ten from which the Xchromosomes segregate to one

pole and the Ychromosomes to the other to form female-

and male-producing sperm76. This bizarre system arose

by sequential exchanges between an ancient sex chromo-

some pair and four autosome pairs78. Surprisingly, plat-

ypus X and Ychromosomes have homology not to the

mammalian X and Ychromosomes but to the bird Z and

W chromosomes9. Monotremes have no SRY gene (SOX3

is autosomal16); the most convincing candidate sex-

determining gene is AMH (anti-Mullerian hormone;

which has a fundamental role in the sex determination

pathway in reptiles and fish)60.

Although the non-pairing regions of the multiple

Xchromosomes make up at least 12% of the length

of the monotreme genome, there is little evidence for

global dosage compensation. There are inconsistent

reports of delayed DNA replication and differential con-

densation75,79,80 but no molecular evidence of epigenetic

changes65.

Allele-specific PCR (a type of allele-specific assay)

showed that both alleles of several X-borne genes were

transcribed in fibroblasts81, and RNA-seq showed a nearly

twofold excess of expression in females over males in

several tissues (FIG.3), implying that there is little dosage

compensation29. However, RNA-FISH of X-specific genes

in the fibroblasts of the female platypus revealed up to

50% of 1X-active cells for several genes81, which suggests

partial stochastic silencing of at least some genes, as is also

observed for genes on the marsupial Xchromosome and

for escaper genes on the human Xchromosome.

Is the bird Z chromosome dosage-compensated?

In birds, the Z chromosome is highly conserved

between species82,83 and contains almost exactly the

same set of genes84. However, the W chromosome has

degraded to different extents in different bird lineages,

being highly differentiated in most birds but almost

Nature Reviews | Genetics

OpossumMouseHuman

Boa

Zebra ﬁnch

MHM

1.1

1.3

1.5

1.7

Mammals

Tongue sole

Rattlesnake

Snakes

Chicken

Birds

Fish

Tongue sole Z chromosome

Snake Z chromosome

Chicken Z chromosome

ZZ/ZW

Rattlesnake Z Boa Z

ZZm/ZWf ZZm/ZWm

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Allele-specific assay

This type of method can be

used to distinguish between

two alternative forms of a gene

by using probes or primers that

bind only to one or the other

alternative nucleotide

sequences.

Quantitative PCR

(qPCR). Quantitative (real-time)

PCR measures the amount of a

specific sequence in a sample

by tracking the production of

amplification products over

PCR cycles.

Microarray analysis

Expression microarrays assay

for the presence of RNA

sequences in a sample by

binding sample to cDNAs

(DNA copies of mRNA)

arrayed on a substrate.

identical cytologically to the Z chromosome in the dis-

tantly related flightless (ratite) birds such as the emu and

ostrich.

The chicken Z chromosome contains nearly 1,000

genes that are absent from the W chromosome. Early

cytogenetic studies detected no heterochromatic Z chro-

mosome, and isozyme studies of a Z-linked enzyme

showed that both alleles were expressed in blood85.

Dosage compensation was observed by quantitative PCR

(qPCR) for some genes86.

Genome sequences from chickens and several other

birds have allowed detailed analyses at the genome and

transcriptome levels17. Like the human Xchromosome,

the chicken Z chromosome is enriched in LINE ele-

ments, but these are not associated with genes that are

dosage-compensated87. Microarray analysis of the levels

of transcription in male and female chickens showed

that Z genes are expressed 30–40% more strongly in ZZ

males than in ZW females88,89. Global expression analysis

with RNA-seq29 confirmed that expression in males is

33% higher than in females (FIG.3). A few Z genes were

completely dosage-compensated (male/female ratio

of 1.0) and a few were completely non-compensated

(male/female ratio of 2.0), but most were somewhere

between these two extremes. RNA-FISH studies of Z

genes in male and female chickens provide a picture of a

stochastic process that is similar to that in monotremes

and marsupials and in the escaper genes on the human

Xchromosome90. Thus, dosage compensation in birds

does occur86, but it is partial and gene-by-gene91.

Over most of the chicken Z chromosome, genes show

no regional pattern of dosage compensation92. However,

there is a small ‘dosage valley’ within which genes are

more dosage-compensated. This region has dramatic

differences in chromatin conformation between the

sexes, being open in females but hypermethylated and

condensed in males88,92. It contains an enigmatic locus

called MHM (Male HyperMethylated) that shows differ-

ential methylation and configuration between the two Z

chromosomes in males93. MHM is methylated and silent

in males, but in females MHM is unmethylated and asso-

ciated with acetylated histones and is transcribed into a

long ncRNA, which accumulates at its transcription site

near the sex-determining DMRT1 locus94.

Analysis of the transcription of Z-borne genes in

other bird species (zebra finch, crow and whitetail

flycatcher) confirms that different genes are dosage-

compensated to low and variable extents95,96, but the dos-

age valley seems to be confined to chickens and their close

relatives97. No dosage compensation was observed for the

genes in the small segment of the ostrich Z chromosome

that is different between the Z and W chromosomes98.

Snake sex chromosomes. Snakes also have a ZZ male/

ZW female sex chromosome system, but gene mapping

has shown that the snake Z chromosome is homolo-

gous to bird chromosome 2 rather than to the bird Z

chromosome99,100. Curiously, repetitive sequences that

are specific to sex chromosomes are shared between the

snake and bird Z chromosomes101, suggesting a com-

mon origin. One hypothesis is that a common ancestor

had a super-sex chromosome that contained both these

regions. DMRT1 is autosomal in snakes, and the snake

sex-determining gene is unknown.

Snake Z and W chromosomes occupy a special place in

sex chromosome theory because, as pointed out by Susumo

Ohno1, they illustrate stages in W chromosome degrada-

tion. Of the three major snake families, boids (pythons

and their relatives) have a W chromosome cytologically

indistinguishable from the Z chromosome, viperids

have extremely differentiated W chromosomes, and

colubrids are somewhere in themiddle.

A 2013 genomic study of the number and expres-

sion of genes on the Z chromosome in boa, garter snake

(colubrid) and rattlesnake (viper)102 revealed no genomic

differences between male and female boa. Presumably,

either sex in boids is conferred by an allelic difference

beyond the resolution of short-read sequencing or the

sex-determining locus lies on an unrelated chromo-

some. However, the viper and, surprisingly, the colubrid

showed sex differences in the numbers of sequence reads

at the genome level for almost all the genes on the Z

chromosome.

Transcription of the Z-specific genes in the colubrid

and viper produced a profile similar to that of genes on

the non-homologous bird Z chromosome. Most genes

showed male/female differences of somewhere between

1.0 and 2.0 (FIG.3). There was no sign of gene dosage

compensation at the chromosome-wide or regionalle vels.

Dosage compensation in fish. Fish display richly inform-

ative variation of sex chromosomes and sex-linked genes

but there have been few studies of dosage compensation

in this group. A paper published in 2015 reported early

signs of the establishment of a dosage compensation sys-

tem in the minimally differentiated sex chromosomes

in the threespine stickleback, which were detectable as

the upregulation of genes on the older stratum of the

Xchromosome in males103. The establishment of this

dosage compensation system was suggested to be initi-

ated by the female-biased expression of many genes on

the Xchromosome104.

A detailed analysis of the genome, transcriptome and

methylome of the half-smooth tongue sole has revealed

signs of dosage compensation. This species has a

ZW chromosome pair that is only 30 million years old

but that has already greatly diverged. Remarkably, the

sole ZW pair has considerable homology to the bird

ZW pair, and DMRT1 fulfils the criteria for being the

sex-determining gene in this species. However, gene

dosage differences between ZZ males and ZW females

are apparently insufficient to define sex, because

the DMRT1 locus is silenced by methylation in ZW

females105. Incubation at a high temperature removes

this methylation and produces fertile ZW pseudomales,

which implies that sex is determined by an epigenetic

mechanism in thisfish.

In this species, dosage compensation can be directly

assessed in the same sex by comparing the transcrip-

tion of Z-borne genes in the testes of ZW and ZZ

males. A study showed that genes on most of the Z

chromosome are expressed at an average male/female

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Ohno’s hypothesis

A hypothesis that states that

the first step of the evolution of

Xchromosome inactivation was

the upregulation of X-borne

genes in males to maintain

parity with the expression

of interacting autosomal

genes. This resulted in the

overexpression of X-borne

genes in females, which was

countered by Xchromosome

inactivation.

ratio of 1.3 between ZZ and ZW males (FIG.3), which

implies variable and partial dosage compensation106.

However, strong dosage compensation was observed

in a 4 Mb region of the Z chromosome. This region

was highly divergent from the W chromosome and

contained many genes that are involved in male

development. This dosage-compensated region was

replete with methylated cytosines, which suggests that

DNA methylation is important for regulating dosage

compensation.

The evolution of dosage compensation systems

Dosage compensation and sex chromosome degeneration.

It seems obvious that the need for dosage compensation

would arise only following gene loss from t he sex-specific

chromosome, thus dosage compensation would keep

pace with degradation. It is therefore important to

understand the progress of chromosome degradation.

Degradation is not a smooth process. The pres-

ence of ‘geological strata’ on the mammal Y and bird Z

chromosomes60,107 provides evidence that degradation

proceeded in ‘fits and starts’, as regions were isolated

from recombination by inversion. However, evolution-

ary ‘tidemarks’ of retreating pseudoautosomal bound-

aries, variation between species and polymorphisms in

the human PAR108–111 show that inactivation could also

creep slowly along the mammalian Xchromosome. The

different sizes of the pseudoautosomal regions in differ-

ent mammals109 show that Ychromosome degradation

proceeded at different rates in different lineages.

Ychromosome genes were probably not lost instanta-

neously but gradually faded away, so that the acquisition

of dosage compensation could proceed slowly. Gradual

inactivation is implied by the presence of partially active

genes and recently inactivated pseudogenes near the

pseudoautosomal boundary on the human Ychromo-

some108. Some of these genes (such as steroid sulfatase)

remain 2X-active, even though their Y partners suffered

partial deletion. Some are inactivated in certain tissues

but escape inactivation in others, and can even be inacti-

vated in some women and not in others: polymorphisms

that attest to the gradual degradation and loss of Y

chromosome genes52.

What genes really need to be dosage-compensated?

We must also consider which genes really need to be

dosage-compensated once their Y partners are inac-

tivated or lost. At one end of the spectrum are highly

dosage-sensitive genes for which haploinsufficiency

would be lethal or deleterious; importantly, such genes

are highly represented among those that retain an

active partner on the Ychromosome60,112. However, for

many genes, dosage is not a problem; for example, a

deficiency for genes that encode enzymes is often a true

recessive, with heterozygotes having a normal pheno-

type, which implies that there are many ways to regulate

enzyme activity other than at the transcriptionallevel.

Some genes may not require dosage compensation

because they have evolved a sex-specific function. For

example, a spermatogenesis gene that is only expressed

in males does not need to be compensated. Biased

expression is common for genes on sex chromosomes,

and the human X and chicken Z chromosomes have

accumulated testis-specific genes113,114. In birds, and

in the tongue sole, most genes on the Z chromosome

are hypertranscribed in males, and there is a twofold

excess of expression of sex-related genes in males com-

pared with females. By contrast, the mouse Xchromo-

some seems to have accumulated female-biased genes

that are expressed in the ovary and placenta, whereas

late-expressing spermatogenesis genes have moved off

the Xchromosome115. In line with the suggestion that

sex-biased genes accumulate on sex chromosomes,

female-biased genes are concentrated in the unpaired

region of the partially differentiated Xchromosome of

the three-spine stickleback, perhaps making up for a

lack of dosage compensation in this species116.

If many or most of the genes are not dosage sensitive,

then selection for the inactivation of a recently unpaired

region of the Xchromosome would be weak until degen-

eration hits a gene for which haploinsufficiency is severe

or lethal, or a damaging level of smaller deficiencies

accumulates. Thus, we might expect recruitment into the

inactivation system to proceed in fits and starts along the

Xchromosome as strong selection begins to compensate

for one or a few dosage-sensitivegenes.

Dosage compensation by the upregulation of gene

expression. Ohno1 first proposed that the initial step

of mammalian Xchromosome inactivation was the

upregulation of genes on the single Xchromosome of

males to maintain parity with autosomal genes (Ohno’s

hypothesis) (FIG.4). The upregulation of X-borne genes

occurs in Drosophila spp. but is, sensibly, confined to

males4. However, in mammals, the upregulation of genes

on the Xchromosome produces an awkward excess of

Xchromosome product in females that is countered

by Xchromosome inactivation117.

Whether X-borne genes are overexpressed compared

with autosomal genes in mammals is still debated118. A

gene that is on the Xchromosome in one mouse species

and on an autosome in another mouse species showed

a twofold difference in expression per Xchromosome

between the two species117. Microarray analyses and,

more recently, an RNA-seq study showed the marked

upregulation of genes on the mouse Xchromosome

in males compared with genes on autosomes, though

this was not sufficient to completely compensate for

the twofold deficiency in Xchromosome gene dos-

age119. Observations of active histone marks bound to

DNA increased RNA stability and RNA polymerase

occupancy, and increased ribosome density are con-

sistent with the upregulation of gene expression in

Xchromosomes120–123.

However, global RNA-seq analysis of all genes on

the mouse Xchromosome (including those with little

or sex-biased transcription) detected no upregulation

of X-chromosome gene expression120,123,124, and neither

did a recent comparison at the protein level125. Even

when non-expressed genes were eliminated from the set

of genes analysed and the transcription of X-chromosome

genes was compared with the transcription of their

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Meiotic sex chromosome

inactivation

(MCSI). Inactivation of the X

and Ychromosomes during

male meiosis in therian

mammals.

orthologues in species with non-homologous sex

chromosomes, there was no evidence of upregula-

tion in placental mammals126. However, similar tech-

niques showed upregulation in males of genes on

the Xchromosome in the opossum and on the oldest

Xchromosome in the platypus29,127.

Thus, evidence for the upregulation of genes on

the Xchromosome as the first step in the evolution

of Xchromosome inactivation in placental mammals

remains equivocal. Inconsistent results may reflect the

analysis of different sets of sex-linked genes, and the set

of autosomal genes to which they were compared128,129.

However, it may be that upregulation occurs for some

genes but not for others, in one or both sexes, and

independently in some lineages but not inothers.

In birds, the upregulation of Z-chromosome genes

was observed in ZW females when their expression was

compared with the average for autosomes, in chickens,

zebra finches and crows97,130 but not in flycatchers95;

although comparisons between Z-chromosome and

proto-ZW-chromosome gene expression did show the

upregulation of Z-chromosome genes in females29. A

similar conclusion was made for genes on the tongue

sole Z chromosome, which were significantly upreg-

ulated in females106. Upregulation of X-borne genes

is correlated with the loss of Y-borne genes even

in a plant system131. Thus, the upregulation of genes in

the heterogametic sex does seem to have occurred

independently in several lineages.

Did inactivation evolve from meiotic silencing? Early

studies of paternal Xchromosome inactivation sug-

gested that marsupials represent an early stage in the

construction of the sophisticated multilayered random

Xchromosome inactivation of placental mammals132.

Paternal Xchromosome inactivation was thought

to have been ancestral because it occurs in marsupi-

als and also in the extra-embryonic membranes in

rodents and bovids. Incomplete and gene- and tis-

sue-specific marsupial inactivation was also thought

to be a leaky version of Xchromosome inactivation in

placental mammals57. However, we now know that pla-

cental mammals and marsupials share characteristics

of variable, partial and gene-specific Xchromosome

inactivation.

The idea that paternal inactivation was ancestral to

therians led to the attractive hypothesis that paternal

inactivation was simply a continuation of meiotic sex

chromosome inactivation (MCSI) in the testis, and this

idea was supported by claims that one Xchromosome

was already inactive at the two-cell stage in mice49.

MCSI seems to be a manifestation of an ancient mecha-

nism to silence chromosome regions that are not paired

at meiosis133 and to banish invading DNA sequences.

Marsupials and placental mammals share the silenc-

ing of both X and Ychromosomes during male meio-

sis134,135. Perhaps the Xchromosome is delivered to the

egg in an inactive form. In marsupials, and in the early

differentiating extra-embryonic membranes in rodents

and bovids, this chromosome could simply remain

inactive. In the somatic cells of placental mammals, the

Xchromosome could be reactivated, and this would be

followed by random inactivation.

However, it was observed that genes inactivated

during meiosis were reactivated in the early embryo of

female opossums66. Indeed, it is now clear that mouse

and human embryos go through a 2X-active stage before

either paternal orrandom Xchromosome inactivation

is imposed136.

The appearance of paternal Xchromosome inac-

tivation in some placental mammals in addition to

marsupials need not necessarily mean that this was an

ancestral condition. Paternal inactivation may have

independently evolved as the result of selection to mit-

igate maternal–foetal incompatibility. Alternatively, it

may have evolved in response to sexual antagonism

towards variants of X-borne genes, which, being always

expressed from the single Xchromosome copy in XY

males, were selected for male-advantageous traits at

the expense of females. Paternally imprinted silenc-

ing appears again and again throughout the animal

kingdom. It is a common theme in some invertebrate

systems of chromosome loss and heterochromatiniza-

tion and is likely to be related to the mechanism that

Nature Reviews | Genetics

TDF

Unpaired region on

X chromosome is

upregulated in

both sexes

XCI evolves to counter

upregulation of X-borne

genes in females

XCI spreads to keep up

with the upregulation

of X-borne genes

X Y X

F M

Proto-Y

chromosome

acquires TDF

Y chromosome

degrades

from TDF

Y chromosome

degrades further

Y chromosome

mostly degraded

Figure 4 | Ohno’s hypothesis that Ychromosome degradation drives upregulation

of the unpaired region of the Xchromosome in males (M) and females (F) and is

countered by Xchromosome inactivation in females. A proto‑Ychromosome is

defined by the acquisition of a testis‑determining factor (TDF; red band). Other genes

(green and blue bands) on the proto‑X and proto‑Ychromosomes are active in both sexes

(transcripts are represented by green and blue dots). As the Ychromosome degrades,

genes on the unpaired region of the Xchromosome are upregulated sequentially to

maintain gene expression dosage in males. Upregulation in females is progressively

countered by Xchromosome inactivation (XCI).

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produces allele-specific expression at several imprinted

loci in mammals137. Striking similarities between fac-

ultative heterochromatin, imprinted regions and

the inactive Xchromosome have been noted several

times138–140.

The evolution of chromosome-wide dosage compensa-

tion. The distinguishing feature of mammalian Xchro-

mosome inactivation is its coordinated control of

(almost) the whole Xchromosome. Did this control have

its beginning in the unpaired region early in evolution

and spread when the X and Ychromosomes started to

differentiate? Or was it superimposed on a more ancient

variable and partial inactivation system?

An early localized silencing event must have taken

place in the region of the mammalian Xchromosome

that was first differentiated, presumably near the SOX3

locus that evolved into SRY. ncRNA transcribed within

this region may originally have had a local effect on

the Xchromosome, similar to the effects of of ncRNA

transcripts of Air and Kcnq1 on an imprinted region137.

This silenced domain spread as the Ychromosome

progressively degraded, and it now encompasses all of

the Xchromosome except for the small pseudoautoso-

mal region. Although XIST is 66 Mb from SOX3 on the

human Xchromosome, Gribnau pointed out141 that the

LNX locus that was replaced by XIST is adjacent to SOX3

in the orthologous region of the bird chromosome 4, so

these genes might have been in close proximity on the

ancestral mammalian Xchromosome.

However, the presence of non-contiguous escaper

genes on the human Xchromosome and the variabil-

ity of their expression142 favour the alternative model

of superimposition of global control on an ancient

gene-by-gene dosage compensation mechanism. The

pattern of inactivation on the mouse and human Xchro-

mosomes suggests that this global control is nearly com-

plete on the mouse Xchromosome but is still underway

on the region of the human Xchromosome that was

added to the eutherian X and Ychromosomes (FIG.5).

Similarly, the stochastic transcription of escaper

genes on the human and kangaroo Xchromosomes sup-

ports the occurrence of variable and partial inactivation

of an ancestral therian Xchromosome that evolved soon

after the evolution of SRY and the beginning of X and

Ychromosome differentiation 190–166 MYA. This nas-

cent system seems to have independently come under

the control of non-homologous non-coding genes in

marsupial and placental mammals.

Although mammalian Xchromosome inactivation

has no parallel in the dosage compensation systems of

other vertebrates, there are at least two examples

of regional control that support the hypothesis that

Xchromosome inactivation was superimposed on

an ancient therian gene-by-gene system. The young

Z chromosome of the tongue sole shows variable and

partial dosage compensation but contains a 4 Mb region

replete with dosage-compensated genes, which is rich

in CpG dinucleotides that are subject to differential

methylation106. Similarly, the chicken Z chromosome,

most of which comprises genes with different levels of

dosage compensation with no obvious polarity contains

a dosage valley that includes the MHM locus, which

is hypomethylated and inactive in males but which is

complexed with activating histones and expressed as a

long ncRNA in females92. The Z chromosomes of other

birds have genes with a range of dosage compensation

but lack this valley, which implies that the valley evolved

recently143 and was superimposed on a gene-by-gene

partial compensation system that is present in allbirds.

Re-use of ancient silencing mechanisms. I have dis-

cussed above how non-homologous sex chromosomes

go through a series of changes as the sex-specific

member degrades and the gene content of its part-

ner becomes specialized, a process that is very similar

across different vertebrate groups. Regulation of gene

expression that mitigates dosage differences in verte-

brates also has many features of epigenetic silencing

that are widely distributed across other eukaryotes,

including regulation by ncRNAs and DNA and histone

modifications.

Long ncRNAs are increasingly being recognized as

important controlling mechanisms that have complex

roles in Xchromosome inactivation. Indeed, Xchro-

mosome inactivation is increasingly being seen as a

series of RNA switches that guide and tether proteins to

silenced DNA144. Many imprinted domains also contain

ncRNA137, which seems to perform similar functions in

recruiting chromatin modifiers145.

It may seem remarkable that XIST and RSX both

produce ncRNAs with similar functions in silencing

genes although they have different sequences and quite

independent origins. XIST and other non-coding genes

in the inactivation centre arose from an ancient region

containing protein-coding genes73, which was dis-

rupted in marsupials72 but which accumulated repeti-

tive sequences in placental mammals146. RSX evolved

from non-homologous sequences distant from XIST.

However, there is no shortage of candidate ncRNAs

transcribed from the Xchromosome; several genes

within regions of the mouse Xchromosome that escape

inactivation transcribe long ncRNAs, predominantly

in females147, and this suggests that many ncRNAs may

have been available to take over the control of Xchro-

mosome inactivation in either marsupials or placental

mammals (FIG.5).

Comparisons of the molecular mechanisms involved

in Xchromosome inactivation that are shared with other

epigenetic silencing systems also reveal many

other examples of the re-use of ancient and ubiquitous

mechanisms. The stochastic silencing process in mam-

mal and bird sex chromosomes resembles monoallelic

expression of many autosomal genes148–150 and may have

evolved from it151. Importantly, the product of a gene

that is involved in chromatin condensation, SMCHD1,

regulates not only Xchromosome inactivation but also

clusters of autosomal genes that are expressed monoal-

lelically152. Monoallelically expressed autosomal genes

also share with inactivated X-chromosome genes a

trademark chromatin signature of highly conserved

histone modifications153.

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Epigenetic changes to DNA or to the histones that

bind it are also a common theme in many eukaryote

regulatory pathways, being widely present in other

vertebrate and invertebrate silencing mechanisms.

In mammals, DNA is methylated mostly at CpG

residues in the heterochromatin; CpG methylation at

promoters is confined to the inactive Xchromosome

and imprinted regions. CpG methylation must have

been a recent addition to the Xchromosome inac-

tivation pathway in placental mammals because it

is absent in marsupials. However, DNA methylation is

seen across eukaryotes and is negatively correlated with

gene expression154. DNA methylation controls the con-

figuration and activity of the MHM locus in the dosage

valley of the chicken Z chromosome in males93,94. DNA

methylation has been shown to inactivate the male-

determining DMRT1 locus to produce female tongue

sole, and differential methylation of CpG sequences

is found in the dosage-compensated region that sur-

rounds the DMRT1 locus106. DNA methylation is

involved in parent-specific silencing of imprinted genes

in plants as well as mammals137,155, and is also involved in

silencing by XIST and RSX27,59. DNA methylation of

repetitive sequences of DNA at centromeres is ubiqui-

tous across eukaryotes156, which probably reflects the

ancient role of DNA methylation. This suggests that

epigenetic changes evolved from the suppression of

invading transposable elements157.

Nature Reviews | Genetics

Partially compensated X chromosome

Ancestral mammal X chromosome

Compensation of

dosage-sensitive genes

RSX PAR PA R

Human

Opossum

Autosomal region

added to PAR

Mouse

Marsupials

Placental mammals

Marsupials Placental mammals

RSX

aSOX3

Kangaroo

. . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . .

. . . . . . . . . . . . . . . .. . . . .

. . . . . . . .

. . . . .

. . . . . . .

XIST

Figure 5 | Evolution of Xchromosome inactivation in mammals. a | The

region near SOX3 (the ancestor of SRY) was the first to be unpaired by

Ychromosome degradation, and inactivation of dosage‑sensitive genes

(pink bands) in the expanding unpaired region (white) was selected. As the

unpaired region was extended, non‑coding RNAs transcribed from

non‑homologous loci (red bands) were recruited to coordinate the

inactivation of genes on one Xchromosome. One of these genes, XIST (X

inactive specific transcript), was recruited in eutherians and another, RSX

(RNA on the silent X), in marsupials. b | The spread of Xchromosome

inactivation from the RSX locus in marsupials and the XIST locus in

placental mammals, which coordinate the inactivated regions, is shown.

Escaper genes (green bands) are gradually recruited into the global

methylation system, which leaves approximately 30% of active genes in

the kangaroo, 15% in humans and the opossum and 3% in mice. A large

autosomal region (green) was added to the pseudoautosomal region (PAR)

of the proto‑sex chromosomes before the radiation of placental mammals.

This added region went through the same series of changes, degrading on

the Ychromosome and undergoing partial inactivation on the

Xchromosome as it was progressively recruited into the global X

inactivation system.

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Histone variants and modifications are also very

old, appearing in very divergent eukaryote taxa158. The

variant histone macroH2A that is associated with the

inactive Xchromosome in mammals is also involved

in regulating other functions, such as the cell cycle159.

Post-translational modifications of histones also

control transcription in many systems and include tis-

sue-specific marks. Common to the inactive Xchro-

mosome of all therian mammals is H3K27me3, which

is also bound to the inactive RSX and XIST loci on

the active Xchromosome51. This inactivation mark

is almost ubiquitous in eukaryotes36,160. Similarly,

there are several activating histone acetylation marks

shared by all therian mammals that are also found in

Drosophila spp., yeast and many other eukaryotes161.

Several active and inactive marks that characterize

the two Xchromosomes in mouse and human females

are not differentially present on the inactive Xchro-

mosome in marsupials or on the paternally inactive

Xchromosome in mouse extra-embryonic mem-

branes58,162. Importantly, the profile of inactivating

histone modifications that marsupial and placental

mammals do share is similar to their profile on cen-

tromeric heterochromatin59,64,156, where they silence

transposable elements, a mechanism that is present

across vertebrates and probably other eukaryotes163.

This observation again suggests that elements of the

silencing domain of the therian Xchromosome may

have been recruited from ancient mechanisms that

silence invading DNA sequences.

Thus, although they evolved independently, the

basic mechanisms of silencing in marsupial and pla-

cental mammals and other vertebrates all made use of

ancient epigenetic silencing mechanisms.

Conclusions

Sex chromosomes in different vertebrate groups

evolved independently from different regions of a con-

served vertebrate genome but the processes of sex chro-

mosome differentiation are remarkably parallel across

vertebrate groups. Sex chromosomes differentiate by

degradation of a male-specific Y or a female-specific W

chromosome, creating problems of compensating for

different dosages of genes on the X or Z chromosomes.

Comparisons between sex chromosomes in mammals,

birds, reptiles and fish are now beginning to fill in

details of how this dosage compensation is achieved,

presenting a picture of great diversity.

The most thoroughly investigated sex chromosomes

are those of mammals and birds; however, these are old

sex chromosome systems and the trail has now gone

a bit cold. The identification of young sex-determin-

ing systems — medaka and stickleback fish, and even

some plants — has provided data that have revealed

the first stages of the evolution of dosage compensation

mechanisms.

The well-studied mammalian Xchromosome inac-

tivation system, to which we have habitually compared

other systems, is unique in vertebrates and perhaps not

a useful comparator. It remains unclear what special

selective forces drove the evolution of global control

of X inactivation in therian mammals. In other verte-

brates, the dosage compensation of genes on differenti-

ated sex chromosomes is gene-specific and partial. This

makes sense because not all genes are equally sensitive

to dosage differences; for many genes, a twofold differ-

ence in gene expression does not matter much. As an

alternative to dosage compensation, some genes have

evolved sex-biased expression. The different extents to

which genes are compensated might well be the rea-

son for the inconsistent results obtained by averaging

expression from different sets ofgenes.

Global or regional control may have been super-

imposed on such a basic system. For example, some

genes on the human Xchromosome escape global inac-

tivation but show partial expression from the inactive

Xchromosome. The few examples of regional control

— the dosage valley of the chicken Z chromosome and

the 4 Mb dosage-compensated region of the tongue sole

Z chromosome — might exemplify the beginnings of a

global controlsystem.

Comparison of dosage compensation systems

between distantly related vertebrates has been impor-

tant in teasing apart the layers of silencing. However,

we cannot assume that the re-use of a particular gene

(such as DMRT1) or a phenotype such as paternal inac-

tivation must represent identity by descent. Rather,

it seems that there are many ancient mechanisms

established in the earliest eukaryotes that constitute a

molecular toolbox of ways to silencegenes.

Although dosage compensation systems seem to be

fundamentally different between different taxa, many

common features are shared across divergent lineages

and resemble systems that control the expression of

autosomal genes and even regulatory mechanisms that

are present in taxa very distant from vertebrates. DNA

methylation seems to control gene expression in many

vertebrates, invertebrates and even plants. Histone

modifications that activate or silence transcription are

ubiquitous. Stochastic suppression, seen in the partial

repression of genes on the inactive Xchromosome in

marsupials and humans, as well as birds, seems sim-

ilar to monoallelic expression of autosomal genes.

This makes it likely that all these dosage systems were

constructed from elements of ancient silencing mech-

anisms that are ubiquitous within, and probably well

outside, vertebrates.

A rapidly growing understanding of these mecha-

nisms and their exaptation to a variety of epigenetic

tasks is facilitated by the many genome-sequencing

projects now being undertaken and fully justifies the

exploration of the genomes of non-model vertebrates.

This exploration is being encouraged and streamlined

by the Genome 10K community of scientists164. The

availability of genome-wide methods to explore DNA

modifications, the action of ncRNA, and the intrica-

cies of the action of histones and other proteins that

cooperate to form silencing domains, will dramatically

increase our understanding of epigenetic processes, a

topic of burgeoning interest and practical importance

as we begin to realize how the environment can alter

gene expression in development.

REVIEWS

NATURE REVIEWS

GENETICS ADVANCE ONLINE PUBLICATION

1. Ohno,S. Sex Chromosomes and Sex-linked Genes

(Springer-Verlag, 1967).

Ohno’s classic book, containing his theory of sex

chromosome differentiation and the hypothesis

that upregulation of the mammalian Xchromosome

in males selected for Xchromosome inactivation.

2. Graves,J.A.M. Sex chromosome specialization and

degeneration in mammals. Cell 124, 901–914 (2006).

3. Charlesworth,B. Sex chromosomes: evolving dosage

compensation. Curr. Biol. 8, 931–933 (1998).

4. Dementyeva,E.V. & Zakian,S.M. Dosage

compensation of sex chromosome genes in

eukaryotes. Acta Naturae 2, 36–43 (2010).

5. Graves,J.A.M. & Disteche,C.M. Does gene dosage

really matter? J.Biol. 6, 1 (2007).

6. Mank,J.E., Hosken,D.J. & Wedell,N. Some

inconvenient truths about sex chromosome dosage

compensation and the potential role of sexual conflict.

Evolution 65, 2133–2144 (2011).

7. Nanda,I. etal. 300 million years of conserved synteny

between chicken Z and human chromosome 9.

Nat. Genet. 21, 258–259 (1999).

8. Ezaz,T. etal. Molecular marker suggests rapid

changes of sex-determining mechanisms in Australian

dragon lizards. Chromosome Res. 17, 91–98 (2009).

9. Veyrunes,F. etal. Bird-like sex chromosomes of

platypus imply recent origin of mammal sex

chromosomes. Genome Res. 18, 965–973 (2008).

10. Graves,J.A.M. The origin and function of the

mammalian Ychromosome and Y-borne genes—an

evolving understanding. Bioessays 17, 311–320

(1995).

11. Kikuchi,K. & Hamaguchi,S. Novel sex-determining

genes in fish and sex chromosome evolution. Dev.

Dyn. 242, 339–353 (2013).

12. Kondo,M., Nanda,I., Schmid,M. & Schartl,M.

Sex determination and sex chromosome evolution:

insights from medaka. Sex. Dev. 3, 88–98 (2009).

13. Just,W. etal. Ellobius lutescens: sex determination

and sex chromosome. Sex. Dev. 1, 211–221 (2007).

14. Kuroiwa,A., Ishiguchi,Y., Yamada,F., Shintaro,A. &

Matsuda,Y. The process of a Y-loss event in an XO/XO

mammal, the Ryukyu spiny rat. Chromosoma 119 ,

519–526 (2010).

15. Foster,J.W. & Graves,J.A.M. An SRY-related

sequence on the marsupial Xchromosome:

implications for the evolution of the mammalian

testis-determining gene. Proc. Natl Acad. Sci. USA 91 ,

1927–1931 (1994).

16. Wallis,M.C. etal. Sex determination in platypus and

echidna: autosomal location of SOX3 confirms the

absence of SRY from monotremes. Chromosome Res.

15, 949–959 (2007).

17. International Chicken Genome Sequencing

Consortium. Sequence and comparative analysis of

the chicken genome provide unique perspectives on

vertebrate evolution. Nature 432, 695–716 (2004).

18. Smith,C.A. etal. The avian Z-linked gene DMRT1 is

required for male sex determination in the chicken.

Nature 461, 267–271 (2009).

19. Raymond,C.S., Kettlewell,J.R., Hirsch,B.,

Bardwell,V.J. & Zarkower,D. Expression of Dmrt1 in

the genital ridge of mouse and chicken embryos

suggests a role in vertebrate sexual development.

Dev. Biol. 215, 208–220 (1999).

20. Raymond,C.S. etal. Evidence for evolutionary

conservation of sex-determining genes. Nature 3 91,

691–695 (1998).

21. O’Meally,D., Ezaz,T., Georges,A., Sarre,S.D. &

Graves,J.A.M. Are some chromosomes particularly

good at sex? Insights from amniotes. Chromosome

Res. 20, 7–19 (2012).

22. Graves,J.A.M. & Peichel,C.L. Are homologies in

vertebrate sex determination due to shared ancestry

or to limited options? Genome Biol. 11, 205 (2010).

23. Mank,J.E. Sex chromosome dosage compensation:

definitely not for everyone. Trends Genet. 29,

677–683 (2013).

24. Disteche,C.M. Dosage compensation of the sex

chromosomes. Annu. Rev. Genet. 46, 537–560

(2012).

25. Luo,Z.X., Yuan,C.X., Meng,Q.J. & Ji,Q.A.

Jurassic eutherian mammal and divergence of

marsupials and placentals. Nature 476, 442–445

(2011).

26. Lyon,M.F. Gene action in the X-chromosome of the

mouse (Mus musculus L.). Nature 190, 372–373

(1961).

27. Galupa,R. & Heard,E. X-chromosome inactivation:

new insights into cis and trans regulation. Curr. Opin.

Genet. Dev. 31, 57–66 (2015).

28. Deng,X., Berletch,J.B., Nguyen,D.K. &

Disteche,C.M. Xchromosome regulation: diverse

patterns in development, tissues and disease. Nat.

Rev. Genet. 15, 367–378 (2014).

29. Julien,P. etal. Mechanisms and evolutionary patterns

of mammalian and avian dosage compensation.

PLoS Biol. 10, e1001328 (2012).

This paper presents a direct visualization of

expression levels of genes on sex chromosomes by

analysis of transcriptomes from males and females

of major mammalian and bird lineages.

30. Sado,T. & Sakaguchi,T. Species-specific differences in

Xchromosome inactivation in mammals. Reproduction

146, 131–139 (2013).

31. Al Nadaf,S. etal. A cross-species comparison of

escape from X inactivation in Eutheria: implications for

evolution of Xchromosome inactivation. Chromosoma

121, 71–78 (2012).

32. Chow,J.C. etal. LINE-1 activity in facultative

heterochromatin formation during Xchromosome

inactivation. Cell 141, 956–969 (2010).

33. Graves,J.A.M. & Gartler,S.M. Mammalian

Xchromosome inactivation: testing the hypothesis of

transcriptional control. Somat. Cell. Mol. Genet. 12,

275–280 (1986).

This paper presents the first demonstration that

Xchromosome inactivation represents

transcriptional repression, a fundamental tenet of

epigenetic silencing.

34. Graves,J.A.M. 5-azacytidine-induced re-expression

of alleles on the inactive Xchromosome in a hybrid

mouse cell line. Exp. Cell Res. 141, 99–105 (1982).

35. Mohandas,T., Sparkes,R.S. & Shapiro,L.J.

Reactivation of an inactive human Xchromosome:

evidence for X inactivation by DNA methylation.

Science 211 , 393–396 (1981).

36. Biterge,B. & Schneider,R. Histone variants: key

players of chromatin. Cell Tissue Res. 356, 457–466

(2014).

37. Peterson,C.L. & Laniel,M.A. Histones and histone

modifications. Curr. Biol. 14, 546–551 (2004).

38. Ferrari,F., Alekseyenko,A.A., Park,P.J. &

Kuroda,M.I. Transcriptional control of a whole

chromosome: emerging models for dosage

compensation. Nat. Struct. Mol. Biol. 21, 118–125

(2014).

39. Deng,X. etal. Bipartite structure of the inactive

mouse Xchromosome. Genome Biol. 16, 152

(2015).

40. Rao,S.S. etal. A 3D map of the human genome at

kilobase resolution reveals principles of chromatin

looping. Cell 159, 1665–1680 (2014).

References 39 and 40 present stunning Hi‑C data

showing that the inactive Xchromosome assumes a

very different three‑dimensional interphase

structure from the structures of the active

Xchromosome and the autosomes.

41. Holwerda,S.J. etal. Allelic exclusion of the

immunoglobulin heavy chain locus is independent of

its nuclear localization in mature Bcells. Nucleic Acids

Res. 41, 6905–6916 (2013).

42. Brown,C.J. etal. A gene from the region of the

human X inactivation centre is expressed exclusively

from the inactive Xchromosome. Nature 349, 38–44

(1991).

43. Escamilla-Del-Arenal,M., da Rocha,S.T. & Heard,E.

Evolutionary diversity and developmental regulation

of X-chromosome inactivation. Hum. Genet. 130,

307–327 (2011).

44. Okamoto,I. etal. Eutherian mammals use diverse

strategies to initiate X-chromosome inactivation

during development. Nature 472, 370–374 (2011).

45. Dupont,C. & Gribnau,J. Different flavors of

X-chromosome inactivation in mammals. Curr. Opin.

Cell Biol. 25, 314–321 (2013).

46. Wutz,A. Gene silencing in X-chromosome inactivation:

advances in understanding facultative

heterochromatin formation. Nat. Rev. Genet. 12,

542–553 (2011).

47. Chu,C. etal. Systematic discovery of Xist RNA binding

proteins. Cell 161, 404–416 (2015).

48. Takagi,N. Imprinted X-chromosome inactivation:

enlightenment from embryos invivo. Semin. Cell Dev.

Biol. 14, 319–329 (2003).

49. Huynh,K.D. & Lee,J.T. Imprinted X inactivation

in eutherians: a model of gametic execution

and zygotic relaxation. Curr. Opin. Cell Biol. 13,

690–697 (2001).

50. Wang,X., Soloway,P.D. & Clark,A.G. Paternally

biased X inactivation in mouse neonatal brain.

Genome Biol. 11, 79 (2010).

51. Fukuda,A. etal. The role of maternal-specific

H3K9me3 modification in establishing imprinted

X-chromosome inactivation and embryogenesis in

mice. Nat. Commun. 5, 5464 (2014).

52. Carrel,L. & Willard,H.F. X-inactivation profile reveals

extensive variability in X-linked gene expression in

females. Nature 434, 400–404 (2005).

53. Cotton,A.M. etal. Analysis of expressed SNPs

identifies variable extents of expression from the

human inactive Xchromosome. Genome Biol. 14,

R122 (2013).

54. Yen,Z.C., Meyer,I.M., Karalic,S. & Brown,C.J.

A cross-species comparison of X-chromosome

inactivation in Eutheria. Genomics 90, 453–463

(2007).

55. Berletch,J.B. etal. Escape from X inactivation

varies in mouse tissues. PLoS Genet. 11, e1005079

(2015).

56. Mikkelsen,T.S. etal. Genome of the marsupial

Monodelphis domestica reveals innovation

in non-coding sequences. Nature 447, 167–177

(2007).

57. Cooper,D.W., Johnston,P.G., Graves. J.A.M. &

Watson,J.M. X-inactivation in marsupials and

monotremes. Seminars Dev. Biol. 4, 117–128

(1993).

58. Koina,E., Chaumeil,J., Greaves,I.K., Tremethick,D.J.

& Graves,J.A.M. Specific patterns of histone marks

accompany Xchromosome inactivation in a marsupial.

Chromosome Res. 17, 115–126 (2009).

59. Wang,X., Douglas,K.C., Vandeberg,J.L.,

Clark,A.G. & Samollow,P.B. Chromosome-wide

profiling of X-chromosome inactivation and

epigenetic states in fetal brain and placenta of the

opossum, Monodelphis domestica. Genome Res. 24,

70–83 (2014).

60. Cortez,D. etal. Origins and functional evolution of

Ychromosomes across mammals. Nature 508,

488–493 (2014).

In this paper, Ychromosome evolution is traced

across major mammalian lineages by genome and

transcriptome sequencing, confirming the

independent origin and punctuated differentiation

of this chromosome.

61. Al Nadaf,S. etal. Activity map of the tammar

Xchromosome shows that marsupial X inactivation is

incomplete and escape is stochastic. Genome Biol. 11,

R122 (2010).

62. Rodriguez-Delgado,C.L., Waters,S.A. & Waters,P.D.

Paternal X inactivation does not correlate with

Xchromosome evolutionary strata in marsupials.

BMC Evol. Biol. 14, 267 (2014).

63. Kaslow,D.C. & Migeon,B.R. DNA methylation

stabilizes Xchromosome inactivation in eutherians but

not in marsupials: evidence for multistep maintenance

of mammalian X dosage compensation. Proc. Natl

Acad. Sci. USA 84, 6210–6214 (1987).

64. Chaumeil,J. etal. Evolution from XIST-independent to

XIST-controlled X-chromosome inactivation: epigenetic

modifications in distantly related mammals. PLoS ONE

6, e19040 (2011).

65. Rens,W., Wallduck,M.S., Lovell,F.L.,

Ferguson-Smith,M.A. & Ferguson-Smith,A.C.

Epigenetic modifications on Xchromosomes in

marsupial and monotreme mammals and implications

for evolution of dosage compensation. Proc. Natl

Acad. Sci. USA 107, 17657–17662 (2010).

66. Mahadevaiah,S.K. etal. Key features of the X

inactivation process are conserved between

marsupials and eutherians. Curr. Biol. 19,

1478–1484 (2009).

67. Wakefield,M.J., Keohane,A.M., Turner,B.M. &

Graves,J.A.M. Histone underacetylation is an

ancient component of mammalian Xchromosome

inactivation. Proc. Natl Acad. Sci. USA 94,

9665–9668 (1997).

68. Goto,T. & Monk,M. Regulation of X-chromosome

inactivation in development in mice and humans.

Microbiol. Mol. Biol. Rev. 62, 362–378 (1998).

69. Davidow,L.S. etal. The search for a marsupial XIC

reveals a break with vertebrate synteny. Chromosome

Res. 15, 137–146 (2007).

70. Shevchenko,A.I. etal. Genes flanking Xist in mouse

and human are separated on the Xchromosome

in American marsupials. Chromosome Res. 15,

127–136 (2007).

71. Hore,T.A., Koina,E., Wakefield,M.J. &

Graves,J.A.M. The region homologous to the

X-chromosome inactivation centre has been disrupted

in marsupial and monotreme mammals. Chromosome

Res. 15, 147–161 (2007).

REVIEWS

ADVANCE ONLINE PUBLICATION www.nature.com/nrg

72. Hore,T.A., Rapkins,R.W. & Graves,J.A.M.

Construction and evolution of imprinted loci in

mammals. Trends Genet. 23, 440–448 (2007).

73. Duret,L., Chureau,C., Samain,S., Weissenbach,J. &

Avner,P. The Xist RNA gene evolved in eutherians by

pseudogenization of a protein-coding gene. Science

312, 1653–1655 (2006).

74. Grant,J. etal. Rsx is a metatherian RNA with Xist-like

properties in X-chromosome inactivation. Nature 487,

254–258 (2012).

This paper describes a locus, non‑homologous to

XIST and independently evolved, that controls the

inactivation of the marsupial Xchromosome by

inducing a silencing domain.

75. Murtagh,C.E.A. A unique cytogenetic system in

monotremes. Chromosoma 65, 37–57 (1977).

76. Grutzner,F. etal. In the platypus a meiotic chain of ten

sex chromosomes shares genes with the bird Z and

mammal Xchromosomes. Nature 432, 913–917

(2004).

77. Rens,W. etal. Resolution and evolution of the

duck-billed platypus karyotype with an

X1Y1X2Y2X3Y3X4Y4X5Y5 male sex chromosome

constitution. Proc. Natl Acad. Sci. USA 101 ,

16257–16261 (2004).

78. Rens,W. etal. The multiple sex chromosomes of

platypus and echidna are not completely identical and

several share homology with the avian Z. Genome Biol.

8, 243 (2007).

79. Wrigley,J.M. & Graves,J.A.M. Sex chromosome

homology and incomplete, tissue-specific

X-inactivation suggest that monotremes represent an

intermediate stage of mammalian sex chromosome

evolution. J.Hered. 79, 115–118 (1988).

80. Ho,K.K., Deakin,J.E., Wright,M.L., Graves,J.A.M.

& Grutzner,F. Replication asynchrony and differential

condensation of Xchromosomes in female platypus

(Ornithorhynchus anatinus). Reprod. Fertil. Dev. 21,

952–963 (2009).

81. Deakin,J.E., Hore,T.A., Koina,E. & Graves,J.A.M.

The status of dosage compensation in the multiple

Xchromosomes of the platypus. PLoS Genet. 4,

e1000140 (2008).

82. Shetty,S., Griffin,D.K. & Graves,J.A.M.

Comparative painting reveals strong chromosome

homology over 80 million years of bird evolution.

Chromosome Res. 7, 289–295 (1999).

83. Nanda,I., Schlegelmilch,K., Haaf,T., Schartl,M. &

Schmid,M. Synteny conservation of the Z

chromosome in 14 avian species (11 families)

supports a role for Z dosage in avian sex

determination. Cytogenet. Genome Res. 122,

150–156 (2008).

84. Zhou,Q. etal. Complex evolutionary trajectories of

sex chromosomes across bird taxa. Science 346,

6215 (2014).

This paper describes and compares bird sex

chromosomes at the sequence level, confirming the

conservation of the bird Z chromosome and the

different extents of W chromosome degradation.

85. Baverstock,P.R., Adams,M., Polkinghorne,R.W. &

Gelder,M. A sex-linked enzyme in

birds—Z-chromosome conservation but no dosage

compensation. Nature 296, 763–766 (1982).

86. McQueen,H.A. & Clinton,M. Avian sex

chromosomes: dosage compensation matters.

Chromosome Res. 17, 687–697 (2009).

87. Melamed,E. & Arnold,A.P. The role of LINEs

and CpG islands in dosage compensation on the

chicken Z chromosome. Chromosome Res. 17,

727–736 (2009).

88. Itoh,Y. etal. Dosage compensation is less

effective in birds than in mammals. J.Biol. 6, 2

(2007).

89. Ellegren,H. etal. Faced with inequality: chicken do not

have a general dosage compensation of sex-linked

genes. BMC Biol. 5, 40 (2007).

90. Livernois,A.M., Graves,J.A.M. & Waters,P.D.

The origin and evolution of vertebrate sex

chromosomes and dosage compensation. Heredity

108, 50–58 (2012).

91. Mank,J.E. & Ellegren,H. All dosage compensation is

local: gene-by-gene regulation of sex-biased

expression on the chicken Z chromosome. Heredity

102, 312–320 (2009).

92. Melamed,E. & Arnold,A.P. Regional differences in

dosage compensation on the chicken Z chromosome.

Genome Biol. 8, R202 (2007).

The authors of this paper demonstrate a dosage

valley on the chicken Z chromosome that shows

some regional dosage compensation.

93. Itoh,Y., Kampf,K. & Arnold,A.P. Possible differences

in the two Z chromosomes in male chickens and

evolution of MHM sequences in Galliformes.

Chromosoma 120, 587–598 (2011).

94. Teranishi,M. etal. Transcripts of the MHM region on

the chicken Z chromosome accumulate as non-coding

RNA in the nucleus of female cells adjacent to the

DMRT1 locus. Chromosome Res. 9, 147–165 (2001).

95. Uebbing,S., Kunstner,A., Makinen,H. & Ellegren,H.

Transcriptome sequencing reveals the character

of incomplete dosage compensation across

multiple tissues in flycatchers. Genome Biol. Evol. 5,

1555–1566 (2013).

96. Naurin,S., Hansson,B., Hasselquist,D., Kim,Y.H. &

Bensch,S. The sex-biased brain: sexual dimorphism in

gene expression in two species of songbirds. BMC

Genomics 12, 37 (2011).

97. Itoh,Y. etal. Sex bias and dosage compensation in the

zebra finch versus chicken genomes: general and

specialized patterns among birds. Genome Res. 20,

512–518 (2010).

98. Adolfsson,S. & Ellegren,H. Lack of dosage

compensation accompanies the arrested stage of sex

chromosome evolution in ostriches. Mol. Biol. Evol.

30, 806–810 (2013).

99. Kawai,A. etal. Different origins of bird and reptile sex

chromosomes inferred from comparative mapping of

chicken Z-linked genes. Cytogenet. Genome Res. 11 7 ,

92–102 (2007).

100. Matsubara,K. etal. Evidence for different origin of

sex chromosomes in snakes, birds, and mammals and

step-wise differentiation of snake sex chromosomes.

Proc. Natl Acad. Sci. USA 103, 18190–18195

(2006).

101. O’Meally,D. etal. Non-homologous sex chromosomes

of birds and snakes share repetitive sequences.

Chromosome Res. 18, 787–800 (2010).

102. Vicoso,B., Emerson,J.J., Zektser,Y., Mahajan,S. &

Bachtrog,D. Comparative sex chromosome genomics

in snakes: differentiation, evolutionary strata, and lack

of global dosage compensation. PLoS Biol. 11,

e1001643 (2013).

By assembling and comparing the genomic

sequences of male and female snakes from

different families, the authors of this paper show

almost complete W chromosome degradation in

two families and the absence of global Z

chromosome dosage compensation.

103. Schultheiss,R., Viitaniemi,H.M. & Leder,E.H.

Spatial dynamics of evolving dosage compensation in

a young sex chromosome system. Genome Biol. Evol.

7, 581–590 (2015).

104. Reinius,B. etal. Abundance of female-biased and

paucity of male-biased somatically expressed genes

on the mouse X-chromosome. BMC Genomics 13, 607

(2012).

105. Chen,S. etal. Whole-genome sequence of a flatfish

provides insights into ZW sex chromosome evolution

and adaptation to a benthic lifestyle. Nat. Genet. 46,

253–260 (2014).

106. Shao,C. etal. Epigenetic modification and inheritance

in sexual reversal of fish. Genome Res. 24, 604–615

(2014).

References 105 and 106 report the discovery of a

fish with epigenetic control of sex determination

(methylation of DMRT1) and the beginnings of a

regional control of Z chromosome gene dosage.

107. Lahn,B.T. & Page,D.C. Four evolutionary strata on

the human Xchromosome. Science 286, 964–967

(1999).

108. Graves,J.A.M., Wakefield,M.J. & Toder,R.

The origin and evolution of the pseudoautosomal

regions of human sex chromosomes. Hum. Mol. Genet.

7, 1991–1996 (1998).

109. Raudsepp,T., Das,P.J., Avila,F. & Chowdhary,B.P.

The pseudoautosomal region and sex chromosome

aneuploidies in domestic species. Sex. Dev. 6, 72–83

(2012).

110 . Mensah,M.A. etal. Pseudoautosomal region 1

length polymorphism in the human population.

PLoS Genet. 10, e1004578 (2014).

111. White,M.A., Ikeda,A. & Payseur,B.A. A pronounced

evolutionary shift of the pseudoautosomal region

boundary in house mice. Mamm. Genome 23,

454–466 (2012).

112 . Bellott,D.W. etal. Mammalian Ychromosomes retain

widely expressed dosage-sensitive regulators. Nature

508, 494–499 (2014).

113 . Wang,J. etal. Imprinted X inactivation maintained

by a mouse Polycomb group gene. Nat. Genet. 28,

371–375 (2001).

114 . Bellott,D.W. etal. Convergent evolution of chicken Z

and human Xchromosomes by expansion and gene

acquisition. Nature 466, 612–616 (2010).

115 . Khil,P.P., Smirnova,N.A., Romanienko,P.J. &

Camerini-Otero,R.D. The mouse Xchromosome is

enriched for sex-biased genes not subject to selection

by meiotic sex chromosome inactivation. Nat. Genet.

36, 642–646 (2004).

116 . Leder,E.H. etal. Female-biased expression on the

Xchromosome as a key step in sex chromosome

evolution in threespine sticklebacks. Mol. Biol. Evol.

27, 1495–1503 (2010).

117 . Heard,E. & Disteche,C.M. Dosage compensation

in mammals: fine-tuning the expression of the

Xchromosome. Genes Dev. 20, 1848–1867 (2006).

118 . Veitia,R.A., Veyrunes,F., Bottani,S. & Birchler,J.A.

X chromosome inactivation and active X upregulation

in therian mammals: facts, questions, and hypotheses.

J.Mol. Cell. Biol. 7, 2–11 (2015).

119 . Nguyen,D.K. & Disteche,C.M. Dosage compensation

of the active Xchromosome in mammals. Nat. Genet.

38, 47–53 (2006).

120. Deng,X. etal. Mammalian X upregulation is

associated with enhanced transcription initiation, RNA

half-life, and MOF-mediated H4K16 acetylation. Dev.

Cell 25, 55–68 (2013).

121. Yildirim,E., Sadreyev,R.I., Pinter,S.F. & Lee,J.T.

X-chromosome hyperactivation in mammals via

nonlinear relationships between chromatin states and

transcription. Nat. Struct. Mol. Biol. 19, 56–61

(2012).

122. Faucillion,M.L. & Larsson,J. Increased expression

of X-linked genes in mammals is associated with a

higher stability of transcripts and an increased

ribosome density. Genome Biol. Evol. 7, 1039–1052

(2015).

123. Xiong,Y. etal. RNA sequencing shows no dosage

compensation of the active X-chromosome. Nat.

Genet. 42, 1043–1047 (2010).

124. Pessia,E., Engelstadter,J. & Marais,G.A. The

evolution of Xchromosome inactivation in mammals:

the demise of Ohno’s hypothesis? Cell. Mol. Life Sci.

71, 1383–1394 (2014).

125. Chen,X. & Zhang,J. No x-chromosome dosage

compensation in human proteomes. Mol. Biol. Evol.

32, 1456–1460 (2015).

126. Pessia,E., Makino,T., Bailly-Bechet,M.,

McLysaght,A. & Marais,G.A. Mammalian

Xchromosome inactivation evolved as a dosage-

compensation mechanism for dosage-sensitive genes

on the Xchromosome. Proc. Natl Acad. Sci. USA 109 ,

5346–5351 (2012).

127. Lin,F., Xing,K., Zhang,J. & He,X. Expression

reduction in mammalian Xchromosome evolution

refutes Ohno’s hypothesis of dosage compensation.

Proc. Natl Acad. Sci. USA 109, 11752–11757

(2012).

128. Jue,N.K. etal. Determination of dosage

compensation of the mammalian Xchromosome by

RNA-seq is dependent on analytical approach. BMC

Genomics 14, 150 (2013).

129. Castagne,R. etal. The choice of the filtering method in

microarrays affects the inference regarding dosage

compensation of the active X-chromosome. PLoS ONE

6, e23956 (2011).

130. Wolf,J.B. & Bryk,J. General lack of global dosage

compensation in ZZ/ZW systems? Broadening the

perspective with RNA-seq. BMC Genomics 12, 91

(2011).

131. Muyle,A. etal. Rapid denovo evolution of

Xchromosome dosage compensation in Silene

latifolia, a plant with young sex chromosomes. PLoS

Biol. 10, http://dx.doi.org/10.1371/journal.

pbio.1001308 (2012).

132. Cooper,D.W. Directed genetic change model for

Xchromosome inactivation in eutherian mammals.

Nature 230, 292–294 (1971).

133. Turner,J.M. Meiotic sex chromosome inactivation.

Development 134, 1823–1831 (2007).

134. Hornecker,J.L., Samollow,P.B., Robinson,E.S.,

Vandeberg,J.L. & McCarrey,J.R. Meiotic sex

chromosome inactivation in the marsupial

Monodelphis domestica. Genesis 45, 696–708

(2007).

135. Namekawa,S.H., VandeBerg,J.L., McCarrey,J.R. &

Lee,J.T. Sex chromosome silencing in the marsupial

male germ line. Proc. Natl Acad. Sci. USA 10 4,

9730–9735 (2007).

136. Ohhata,T. & Wutz,A. Reactivation of the inactive

Xchromosome in development and reprogramming.

Cell. Mol. Life Sci. 70, 2443–2461 (2013).

REVIEWS

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137. Barlow,D.P. & Bartolomei,M.S. Genomic imprinting

in mammals. Cold Spring Harb. Perspect. Biol. 6,

a018382 (2014).

138. Chandra,H.S. & Brown,S.W. Chromosome

imprinting and the mammalian Xchromosome. Nature

253, 165–168 (1975).

139. Reik,W. & Lewis,A. Co-evolution of X-chromosome

inactivation and imprinting in mammals. Nat. Rev.

Genet. 6, 403–410 (2005).

140. Autuoro,J.M., Pirnie,S.P. & Carmichael,G.G.

Long noncoding RNAs in imprinting and

Xchromosome inactivation. Biomolecules 4, 76–100

(2014).

141. Gribnau,J. & Grootegoed,J.A. Origin and evolution

of Xchromosome inactivation. Curr. Opin. Cell Biol.

24, 397–404 (2012).

142. Peeters,S.B., Cotton,A.M. & Brown,C.J. Variable

escape from X-chromosome inactivation: identifying

factors that tip the scales towards expression.

Bioessays 36, 746–756 (2014).

143. Arnold,A.P., Itoh,Y. & Melamed,E. A bird’s-eye view

of sex chromosome dosage compensation. Annu. Rev.

Genomics Hum. Genet. 9, 109–127 (2008).

144. Gendrel,A.V. & Heard,E. Noncoding RNAs and

epigenetic mechanisms during X-chromosome

inactivation. Annu. Rev. Cell Dev. Biol. 30, 561–580

(2014).

145. Froberg,J.E., Yang,L. & Lee,J.T. Guided by RNAs:

X-inactivation as a model for lncRNA function.

J.Mol. Biol. 425, 3698–3706 (2013).

146. Romito,A. & Rougeulle,C. Origin and evolution of the

long non-coding genes in the X-inactivation center.

Biochimie 93, 1935–1942 (2011).

147. Reinius,B. etal. Female-biased expression of long

non-coding RNAs in domains that escape

X-inactivation in mouse. BMC Genomics 11, 614

(2010).

148. Zwemer,L.M. etal. Autosomal monoallelic expression

in the mouse. Genome Biol. 13, R10 (2012).

149. Chess,A. Mechanisms and consequences of

widespread random monoallelic expression. Nat. Rev.

Genet. 13, 421–428 (2012).

150. Deng,Q., Ramskold,D., Reinius,B. & Sandberg,R.

Single-cell RNA-seq reveals dynamic, random

monoallelic gene expression in mammalian cells.

Science 343, 193–196 (2014).

151. Ohlsson,R., Paldi,A. & Graves,J.A.M. Did genomic

imprinting and Xchromosome inactivation arise from

stochastic expression? Trends Genet. 17, 136–141

(2001).

This paper proposes the hypothesis that epigenetic

control arose from an ancient mechanism of

monoallelic expression.

152. Mould,A.W. etal. Smchd1 regulates a subset of

autosomal genes subject to monoallelic expression in

addition to being critical for X inactivation. Epigenet.

Chromatin 6, 19 (2013).

153. Nag,A., Vigneau,S., Savova,V., Zwemer,L.M. &

Gimelbrant,A.A. Chromatin signature identifies

monoallelic gene expression across mammalian cell

types. G3 5, 1713–1720 (2015).

154. Li,Q. etal. Genome-wide mapping of DNA

methylation in chicken. PLoS ONE 6, e19428 (2011).

155. Feil,R. & Berger,F. Convergent evolution of genomic

imprinting in plants and mammals. Trends Genet. 23,

192–199 (2007).

156. Saksouk,N. etal. Redundant mechanisms to form

silent chromatin at pericentromeric regions rely on

BEND3 and DNA methylation. Mol. Cell 56, 580–594

(2014).

157. He,X.J., Ma,Z.Y. & Liu,Z.W. Non-coding RNA

transcription and RNA-directed DNA methylation in

Arabidopsis. Mol. Plant 7, 1406–1414 (2014).

158. Talbert,P.B. & Henikoff,S. Histone variants—ancient

wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol.

11, 264–275 (2010).

159. Gamble,M.J. & Kraus,W.L. Multiple facets of the

unique histone variant macroH2A: from genomics to

cell biology. Cell Cycle 9, 2568–2574 (2010).

160. Banaszynski,L.A., Allis,C.D. & Lewis,P.W.

Histone variants in metazoan development. Dev. Cell

19, 662–674 (2010).

161. Ebert,A., Lein,S., Schotta,G. & Reuter,G.

Histone modification and the control of

heterochromatic gene silencing in Drosophila.

Chromosome Res. 14, 377–392 (2006).

162. Zakharova,I.S. etal. Histone H3 trimethylation at

lysine 9 marks the inactive metaphase Xchromosome

in the marsupial Monodelphis domestica.

Chromosoma 120, 177–183 (2011).

163. Rigal,M. & Mathieu,O. A “mille-feuille” of silencing:

epigenetic control of transposable elements. Biochim.

Biophys. Acta 1809, 452–458 (2011).

164. Koepfli,K.P., Paten,B., Genome,K.C.o. S. &

O’Brien,S.J. The Genome 10K Project: a way forward.

Annu. Rev. Anim. Biosci. 3, 57–111 (2015).

Competing interests

The author declares no competing interests.

REVIEWS

ADVANCE ONLINE PUBLICATION www.nature.com/nrg

Characterizing intra-chromosomal homologous recombination on the human Y chromosome: An examination of amplicon copy number variation and gene conversion activity

Thesis

Full-text available

Sep 2023

Valdis Björt Guðmundsdóttir

The Y chromosome in humans has several peculiarities relative to the rest of the genome, with its lack of recombination for the most part, the accumulation of heterochromatic sequences and sparsity of functional genes. Nevertheless, and in fact because of some of those properties, the human Y chromosome provides a powerful tool for the study of phylogenetics, population genetics, genealogy and forensics. Yet it is a somewhat neglected subject of research, one reason being the overrepresentation of repetitive sequences which presents challenges to the short-read mapping of whole-genome sequencing. The complex landscape of the ampliconic regions, which harbour genes expressed in testes and therefore important for maleness, exemplify this well. The studies presented in this thesis provide an examination of intra-chromosomal homologous recombination events on the Y chromosome, in the form of duplications and/or deletions of whole amplicon units and the activity of gene conversion in the palindromes and its implications for Y chromosome degeneration, male fertility and phenotypic effects. First, we present a detailed analysis of the rate and nature of gene conversion events in palindromes using paralog-combined reads and patrilineal genealogies and demonstrate how this can be used to improve our understanding of the dynamic relationship between mutation and gene conversion and how they influence the evolution of the palindromic sequences and the genes within them. Our results point towards the homogenisation of paralogous sequences along with a bias towards C and G alleles as being the main ongoing mechanisms in intra-palindromic Y-Y gene conversion. Second, we estimate the de novo mutation rate and the long-term evolution of copy number in amplicon units in human populations. In addition, we explore the effects of copy number variations on a variety of phenotypic traits. Intriguingly, we conclude that the phenotypic impact of the Y ampliconic copy number variation is somewhat limited in humans. Overall, this thesis sheds light on the role of intra-chromosomal gene conversion in the preservation of the most functionally important parts of the human Y chromosome and provides evidence for weak selection against non-reference copy number carriers.

Multiple Transitions between Y Chromosome and Autosome in Tago’s Brown Frog Species Complex

Article

Full-text available

Feb 2024

Sex chromosome turnover is the transition between sex chromosomes and autosomes. Although many cases have been reported in poikilothermic vertebrates, their evolutionary causes and genetic mechanisms remain unclear. In this study, we report multiple transitions between the Y chromosome and autosome in the Japanese Tago’s brown frog complex. Using chromosome banding and molecular analyses (sex-linked and autosomal single nucleotide polymorphisms, SNPs, from the nuclear genome), we investigated the frogs of geographic populations ranging from northern to southern Japan of two species, Rana tagoi and Rana sakuraii (2n = 26). Particularly, the Chiba populations of East Japan and Akita populations of North Japan in R. tagoi have been, for the first time, investigated here. As a result, we identified three different sex chromosomes, namely chromosomes 3, 7, and 13, in the populations of the two species. Furthermore, we found that the transition between the Y chromosome (chromosome 7) and autosome was repeated through hybridization between two or three different populations belonging to the two species, followed by restricted chromosome introgression. These dynamic sex chromosome turnovers represent the first such findings in vertebrates and imply that speciation associated with inter- or intraspecific hybridization plays an important role in sex chromosome turnover in frogs.

Two novel genomes of fireflies with different degrees of sexual dimorphism reveal insights into sex-biased gene expression and dosage compensation

Preprint

Full-text available

Dec 2023

Sexual dimorphism arises because of divergent fitness optima between the sexes. Phenotypic divergence between sexes can range from mild to extreme, as observed in various species of bioluminescent beetles - fireflies. Fireflies present various degrees of sexual dimorphism, including female neoteny, posing a unique framework to investigate the evolution of sexually dimorphic traits across species. In this work, we present novel assembled genomes of two firefly species, Lamprohiza splendidula and Luciola italica, species with different degrees of sexual dimorphism. We uncovered high synteny conservation of the X-chromosome across ~ 150 Mya. We also found full X-chromosome dosage compensation in our two fireflies hinting at common mechanism upregulating the single male X-chromosome. Different degrees of sex-biased expressed genes were found across two body parts showing different proportions of expression congruence between species. Interestingly, we did not find X-chromosome enrichment of sex-biased genes, but retrieved autosomal enrichment of sex-biased genes. We further uncovered higher nucleotide diversity in the intronic regions of sex-biased genes, hinting at a maintenance of heterozygosity through sexual selection. We identified different levels of sex-biased gene expression divergence including sex-biased genes conserved between species. Divergent and conserved sex-biased genes are candidate to test their role in sexually dimorphic traits.

Genomic reconsideration of fish non-monophyly: why cannot we simply call them all ‘fish’?

Article

Full-text available

Dec 2023
ICHTHYOL RES

Extant ‘fishes’ belong to jawless, cartilaginous, actinopterygian, or sarcopterygian fish lineages. They comprise a non-monophyletic group of vertebrates from which tetrapods are excluded, and they are therefore paraphyletic. Recent advances in whole-genome sequencing have shed light on phylogenetic relationships, divergence times among major fish lineages, and the molecular basis of phenotypic diversity. This review encompasses the diversity of extant fishes and explores the variation in genomic organization and its evolutionary origins. This review begins with evaluating available genomic sequence resources with a focus on literally complete (‘telomere-to-telomere’) sequencing. Next, it discusses among-lineage variations in genomic contents, considering karyotype reports, genome sizes, and whole-genome duplication events. Additionally, we investigate three families of protein-coding genes, visual opsins, aquaporins (Aqps), and Hox genes, as they offer insights into morphological and physiological differences among major fish lineages. Overall, our technical basis of analyzing fish genomes and the knowledge of genomic organization provide valuable insights into our vertebrate-wide understanding of how molecular mechanisms specifying variable phenotypes are encoded in genomic sequence information.

A rapid approach for sex assignment by RAD-seq using a reference genome

Article

Full-text available

Apr 2024
PLOS ONE

Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of two ad hoc indexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.

Overview of chicken embryo genes related to sex differentiation

Article

Mar 2024

Sex determination in chickens at an early embryonic stage has been a longstanding challenge in poultry production due to the unique ZZ:ZW sex chromosome system and various influencing factors. This review has summarized the genes related to the sex differentiation of chicken early embryos (mainly Dmrt1 , Sox9 , Amh , Cyp19a1 , Foxl2 , Tle4z1 , Jun , Hintw , Ube2i , Spin1z , Hmgcs1 , Foxd1 , Tox3 , Ddx4 , cHemgn and Serpinb11 in this article), and has found that these contributions enhance our understanding of the genetic basis of sex determination in chickens, while identifying potential gene targets for future research. This knowledge may inform and guide the development of sex screening technologies for hatching eggs and support advancements in gene-editing approaches for chicken embryos. Moreover, these insights offer hope for enhancing animal welfare and promoting conservation efforts in poultry production.

Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster ( Heloderma suspectum ) Revealed by De Novo Genome Assembly

Article

Full-text available

Feb 2024

Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z-chromosome scaffolds. These putative Z-chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.

Female long-term sperm storage results in viable offspring in the Himalayan Mountain Pitviper, Ovophis monticola

Article

Full-text available

Jan 2024
ZOO BIOL

The ability of females to store sperm for extended periods in their reproductive tracts (termed long-term sperm storage, LTSS) has been reported across a diversity of vertebrate taxa. The evolutionary, ecological, and physiological significance of LTSS is wide-ranging and includes the ability to produce offspring when mates may be temporally scarce by way of decoupling copulation from ovulation, inbreeding avoidance, and the generation and maintenance of genetic diversity in progeny. Among vertebrate lineages, nonavian reptiles exhibit a remarkable capacity for LTSS, with the production of viable offspring reported after periods exceeding 6 years since prior contact with a potential mate. Given that female reptiles are able to store viable sperm for prolonged periods, it is important to disentangle LTSS from that of facultative parthenogenesis (FP), a reproductive trait which appears widespread among all reptile lineages. The implications of this distinction are particularly important in the context of the development and management of captive breeding programs. To accurately determine between the two reproductive strategies, genomic screening is highly recommended. Following a period of isolation for 13 months from a potential male mate, a female Himalayan Mountain Pitviper (Ovophis monticola) produced a clutch of three male offspring. Here, through genome-scale analyses of the female and her progeny, we document the first record of LTSS in this genus and exclude FP as the alternative hypothesis.

Unleashing diversity through flexibility: The evolutionary journey of sex chromosomes in amphibians and reptiles

Article

Dec 2023

Sex determination systems have greatly diversified between amphibians and reptiles, with such as the different sex chromosome compositions within a single species and transition between temperature‐dependent sex determination (TSD) and genetic sex determination (GSD). In most sex chromosome studies on amphibians and reptiles, the whole‐genome sequence of Xenopous tropicalis and chicken have been used as references to compare the chromosome homology of sex chromosomes among each of these taxonomic groups, respectively. In the present study, we reviewed existing reports on sex chromosomes, including karyotypes, in amphibians and reptiles. Furthermore, we compared the identified genetic linkages of sex chromosomes in amphibians and reptiles with the chicken genome as a reference, which is believed to resemble the ancestral tetrapod karyotype. Our findings revealed that sex chromosomes in amphibians are derived from genetic linkages homologous to various chicken chromosomes, even among several frogs within single families, such as Ranidae and Pipidae. In contrast, sex chromosomes in reptiles exhibit conserved genetic linkages with chicken chromosomes, not only across most species within a single family, but also within closely related families. The diversity of sex chromosomes in amphibians and reptiles may be attributed to the flexibility of their sex determination systems, including the ease of sex reversal in these animals.

The Scorpionfly ( Panorpa cognata ) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome

Article

Full-text available

Nov 2023

Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.

Complex evolutionary trajectories of sex chromosomes across bird taxa

Article

Full-text available

Dec 2014
SCIENCE

Bipartite structure of the inactive mouse X chromosome

Article

Full-text available

Aug 2015
GENOME BIOL

In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. We find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a hinge region. Comparison with the recently reported bipartite 3D structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the hinge is conserved and located near the Dxz4/DXZ4 locus. In mouse, the hinge region also contains a minisatellite Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation, compared to the active alleles and to genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele. By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.

Chromatin Signature Identifies Monoallelic Gene Expression Across Mammalian Cell Types

Article

Full-text available

Jun 2015

Monoallelic expression of autosomal genes (MAE) is a widespread epigenetic phenomenon which is poorly understood, due in part to current limitations of genome-wide approaches for assessing it. Recently, we reported that a specific histone modification signature is strongly associated with MAE, and demonstrated that it can serve as a proxy of MAE in human lymphoblastoid cells. Here, we use murine cells to establish that this chromatin signature is conserved between mouse and human, and is associated with MAE in multiple cell types. Our analyses reveal extensive conservation in the identity of MAE genes between the two species. By analyzing MAE chromatin signature in a large number of cell and tissue types, we show that it remains consistent during terminal cell differentiation and is predominant among cell-type specific genes, suggesting a link between MAE and specification of cell identity. Copyright © 2015 Author et al.

Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development (Nature (2011) 472 (370-374))

Article

Jun 2011

Sex Chromosomes and Sex-Linked Genes

Article

Jan 1967
Monogr Endocrinol

Susumu Ohno

Natural selection operates among individual organisms which differ in their genetic constitution. The degree of hereditary variability within a species is greatly enhanced by cross-fertilization. Indeed, the mechanism of sexual reproduction occurred very early in evolution, for it is seen today even in bacteria. In Escherichia coli, fertilization occurs by passage of the single chromosome from the male into the female bacterium (LEDERBERG, 1959). In multicellular organisms, the separation of germ from soma, and the production of haploid gametes became mandatory. The gametes were of two types. One, extremely mobile, was designed to seek out and penetrate the other, which loaded with nutrients, received the mobile gamete and intiated the development of a new individual. The foundation for true bisexuality was thus laid. In the primitive state of bisexuality, whether an individual is to be a sperm-producing male or an egg-producing female appears to be decided rather haphazardly. In the worm, Banelia viridis, the minute males are parasites in the female. Larvae that become attached to the proboscis of an adult female become males, while unattached larvae sink to the bottom and become females (BALTZER, 1935). The more sophisticated state of bisexuality was initiated by setting aside a particular pair of chromosomes for specialization and making either the male or the female a heterogametic sex. Sex chromosomes as we know them were thus born.

Sex Chromosomes and Sex-linked Genes

Book

Jan 1966

Susumu Ohno

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

Article

Jul 2016

Male meiotic sex chromosome inactivation and meiotic silencing

Chapter

Apr 2007

Until recently, meiotic sex chromosome inactivation (MSCI) was regarded as an oddity of spermatogenesis with an ill-defined function. Recent experiments, especially those on the flatworm Caenorhabditis elegans and on mice, have now challenged this view. In this review, we summarize the molecular mechanisms involved in MSCI, which in mice utilizes members of the DNA repair pathway including BRCA1, ATR, and histone H2AX. MSCI is driven by the asynaptic nature of the sex chromosomes during pachytene of male meiosis, and therefore represents an example of a recently identified more general silencing mechanism - meiotic silencing of unsynapsed chromatin (MSUC) - that serves to transcriptionally repress any unsynapsed chromatin in males or females. It is well established that during pachytene, there is also a "checkpoint" response to the presence of unsynapsed chromatin; and following from studies in yeast, it is thought that the checkpoint is triggered by the presence of DNA double-strand breaks (DSBs) that remain unrepaired in unsynapsed regions. The possible links between MSUC and this pachytene checkpoint are discussed. It has recently been proposed that, inmammals, MSCI serves to provide preimplantation XX embryos with a preinactivated paternal X chromosome (imprinted XCI). New studies show that although MSCI is causally linked to a substantial degree of postmeiotic X and Y silencing in round spermatids, MSCI and imprinted XCI can be dissociated. In summary, recent studies of MSCI, in addition to clarifying the molecular basis of the epigenetic processes that lead to inactivation, have shown it to be a manifestation of a more general response to unsynapsed chromatin that may be a component of the pachytene checkpoint response and that is maintained into spermatid development. © 2007 by World Scientific Publishing Co. Pte. Ltd. All rights reserved.

Gene action in the X chromosome of the mouse

Article

Jan 1961

M.F. Lyon

Four evolutionary strata on the human X chromosome (vol 286, pg 964, 1999)

Article

Dec 1999

Evolution of vertebrate sex chromosomes and dosage compensation

Abstract

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