Out of Balance: R-loops in Human Disease

Abstract

R-loops are cellular structures composed of an RNA/DNA hybrid, which is formed when the RNA hybridises to a complementary DNA strand and a displaced single-stranded DNA. R-loops have been detected in various organisms from bacteria to mammals and play crucial roles in regulating gene expression, DNA and histone modifications, immunoglobulin class switch recombination, DNA replication, and genome stability. Recent evidence suggests that R-loops are also involved in molecular mechanisms of neurological diseases and cancer. In addition, mutations in factors implicated in R-loop biology, such as RNase H and SETX (senataxin), lead to devastating human neurodegenerative disorders, highlighting the importance of correctly regulating the level of R-loops in human cells. In this review we summarise current advances in this field, with a particular focus on diseases associated with dysregulation of R-loop structures. We also discuss potential therapeutic approaches for such diseases and highlight future research directions.

Full text

Review
Out of Balance: R-loops in Human Disease
Matthias Groh, Natalia Gromak*
Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
Abstract: R-loops are cellular structures composed of an
RNA/DNA hybrid, which is formed when the RNA
hybridises to a complementary DNA strand and a
displaced single-stranded DNA. R-loops have been
detected in various organisms from bacteria to mammals
and play crucial roles in regulating gene expression, DNA
and histone modifications, immunoglobulin class switch
recombination, DNA replication, and genome stability.
Recent evidence suggests that R-loops are also involved in
molecular mechanisms of neurological diseases and
cancer. In addition, mutations in factors implicated in R-
loop biology, such as RNase H and SETX (senataxin), lead
to devastating human neurodegenerative disorders,
highlighting the importance of correctly regulating the
level of R-loops in human cells. In this review we
summarise current advances in this field, with a particular
focus on diseases associated with dysregulation of R-loop
structures. We also discuss potential therapeutic ap-
proaches for such diseases and highlight future research
directions.
Introduction
R-loops are three-stranded structures, which form when RNA
hybridises to a complementary DNA strand, forming an RNA/
DNA hybrid, resulting in displacement of the other DNA strand in
this process (Figure 1). The first R-loops were described in 1976,
when their formation in vitro in the presence of 70% formamide
was visualised by electron microscopy (Figure 1) [1]. These
structures were thermodynamically more stable than duplex
DNA, and they remained intact following removal of formamide.
This technique of RNA/DNA hybridisation has been used in over
140 studies to map gene organisation, transcription initiation sites,
and the direction of transcription, as well as measure the quantities
of cellular RNAs [2].
The first evidence for R-loop formation in live bacteria was
obtained in 1994 [3]. This was followed by numerous studies
showing that R-loops exist in different organisms (Figure 1) [4–6].
In living cells, R-loops are thought to form in cis during
transcription, when nascent RNA hybridises to the DNA template
behind the elongating RNA polymerase (Pol) [4]. However, in
contrast to this popular view of cotranscriptional R-loops, recent
studies suggest that RNA transcribed at one locus can hybridise to
homologous DNA at another locus, thus leading to R-loop
formation in trans [7]. In the last five years, the use of an antibody
(S9.6) recognising RNA/DNA hybrids has revolutionised the R-
loop field [8]. Initially, the S9.6 antibody, which detects hybrids as
small as six bp with an affinity of 0.6 nM, was developed as a tool
to enhance the DNA/RNA hybridisation signal in DNA
microarray studies [9,10]. More recently, it has been used to
detect R-loops in vivo and uncover their contribution to
fundamental biological processes in yeast [11,12], plants [13],
mice [14,15], and humans [16–18].
The picture emerging from these studies suggests that R-loops
can be both beneficial and deleterious to cells. Paradoxically, while
they are required for important biological processes, they can also
promote DNA damage and genome instability. In particular, R-
loops have been shown to play an essential positive function in
Escherichia coli plasmid and human mitochondrial DNA replica-
tion [19,20] and during immunoglobulin class switch recombina-
tion, which contributes to the antibody isotype diversity in
activated B cells [21]. R-loops form on many genes in yeast and
human cells [18,22] and have been implicated in regulation of
gene expression. R-loops can repress transcription and promote
transcriptional termination [16,23,24]. Furthermore, R-loops are
clearly associated with epigenetic mechanisms governing tran-
scription, including DNA methylation and posttranslational
histone modifications [18,25–27]. In spite of this growing list of
beneficial R-loop functions, it is also evident that R-loops can be a
dangerous source of DNA damage. They can sensitize DNA to
damaging agents [28], induce transcription-associated recombi-
nation [24], double-strand breaks (DSBs) [29,30], chromosome
breaks, and fragile site instability [31–33], and cause chromosome
loss [34]. Therefore, cells need to tightly regulate the levels of R-
loops to exploit their unique features. Altering the physiological R-
loop balance can impair R-loop-regulated processes, cause
genome instability, and may lead to human diseases. Consequent-
ly, defining the roles of R-loops in the multitude of biological
processes and human disease is likely to develop into one of the
most important and influential areas of R-loop research in the
future.
Proteins in R-loop Biology
The number of proteins associated with R-loop biology has
increased in the last few years, reflecting the diversity of R-loop
processes (Table S1) [4–6]. Many proteins can regulate cellular R-
loop levels either directly or indirectly, mostly by preventing RNA
from hybridising to DNA, thus reducing excessive R-loop
accumulation. Among these are proteins required for efficient
transcriptional elongation, termination, polyadenylation, RNA
splicing, packaging, and export [16,24,28,30,31,34,35]. DNA
topology itself can influence hybridisation of RNA to DNA, and
topoisomerases consequently play important roles in modulating
Citation: Groh M, Gromak N (2014) Out of Balance: R-loops in Human
Disease. PLoS Genet 10(9): e1004630. doi:10.1371/journal.pgen.1004630
Editor: Nancy Maizels, University of Washington School of Medicine, United
States of America
Published September 18, 2014
Copyright: ß2014 Groh, Gromak. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
Funding: NG is supported by a Royal Society University Research Fellowship and
MRC NIRG (MR/J007870/1). MG is supported by a PhD studentship from Ataxia
UK/Motor Neuron Disease Association (Gromak/Jun11/6278). The funders had no
role in the preparation of the article.
Competing Interests: The authors have declared that no competing interests
exist.
* Email: natalia.gromak@path.ox.ac.uk
PLOS Genetics | www.plosgenetics.org 1 September 2014 | Volume 10 | Issue 9 | e1004630

R-loop levels [27,33]. Proteins involved in maintenance of genome
integrity can also regulate R-loops, suggesting a dynamic interplay
between DNA repair and R-loop formation [7]. Importantly, cells
possess dedicated enzymes, including the members of the RNase
H family that specifically degrade the RNA in R-loops [36], and
helicases that can unwind RNA/DNA hybrids [12,16].
Recent evidence shows that R-loops can directly affect many
gene expression–associated processes, including DNA methyla-
tion, posttranslational histone modifications, and transcription, by
influencing the function of regulatory proteins [16,18,25,26].
Despite the growing number of proteins involved in R-loop
homeostasis and human disease, many questions still remain
unanswered. For many proteins with documented in vitro RNA/
DNA helicase activity (e.g., Pif1, the MCM complex), in vivo
evidence is generally still lacking (Table S1) [37,38]. Moreover, the
molecular mechanisms underlying interactions between proteins
and R-loops are poorly understood, and in many cases the
connections to disease remain obscure.
R-loops and Neurological Diseases
The biological importance of R-loops in humans is supported
by the fact that mutations in proteins implicated in R-loop
resolution cause devastating human diseases, often related to
neurodegeneration. Mutations in the putative RNA/DNA helicase
SETX cause neurodegenerative diseases, the dominant juvenile
form of amyotrophic lateral sclerosis type 4 (ALS4), and a recessive
form of ataxia oculomotor apraxia type 2 (AOA2) (Figure 2A).
These diseases are characterised by progressive degeneration of
motor neurons in the brain and spinal cord, muscle weakness and
atrophy [39–41].
In addition to its predicted function as an RNA/DNA helicase,
SETX interacts with proteins involved in diverse aspects of RNA
metabolism [42]. Moreover, a single amino acid mutation, which
compromises the function of the yeast homologue Sen1, dramat-
ically changes the Pol II distribution genome-wide, further
supporting the view that SETX/Sen1 functions in the regulation
of transcription [43]. Recently, we demonstrated that SETX is
implicated in transcriptional termination by Pol II in humans [16].
It is required to resolve R-loops at termination elements, releasing
RNA for degradation by the 59–39‘‘torpedo’’ exonuclease Xrn2
prior to termination (Figure 2A) [16,44]. Mutations in the yeast
homologue, Sen1, also lead to a transcriptional termination defect,
associated with accumulation of R-loops and genome instability
[12]. In line with its function in R-loop resolution, SETX/Sen1 is
also involved in maintaining genome integrity by coordinating
transcription, DNA replication, and the DNA damage response
[45–47]. SETX can target the 39–59RNA degradation complex,
the exosome, to sites of transcription-induced DNA damage [48].
Furthermore, SETX protects genome integrity by coordinating
meiotic recombination with transcription during spermatogenesis
and gene silencing during meiotic sex chromosome inactivation [14].
In particular, Setx knock-out mice accumulated DNA double strand
breaks and R-loops and failed to disassemble Rad51 filaments. This
resulted in a failure to cross over, likely due to collision between R-
loops with Holliday junctions [14]. These defects in Setx knock-out
mice lead to male infertility, raising the question as to how this relates
to fertility of male AOA2/ALS4 patients.
Studies in neuronal cells have demonstrated a role for SETX in
neuronal differentiation through fibroblast growth factor 8 (FGF8)
signalling, providing one explanation for the effects of loss-of-
function AOA2 mutations [49]. Surprisingly, overexpression of
dominant mutant forms of SETX did not affect neuritogenesis,
suggesting that a different function of SETX may be affected in
ALS4 patients. However, the interplay between the function of
SETX in R-loop resolution, genome maintenance, and neuronal
differentiation is still unclear. In a recent study, Lavin and
colleagues examined cells from mice with disrupted Atm,Tdp1,
Setx,orAptx genes, which cause ataxia telangiectasia (AT),
spinocerebellar ataxia with axonal neuropathy 1 (SCAN1), AOA2,
and ataxia oculomotor apraxia type 1 (AOA1) disorders,
respectively [15]. These diseases are characterised by a defective
response to DNA damage, suggesting that R-loops may be
implicated in triggering genome instability. Indeed, R-loops were
found to be enriched in proliferating cells (testes), but not in the
brain tissues from Setx,Atm,Tdp1 or Aptx knock-out mice [15].
The enrichment of R-loops in testes correlated with high levels of
DNA damage and apoptosis. The lack of R-loops in brain tissue
questions the association between R-loops and neurodegeneration.
This result is surprising, because inducible R-loops have been
previously detected in neuronal cells at the Snord116 locus, which
is associated with the neurodevelopmental disorder Angelman
syndrome, as discussed below [50]. Furthermore, R-loops were
implicated in inducing DNA damage in nonproliferating cells and
post-mitotic neurons and proposed to contribute to the neurode-
generation seen in AT patients [29]. It is possible that R-loops are
regulated by different mechanisms in proliferating cells and post-
mitotic neurons, thereby leading to different R-loop kinetics and so
preventing their detection in some model systems. In particular, R-
loop accumulation may reflect collisions between transcription and
replication machineries [32,51], events which do not occur in
postmitotic neurons. It should be noted that the mouse models
currently used may not fully recapitulate all aspects of human
neurodegeneration.
Figure 1. History of R-loop research. The diagram depicts major developments in the R-loop field and diseases associated with R-loop
dysregulation.
doi:10.1371/journal.pgen.1004630.g001
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Figure 2. R-loops and human diseases. The diagram depicts the role of R-loops in human diseases. Loss of wild type protein function is depicted
by red crosses. A. Ataxia and motor neuron diseases. Mutations in human RNA/DNA helicase senataxin are associated with AOA2/ALS4 disorders and
lead to R-loop accumulation and defects in transcriptional termination by Pol II [16], the maintenance of genome integrity [46], meiotic
recombination during spermatogenesis, gene silencing during meiotic sex chromosome inactivation [14], and neuronal differentiation [49]. B.
Aicardi-Goutie
`res syndrome (AGS). AGS is associated with mutations in all three subunits of RNase H2, ssDNA 39–59exonuclease TREX1 (DNASEIII),
dsRNA-editing enzyme ADAR1, and dNTP triphosphatase SAMHD1; these trigger accumulation of unprocessed nucleic acids, including genomic DNA
with incorporated ribonucleotides, R-loops, and retroelement-derived nucleic acids, and result in the immune response characteristic of AGS [65]. C.
Trinucleotide expansion diseases. R-loops form over expanded repeats and result in decreased initiation and elongation of RNA Pol II and formation
of repressive chromatin marks, which silence the host gene containing expanded repeats [75]. D. Genome instability in cancer. Loss of proteins
protecting against abnormal R-loop accumulation, such as FIP1L1, leads to genome instability, one hallmark of cancer [31]. Yellow stars denote
double-stranded DNA breaks. E. AID-mediated mutagenesis and translocations in cancer. Single-stranded DNA in R-loops is a substrate for cytidine
deamination by activation-induced cytidine deaminase, leading to mutagenesis as indicated by orange stars [21,88]. These mutations can cause DSB
formation, leading to chromosomal translocations. The IgH/c-MYC translocation brings the strong IgH enhancers, shown as yellow box, close to
c-MYC, leading to its overexpression in Burkitt’s lymphoma [87]. Transcription of IgH/c-MYC starts from a previously inactive promoter downstream of
the translocation break point. The IgH locus is depicted in blue, c-MYC gene is in grey. The translocation breakpoint is indicated by a dashed black
line. F. Senescence. R-loops formed by the noncoding RNA TERRA accumulate at telomeres in cells deficient of Hpr1 and RNase H. In the absence of
telomerase, these R-loops promote Rad52-dependent telomere elongation and delayed senescence. In the absence of telomerase and Rad52, R-loops
promote telomere shortening and premature senescence [94].
doi:10.1371/journal.pgen.1004630.g002
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RNase H and Aicardi-Goutie
`res Syndrome (AGS)
In addition to their generation during transcription, RNA/
DNA hybrids can arise due to incorporation of ribonucleotides
into DNA by DNA polymerases during replication. RNase H
enzymes are endonucleases that cleave the RNA of RNA/DNA
hybrids in a sequence-independent manner, thus maintaining
genome stability by resolving R-loops that form during transcrip-
tion and by removing misincorporated ribonucleotides from the
DNA [36]. Eukaryotic cells have two types of these enzymes,
RNase H1 and RNase H2, which have different enzymatic and
site-specific activities [52]. In particular, RNase H1 requires a tract
of at least four ribonucleotides to cleave the RNA/DNA hybrid,
whereas RNase H2 can incise 59to a single ribonucleotide
incorporated within a DNA molecule [36,52]. Therefore, only
RNase H2 can process single ribonucleotides in the DNA, but
both enzymes are capable of eliminating RNA/DNA hybrids.
Unlike in bacteria and unicellular eukaryotic organisms, where
RNase H enzymes are dispensable for viability, both RNase H
enzymes are essential in higher eukaryotes. RNase H1 has been
implicated in mitochondrial DNA (mtDNA) replication during
mouse development, a process likely to be associated with
processing of RNA primers during mtDNA replication [53].
RNase H2 is composed of three different subunits, the catalytic
subunit 2A, and two other subunits, 2B and 2C, all of which are
required for enzyme activity. RNase H2 has been implicated in
recognition and removal of ribonucleotides incorporated into
DNA and hydrolysis of Okazaki fragment RNA primers during
DNA replication [36,54–57]. In addition, recent studies point
towards a role of RNase H2 in R-loop resolution during
transcription in vivo [11,58]. In particular, deletion of Saccharo-
myces cerevisiae RNase H2 imposes transcriptional blocks and R-
loop accumulation over rDNA regions in cells depleted of
Topoisomerase I [11] and transcriptional down-regulation of
genes with higher guanine-cytosine (GC) content at the promoter
regions, which are likely to form stable R-loops [58].
In humans, mutations in any of the three subunits of RNase H2
cause Aicardi-Goutie`res syndrome (AGS), a neurological inflam-
matory disorder, which resembles a congenital viral infection and
is associated with accumulation of ribonucleotides in the DNA
(Figure 2B) [59,60]. Interestingly, AGS can also be triggered by
mutations in single-stranded DNA (ssDNA) 39–59exonuclease
TREX1(DNASEIII) [61], double-stranded RNA (dsRNA)-editing
enzyme ADAR1 [62], and dNTP triphosphatase SAMHD1[63].
These proteins are involved in diverse pathways of nucleic acid
metabolism, although their functions are not yet fully understood.
They have been implicated in degrading ssDNA arising from
endogenous retroelements or replication stress (TREX1), regulat-
ing the intracellular dNTPs pool available for replication and
reverse transcription of these retroelements (SAMHD1), or
altering the immune response to RNA species through RNA
editing of retroelements and microRNAs (ADAR1) [64]. Muta-
tions in these proteins are associated with an accumulation of
unprocessed nucleic acids, which triggers the immune response
characteristic of AGS [64,65].
So far, pathologies linked to AGS mutations in RNase H2 have
been mainly attributed to genome instability caused by accumu-
lation of ribonucleotides in DNA [56,66]. However, a specific
contribution of R-loops and RNA/DNA hybrids to AGS
pathology has not been yet investigated. This research has been
hampered by the difficulty to uncouple the two activities of RNase
H2; its ability to remove ribonucleotides from the DNA and to
resolve R-loops, both of which are affected when RNase H2 is
deleted [52,56]. Nevertheless, several lines of evidence suggest that
R-loops may be involved in AGS pathology. Thus, an AGS-
related mutation in the yeast RNase H2 enzyme resulted in its
reduced RNA/DNA cleavage activity [52]. Since RNase H2
constitutes ,90% of the total cellular RNA/DNA hybrid cleavage
activity, its loss due to AGS mutations may lead to significant
accumulation of R-loops [56]. The importance of RNase H2 is
further highlighted by the fact that mutations in RNase H1 do not
cause AGS, suggesting that RNase H2 may have unique properties
to degrade RNA/DNA hybrids [52]. Indeed, R-loops arising
during DNA replication may be exclusively degraded by RNase
H2, as they may be inaccessible to RNase H1 [52,67]. A recently
generated S. cerevisiae RNase H2 mutant, which possesses R-loop
degrading activity but fails to remove single ribonucleotides from
the DNA [52], will be a useful tool in addressing the contribution
of unresolved transcription-associated R-loops to AGS pathology.
TREX1, ADAR1 and SAMHD1 process retroelement-derived
nucleic acids and help to suppress retroelements expansion in the
host genome and their recognition by the immune system [64].
Interestingly, recent genome-wide studies have demonstrated that
RNA/DNA hybrids are particularly enriched at retrotransposon
elements in yeast cells [22], suggesting that expansion of retro-
elements due to mutations in TREX1, ADAR1 or SAMHD1 may
lead to increased RNA/DNA hybrid levels, contributing to
autoimmunitity in AGS. Indeed, it has recently been demonstrated
that RNA/DNA hybrids can be sensed by toll-like receptor 9
(TLR9) to induce pro-inflammatory cytokine and antiviral
interferon production in dendritic cells [68].
R-loops in Nucleotide Expansion Diseases
Expansions of repetitive sequences have been linked to over
forty human diseases [69], and R-loops have been proposed to
play a role in their pathology [70–73]. Remarkably, R-loops are
formed following transcription of trinucleotide repeats in vitro, in
bacteria and human cells [70,71,73]. Interestingly, the nontem-
plate DNA strand in many repetitive sequences can adopt unusual
DNA structures, including G-quadruplexes and DNA triplexes,
which may further stabilise R-loops [74]. Moreover, R-loops
formed at CTG repeats promote repeat instability characteristic of
these diseases [71].
Recently, we demonstrated that R-loops form over expanded
GAA and CGG repeats in cells from Friedreich’s Ataxia (FRDA)
and Fragile X syndrome (FXS) patients, respectively (Figure 2C)
[75]. The abundance of these stable R-loops correlates with
expansion size, and they colocalise with the repressive chromatin
marks characteristic of these diseases (Figure 2C). R-loops can also
trigger the formation of repressive chromatin and cause transcrip-
tional silencing of the FXN gene, providing a molecular link
between R-loops and the pathology of expansion diseases [75]. In
line with R-loops formed on expanded ‘‘premutation’’ and ‘‘full
mutation’’ CGG-repeat-containing alleles of the FMR1 gene
[75,76], promoter-bound FMR1 mRNA containing trinucleotide
repeats was shown to promote epigenetic silencing in FXS [77].
Importantly, the involvement of R-loops in expansion diseases is
not limited to trinucleotide repeats, since R-loops associated with
expanded hexanucleotide GGGGCC repeats in C9orf72 contrib-
ute to the molecular event leading to amyotrophic lateral sclerosis
(ALS) and frontotemporal dementia (FTD) [78].
R-loops could contribute to the pathology of expansion diseases
in various ways. Similar to R-loops at the 39ends of human genes,
expansion-associated R-loops may form a structural block, directly
interfering with Pol II transcriptional elongation [16,24]. Alterna-
tively, R-loops may nucleate repressive chromatin over the
expansion region, by analogy with heterochromatin formation at
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centromeres in Schizosaccharomyces pombe [25], or promote
chromatin compaction associated with histone H3S10 phosphor-
ylation, as observed in S. cerevisiae,Caenorhabditis elegans, and
human cells [26]. Furthermore, R-loops could cause the charac-
teristic intergenerational and somatic instability of repeat sequenc-
es [72].
R-loops in Cancer
Genome instability is a hallmark of cancer, and it may actively
drive hereditary tumour development [79,80]. Research in the last
decade has clearly demonstrated that dysregulation of R-loops can
corrupt genome integrity, resulting in increased DNA sensitivity to
damaging agents, formation of DSBs, chromosome breaks, fragile
site instability, chromosome loss, and recombination events [5].
Several mechanisms have therefore evolved to maintain R-loop
levels in balance, and alterations in genome caretaker processes can
affect R-loop levels and genome stability [4]. Moreover, mutations
in proteins controlling R-loop levels have been identified in tumours
(Figure 2D). For example, in eosinophilic leukemia, an oncogenic
translocation renders cleavage and polyadenylation factor FIP1L1
inactive, which has been previously shown to cause increased R-
loop levels, DNA damage and chromosome instability (Figure 2D)
[31]. A similar mechanism was suggested for RNA kinase CLP1,
which is associated with a translocation in mixed lineage leukemia
(MLL) [31]. The histone ubiquitin ligase BRE1 also limits R-loop
levels, and its decreased expression may contribute to the high levels
of genomic instability observed in testicular seminoma [81].
The link between R-loops and cancer has been further
substantiated by the finding that the tumour suppressor BRCA2,
which is mutated in breast and ovarian cancer, is required to prevent
R-loop accumulation and genome instability [82]. These observa-
tions raise the interesting possibility that R-loops may provide
proliferative advantages to tumour cells by promoting genome
instability. This will in turn increase the probability of accumulating
mutations favourable to tumour growth and metastasis. Intriguingly,
recent evidence demonstrates that human oncogenic viruses may
also promote genomic instability through accumulation of R-loops
after infection. Kaposi’s sarcoma-associated herpesvirus (KSHV),
which causes multiple AIDS-related cancers, encodes the ORF57
protein, which can sequester the host hTREX complex, important
for mRNA processing and export [83]. Sequestration of hTREX
leads to KSHV-induced accumulation of R-loops and causes
damage to the host DNA, contributing to tumourigenesis [83].
Whilst some proteins suppress R-loop formation, others may
promote R-loops and so increase genome instability leading to
tumour development. This unexpected function has been shown in
yeast for transcription elongation factor Spt2 and DNA repair
protein Rad51 [7,84]. Overexpression of Spt2 leads to transcription-
dependent chromosomal rearrangements, which are prevented by
RNase H overexpression [84]. Spt2 is structurally related to human
HMG1, which is overexpressed in gastric cancers and malignant
melanomas [84]. However, it is not clear if increased HMG1 levels
promote R-loops and DNA damage in cancer cells. In contrast to its
well-established role in DNA strand exchange during homologous
recombination and DNA repair [85], recent studies have shown that
Rad51 can also mediate R-loop formation and genome instability in
trans, extending the prevailing view that R-loops form cotranscrip-
tionally [7]. Similar to HMG1, RAD51 is overexpressed in human
cancers [7]. However, it remains to be elucidated if RAD51
overexpression in cancers is a consequence of activated DNA repair
pathways, or a cause of genome instability [7].
R-loops have been detected in immunoglobulin (Ig) genes,
where they initiate class switch recombination by exposing single-
stranded DNA, thus providing the substrate for activation-induced
cytidine deaminase (AID), which promotes DSBs and subsequent
translocation between Ig heavy chains [21,86]. Although this
process is essential for generation of antibody isotype diversity,
AID-mediated mutagenesis has also been implicated in patholog-
ical translocations between the Ig loci and other active genes,
leading to production of fusion proteins or oncogenic gene
expression, observed in B cell malignancies (Figure 2E) [87].
Interestingly, R-loops are also found in common translocation
partners of Ig genes, including the oncogene c-MYC [18,27].
Therefore, the simultaneous formation of R-loops in Ig and
transcribed non-Ig genes may induce AID-mediated DSB
formation, leading to pathological translocations (Figure 2E)
[27,88,89]. Interestingly, overexpression of the APOBEC family
of AID-related enzymes in breast cancer have been linked to
genomic mutations, pointing to a potentially broader role of R-
loops and AID/APOBEC-mediated genome instability in cancer
[90].
Changes in gene expression are another central aspect of cancer
[79]. In healthy cells, the expression of tumour suppressor genes
prevents abnormal proliferation and other aspects of tumourigen-
esis [79]. Tumour suppressors are frequently silenced in cancer by
excessive promoter DNA methylation [91]. It has been proposed
that R-loop formation at promoters protects against DNA
methylation by de novo DNA methyltransferase DNMT3B,
thereby keeping genes active [18]. Since R-loops have been
computationally predicted to form at promoters of tumour
suppressor genes BRCA1,RASSF1A, and CDKN2A [92], it is
important to investigate if R-loop levels at these genes are reduced
in cancer and how this relates to the observed DNA hypermethy-
lation.
In contrast to this, efficient transcription of the oncogene c-MYC
requires that R-loop levels are kept low by the activity of DNA
topoisomerase IIIB, which is recruited to arginine-methylated
histones by the tudor domain containing 3 (TDRD3) protein [27].
This R-loop-mediated mechanism of c-MYC gene regulation may
be relevant to tumour progression in breast cancer, which
frequently shows overexpression of both c-MYC and TDRD3
[27,93]. Therefore, it is tempting to speculate that increased
TDRD3 levels suppress R-loops in c-MYC, thereby allowing its
enhanced expression, which correlates with poor cancer prognosis
[93]. However, it still remains to be determined if R-loops play a
specific role in transcription dysregulation in cancer and if this
process differs from R-loop-mediated transcriptional programmes
associated with housekeeping genes.
More recently, R-loops have been implicated in cell senescence, a
mechanism protecting against tumour cell proliferation [79]. In
particular, the telomeric noncoding (nc) RNA TERRA forms R-
loops which are induced when R-loop suppressors such as RNase H
or Thp2 are lost [94,95]. In the absence of telomerase, telomeric R-
loops promote recombination-mediated telomere elongation via
Rad52, and this delays the onset of cellular senescence [94]. In
contrast, in Rad52-deficient cells, R-loop accumulation leads to
telomere shortening and premature senescence [94]. Interestingly,
cells from AOA2 patients with senataxin mutations contain shorter
telomeres, suggesting a possible involvement of SETX in telomere
stability [96]. Telomeric R-loops therefore play a complex and
dynamic role in telomere length maintenance and cellular
proliferative potential (Figure 2F).
In conclusion, multiple lines of evidence point to an involve-
ment of R-loops in cancer biology. Yet it still remains to be
investigated if R-loop levels are indeed regulated differentially in
normal and tumour tissues and if they can directly influence
tumourigenesis.
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R-loop Therapies
R-loops represent a potential therapeutic target. Despite their
importance in gene regulation, they have yet to be fully exploited
in drug design [97]. Various ligands can target RNA/DNA
hybrids, including ethidium bromide, the aminoglycosides neo-
mycin and paramomycin, and the polyamides distamycin and
netropsin [98]. These compounds recognise RNA/DNA hybrids
through intercalation and binding to the nucleic acid groove.
Although exhibiting high binding affinities to RNA/DNA hybrids,
many of these molecules also bind dsDNA and RNA and are
mutagenic, limiting their potential biological applications [98].
However, recent studies suggest that combining the properties of
these ligands can achieve subnanomolar affinity for RNA/DNA
hybrids. In particular, this has been demonstrated for ligands
linking aminoglycosides to derivatives of ethidium bromide [99],
providing a possible approach for the development of potent and
specific RNA/DNA hybrid ligands in future drug design efforts.
Various compounds that modulate DNA supercoiling and inhibit
DNA topoisomerases, including topotecan and camptothecin, can
also affect R-loop formation in vivo [29,50]. In particular,
topoisomerase inhibitors have recently been used to reactivate the
silenced paternal Ube3a gene, which encodes a ubiquitin E3 ligase,
to compensate for the deleted maternal Ube3a in Angelman
syndrome (AS). AS and Prader-Willi syndrome (PWS) are imprinted
neurodevelopmental disorders that are often caused by large
deletions of human chromosome 15q11–q13 over the Snord116
gene locus, but the deletion differs in its parent-of-origin [100]. In
neurons, only the maternal Ube3a allele is expressed, because the
paternal Ube3a allele is silenced by expression of the ncRNA
Ube3a-ATS (Figure 3A) [101]. AS therapies therefore seek to
reactivate the silenced, but genetically intact, paternal Ube3a allele.
Interestingly, R-loops were recently shown to regulate the neuronal
expression of the paternal Ube3a-ATS transcript, which is essential
for transcriptional silencing of the paternal Ube3a gene [50]. In
particular, treatment with the topoisomerase inhibitor topotecan
increased R-loop levels over the Snord116 locus, resulting in
chromatin decondensation, inhibition of Pol II transcription of
Ube3a-ATS, and concomitant increase in Ube3a expression from
the paternal allele (Figure 3B). This R-loop-mediated reactivation
of paternal Ube3a could therefore compensate for the loss of
maternal Ube3a in AS and so potentially holds promise for targeted
therapies for both AS and PWS (Figure 3B).
It has previously been proposed that R-loops in trinucleotide
expansion diseases could be targeted to suppress repeat expansions
or reactivate silenced genes [72]. A recent study provided direct
evidence that a small molecule is able to suppress R-loop formation
at expanded CGG repeats in the FMR1 gene, thereby preventing
FMR1 epigenetic silencing in FXS [77]. As an alternative
approach, R-loop levels may be indirectly modulated by treatments
that target proteins involved in R-loop biology (Table S1). For
instance, genomic instability caused by a widespread increase of R-
loops due to loss of an R-loop suppressing protein could potentially
be reverted by introduction of an alternative R-loop suppressor.
Recent identification of small-molecule inhibitors for RNase H2
may also provide a powerful new tool for the study of R-loop biology
in health and disease [102]. Furthermore, the S9.6 antibody offers
new opportunities for research and development. In particular, it
has already been used in the development of biosensor systems
[103], detection of miRNA targets[104], and as a key component of
human papillomavirus (HPV) diagnostic kit (Qiagen).
The explosion of studies uncovering the role of R-loops in
health and disease in recent years provides the exciting prospect of
developing new targeted therapeutics for many human disorders.
However, due to the ubiquitous nature of R-loops it will be
important to ensure that efficient treatments are specific.
Conclusions and Future Challenges
R-loops have been implicated in many biological processes in
different organisms. R-loops can play positive and negative roles in
gene expression; they can mediate Ig class switch recombination
and transcriptional termination, affect genome stability, transcrip-
tion, cell cycle progression, and cell viability. Despite the diversity
of these biological processes, the molecular mechanisms associated
with R-loop formation in mammalian cells remain largely
unknown. It is unclear how R-loops can regulate gene expression,
how they are maintained and eliminated in the cells, and which
proteins are involved in the regulation of these processes.
The connections between R-loops and human diseases suggest
that cells have evolved mechanisms to distinguish between
deleterious and beneficial R-loops. However, the evidence discussed
above raises an important question: how can R-loop dysregulation
be mechanistically linked to a variety of human diseases with such
diverse pathologies? One explanation may be that R-loops form in
many genomic locations in healthy cells [16,18,22,27]. Therefore,
unsurprisingly, their dysregulation can affect a large number of
disease-associated genes. This is in contrast to gene-specific R-loop
pathologies, associated with mutations, which result in altered R-
loop levels locally, as observed in the repeat expansion diseases
FRDA and FXS [75,77]. Furthermore, R-loops can have different
intrinsic properties. R-loops at expanded GAA repeats in the FXN
gene are highly stable and trigger transcriptional repression, while R-
loops in the highly-expressed c-Actin gene are easily turned over
[75]. This could, in part, be due to differential activity of R-loop
processing proteins on different classes of genes, as proposed in yeast
[22]. Adding another layer of complexity, the formation of R-loops
can be influenced by cell type [77], cell cycle stage [15], gene length,
and/or GC content and transcriptional level [22,105]. Epigenetic
marks including DNA methylation and post-translational histone
modifications can contribute to further modulation of R-loop levels
[18,27]. Thus, R-loops represent cellular structures that share the
same elementary composition, but may possess different dynamic
properties, which can be affected by any of the aforementioned
processes, thus explaining the wide range of diseases associated with
R-loops.
Despite the lack of mechanistic insights into R-loop-associated
diseases, some common themes, underlying their pathology, are
already becoming obvious. First, there is a strong connection
between R-loop dysregulation and induction of DNA damage and
loss of genome integrity, which contributes to cancer development
[31,81,88], repeat expansion diseases [71], and neurodegeneration
[29,45]. Secondly, R-loops can mediate changes in transcription
locally or globally, contributing to pathologies associated with
repeat expansion diseases [75,77,78], Angelman syndrome [50],
and cancer [27]. However, it is a strong possibility that both of
these pathological themes may overlap in many disorders, as
observed in repeat expansion diseases [71,75,77], and novel
disease themes may be revealed in the future.
One of the major challenges in R-loop field is to investigate the
causes and consequences of R-loop formation in additional models
of human disease. Uncovering further aspects of R-loop biology in
human cells will certainly shed light on many basic biological
questions and have major implications for our understanding of
human disease. Future studies will undoubtedly reveal more
diseases associated with R-loop dysregulation and will provide the
basis for novel therapeutic approaches targeting these so far
overlooked structures in gene expression.
PLOS Genetics | www.plosgenetics.org 6 September 2014 | Volume 10 | Issue 9 | e1004630

Supporting Information
Table S1 Proteins implicated in R-loop biology. For
multiprotein complexes, only subunits directly implicated in R-
loop biology are mentioned in the table. *Asterisk indicates that
protein association with R-loops is based on in vitro evidence.
(DOCX)
Text S1 Supplemental references.
(DOCX)
Acknowledgments
We thank Prof. P. Cook, Prof. N. J. Proudfoot, Prof. C. Norbury and L. M.
Silva for critically reading the manuscript.
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PLOS Genetics | www.plosgenetics.org 9 September 2014 | Volume 10 | Issue 9 | e1004630