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The Xist gene and it potential role in creating a silent nuclear compartment. (A) A map of the murine Xist gene is shown, indicating the conserved repeats (A–E). The sequence of the most highly conserved A repeats, involved in the gene silencing function of Xist, is shown. (B) Example of RNA polymerase II immunofluorescence combined with Xist RNA FISH in early differentiating ES cells (top two panels) and embryonic fibroblasts (lower panel). This shows overall exclusion of RNA pol II at the level of the domain of nuclear Xist RNA accumulation as described by Chaumeil et al. (2006). (C) Model for two types of Xist RNA function during the onset of X inactivation, based on Chaumeil et al. (2006).
Source publication
In female mammals, one of the two X chromosomes is converted from the active euchromatic state into inactive heterochromatin during early embryonic development. This process, known as X-chromosome inactivation, results in the transcriptional silencing of over a thousand genes and ensures dosage compensation between the sexes. Here, we discuss the p...
Contexts in source publication
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... territory from which it is expressed ( Brown et al. 1992;Clemson et al. 1996). This restriction does not appear to be dependent on the DNA of the chromosome itself, as the appearance of the Xist RNA domain remains unperturbed after DNase treatment ( Clemson et al. 1996). It has therefore been proposed that Xist RNA may show only an indirect Fig. 2A). The A repeats, located at the 5′ end of the first exon of Xist, are the most conserved of all. Indeed, these repeats were shown to be capable of inducing repression of X-linked genes in an in vitro assay (Allaman-Pillet et al. 2000). To define the functional regions of the Xist tran- script in vivo, male ES cells containing inducible ...
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... set out to determine whether Xist RNA might function at the level of nuclear organiza- tion, using differentiating ES cells to assess changes in nuclear organization relative to chromatin changes and gene silencing. We showed that Xist RNA chromosome coating leads to the rapid exclusion of RNA polymerase II and associated transcription factors (Fig. 2B). This rep- resents the earliest event following Xist RNA accumula- tion described so far and precedes the loss of active histone marks such as H3K9 acetylation and H3K4 di- methylation ( Chaumeil et al. 2006). Only subsequently do genes cease to be transcribed, as detected at the primary transcript level by RNA FISH, which allows the ...
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... study provided the first evidence for a new and early step in the X-inactivation process. It also suggests a novel role for Xist RNA in the formation of a silent nuclear compartment which initially comprised the more repetitive part of the X chromosome (Fig. 2C). This new function for Xist RNA is independent of its A repeats and results in the rapid exclusion of the transcription machinery from the X chromosome chosen to be inactivated. Gene repression occurs subsequently, requires Xist A-repeat action, and is accompanied by a shift from outside to inside this silent nuclear compartment. This ...
Citations
... ANRIL has been shown to prevent senescence induction by repressing the expression of the p15/CDKN2B and p16/CDKN2A genes at the INK4 locus in proliferative cells by locally recruiting the repressive Polycomb complexes [18,19]. Polycomb group proteins are involved in transcriptional gene silencing and heterochromatin formation [20,21] and are mainly within two multimolecular complexes, PRC1 and PRC2. PRC2 contains the EZH2 histone methyl transferase, which methylates K27 of histone H3. ...
Long non-coding RNAs (ncRNAs) are major regulators of gene expression and cell fate. The INK4 locus encodes the tumour suppressor proteins p15INK4b, p16INK4a and p14ARF required for cell cycle arrest and whose expression increases during senescence. ANRIL is a ncRNA antisense to the p15 gene. In proliferative cells, ANRIL prevents senescence by repressing INK4 genes through the recruitment of Polycomb-group proteins. In models of replicative and RASval12 oncogene-induced senescence (OIS), the expression of ANRIL and Polycomb proteins decreases, thus allowing INK4 derepression. Here, we found in a model of RAF1 OIS that ANRIL expression rather increases, due in particular to an increased stability. This led us to search for circular ANRIL isoforms, as circular RNAs are rather stable species. We found that the expression of two circular ANRIL increases in several OIS models (RAF1, MEK1 and BRAF). In proliferative cells, they repress p15 expression, while in RAF1 OIS, they promote full induction of p15, p16 and p14ARF expression. Further analysis of one of these circular ANRIL shows that it interacts with Polycomb proteins and decreases EZH2 Polycomb protein localization and H3K27me3 at the p15 and p16 promoters, respectively. We propose that changes in the ratio between Polycomb proteins and circular ANRIL isoforms allow these isoforms to switch from repressors of p15 gene to activators of all INK4 genes in RAF1 OIS. Our data reveal that regulation of ANRIL expression depends on the senescence inducer and underline the importance of circular ANRIL in the regulation of INK4 gene expression and senescence.
... Hence, epigenetics could be said to deal with mechanisms to establish durable decisions, while gene control may also describe more punctual fluctuations in transcription levels. Still, the distinction between transcription control and epigenetic control of gene expression is probably a semantic one when considering the question at the molecular level since nucleosomes are involved in both cases [36]. DNA-bound histones in the form of nucleosomes are ideally suited to perform molecular memory-related tasks because their residence time on DNA can be of the order of many hours [37][38][39]. ...
The molecular basis of cellular memory is a fascinating topic that progressed with great strides during the last few decades. In the case of cells of the immune system, cellular memory likely extends beyond cell fate determination mechanisms, since immunity can tailor its responses to a potentially hostile environment that is a priori variable if not unpredictable. One particularly versatile innate immune system cell type is the macrophage. These phagocytes occur in all organs and tissues as resident cells or as differentiation products of recruited circulating blood monocytes. They come in many flavours determined by the tissue of residence and by external factors such as microbes. Recently, macrophage epigenome profiling has revealed thousands of chromosomal loci that are differentially active in macrophages, revealing chromosome elements that drive macrophage gene expression. The most dynamic epigenomic mark is nucleosomal histone acetylation. This mark is found at gene promoters and enhancers and correlates very well with gene expression changes. A second mark is H3K4me3, which sharply decorates the promoters of most protein coding genes that are (potentially) expressed. H3K4me3 at promoters is surrounded by its precursor H3K4me1. However, most often H3K4me1 occurs without H3K4me3 at enhancers where it appears together with histone acetylation, but can persist long after acetylation decreased. Hence, the biochemical signal H3K4me1 embodies appears to be a key to the plasticity of macrophage gene expression potential.
... Il a quand même été observé une expression relativement élevée des lncRNAs dans les testicules (Ørom et al., 2010). De plus, il existe un certain nombre d'exemples de lncRNAs fortement exprimés, de façon ubiquitaire et à des niveaux similaires aux ARNm, comme les lncRNAs XIST chez la femelle placentaire (Masui and Heard, 2006), MALAT1 ...
Les longs ARN non codants (lncRNAs) sont définis comme des transcrits de plus de 200nt et n'ayant pas de potentiel codant. Des études récentes ont démontré que les lncRNAs pouvaient être impliqués dans la régulation de la transcription, de la traduction, de la différenciation cellulaire, de l'expression génique, du cycle cellulaire et des modifications de la chromatine. De plus, il a été montré un impact fonctionnel de certains lncRNAs dans le processus de cancérogenèse mais nos connaissances actuelles sur ces molécules dans le cancer, et plus particulièrement dans la leucémie, restent extrêmement limitées. Au cours de cette étude, nous avons analysé l'expression des lncRNAs par RNA-sequencing sur 40 patients atteints de leucémie aiguë myéloblastique (LAM) à caryotype normal. Parmi les 11065 lncRNAs exprimés dans nos échantillons, nous avons identifié une signature de lncRNAs associée à la mutation de NPM1. Afin de mettre en évidence les fonctions putatives des lncRNAs sélectionnés, nous avons utilisé un algorithme de prédiction d'interaction protéine/ARN. De manière intéressante, plus de la moitié des lncRNAs présentent des sites d'interactions potentiels à SUZ12, une sous unité du complexe PRC2 (Polycomb repressive complex 2), connu pour être recruté par des lncRNAs pour la régulation épigénétique de gènes cibles. Par RNA immunoprécipitation (RIP) de SUZ12, nous avons pu démontrer que le lncRNA XLOC_087120 interagissait avec SUZ12. De plus, son expression est anti-corrélée avec celle des gènes voisins codants des histones, suggérant un rôle dans la régulation négative des histones par ce lncRNA. L'impact de la dérégulation de XLOC_087120 sur les histones a été confirmé par des expériences de surexpression et d'inhibition de ce lncRNA dans des lignées de LAM. De plus, même si la mutation NPM1 ne semble pas affecter directement l'expression de ce lncRNA, des expériences d'infection de la forme mutée de NPM1 dans une lignée LAM ont montré que NPM1 pourrait réguler la localisation nucléaire/cytoplasmique de XLOC_087120 et moduler sa fonction de répresseur. En conclusion, ces données suggèrent que les lncRNAs sont des facteurs clés dans la pathogenèse des LAMs.
... In addition, methylation of subtelomeric DNA by DNMTs in human also plays an important role in heterochromatin formation [34]. There are many non-coding RNAs such as Xist and Piwi, which have been proposed to be involved in heterochromatin formation as evidenced by the silencing of one of the two female X chromosomes [35,36]. In accordance, TERRA molecules function similar to Xist, but rather than recruiting the heterochromatin marks to the female X chromosome, these molecules are involved in the recruitment of heterochromatin marks to the telomeric regions [15,37]. ...
... Further, studies have also shown that dysfunctional telomeres can trigger a DNA damage response leading to a phenotype in post mitotic neurons that identifies with cellular senescence in various features [41,42]. TERRA is also reported to be involved in telomeric heterochromatization, displaying a role similar to Xist RNA, which plays an essential role in mammalian development [35,36]. Collectively, we could infer that TERRA may be developmentally regulated and is itself involved in organism development. ...
Telomeric repeat containing RNAs (TERRA) are small RNA molecules synthesized from telomeric regions which were previously considered as silent genomic domains. In normal cells, these RNAs are transcribed in a direction from subtelomeric region towards the chromosome ends, but in case of cancer cells, their expression remains limited or absent. Telomerase is a rate limiting enzyme for cellular senescence, cancer and aging. Most of the studies deal with the manipulation of telomerase enzyme in cancer and aging either by synthetic oligonucleotide or by natural phytochemicals. Here, we collected evidences and discussed intensely about the bio-molecular structure of TERRA, naturally occurring ligands of telomerase, and their genetic and epigenetic regulations in aging associated diseases. Due to their capability to act as naturally occurring ligands of telomerase, these RNAs can overcome the limitations possessed by synthetic oligonucleotides, which are aimed against telomerase. Drugs specifically targeting TERRA molecules could modulate telomerase-mediated telomere lengthening. Thus, targeting TERRA-mediated regulation of telomerase would be a promising therapeutic strategy against cancer and age-associated diseases.
... We explored this idea by testing whether Atf7ip knockdown alters the Xi localization of Xist RNA, and the enrichment of the histone H3K27me3 and the chromatin regulator ASH2L, both of which are known to be recruited to the Xi in an Xist RNA-dependent manner [44,45]. Our FISH and immunostaining approaches demonstrated that Atf7ip knockdown, with or without a low dose 5-aza-2'-dC (0.2 uM), did not change the extent of Xi enrichment/localization of Xist RNA, H3K27me3, and Ash2l ( Figure 3A, B, Additional file 6: Figure S6A, B), indicating that Atf7ip does not influence XCI by regulating Xist expression and the coating of the chromosome by Xist RNA, or by affecting the H3K27me3 pathway. ...
Background
X chromosome inactivation (XCI) is a developmental program of heterochromatin formation that initiates during early female mammalian embryonic development and is maintained through a lifetime of cell divisions in somatic cells. Despite identification of the crucial long non-coding RNA Xist and involvement of specific chromatin modifiers in the establishment and maintenance of the heterochromatin of the inactive X chromosome (Xi), interference with known pathways only partially reactivates the Xi once silencing has been established. Here, we studied ATF7IP (MCAF1), a protein previously characterized to coordinate DNA methylation and histone H3K9 methylation through interactions with the methyl-DNA binding protein MBD1 and the histone H3K9 methyltransferase SETDB1, as a candidate maintenance factor of the Xi.
Results
We found that siRNA-mediated knockdown of Atf7ip in mouse embryonic fibroblasts (MEFs) induces the activation of silenced reporter genes on the Xi in a low number of cells. Additional inhibition of two pathways known to contribute to Xi maintenance, DNA methylation and Xist RNA coating of the X chromosome, strongly increased the number of cells expressing Xi-linked genes upon Atf7ip knockdown. Despite its functional importance in Xi maintenance, ATF7IP does not accumulate on the Xi in MEFs or differentiating mouse embryonic stem cells. However, we found that depletion of two known repressive biochemical interactors of ATF7IP, MBD1 and SETDB1, but not of other unrelated H3K9 methyltransferases, also induces the activation of an Xi-linked reporter in MEFs.
Conclusions
Together, these data indicate that Atf7ip acts in a synergistic fashion with DNA methylation and Xist RNA to maintain the silent state of the Xi in somatic cells, and that Mbd1 and Setdb1, similar to Atf7ip, play a functional role in Xi silencing. We therefore propose that ATF7IP links DNA methylation on the Xi to SETDB1-mediated H3K9 trimethylation via its interaction with MBD1, and that this function is a crucial feature of the stable silencing of the Xi in female mammalian cells.
... PRC2 is thought to be recruited to Xi via Xist RNA, either directly or indirectly (10,13). Different PRC1 complexes are recruited to Xi in at least two ways: via CBX7 binding to the H3K27me3 mark (14,15) and via RYBP, independently of H3K27me3 and CBX7 (16,17). The complexes that lay down or associate with the other histone modifications on Xi are less well characterized. ...
X chromosome inactivation is a remarkable example of chromosome-wide gene silencing and facultative heterochromatin formation.
Numerous histone posttranslational modifications, including H3K9me2 and H3K27me3, accompany this process, although our understanding
of the enzymes that lay down these marks and the factors that bind to them is still incomplete. Here we identify Cdyl, a chromodomain-containing
transcriptional corepressor, as a new chromatin-associated protein partner of the inactive X chromosome (Xi). Using mouse
embryonic stem cell lines with mutated histone methyltransferase activities, we show that Cdyl relies on H3K9me2 for its general
association with chromatin in vivo. For its association with Xi, Cdyl requires the process of differentiation and the presence of H3K9me2 and H3K27me3, which
both become chromosomally enriched following Xist RNA coating. We further show that the removal of the PRC2 component Eed
and subsequent loss of H3K27me3 lead to a reduction of both Cdyl and H3K9me2 enrichment on inactive Xi. Finally, we show that
Cdyl associates with the H3K9 histone methyltransferase G9a and the MGA protein, both of which are also found on Xi. We propose
that the combination of H3K9me2 and H3K27me3 recruits Cdyl to Xi, and this, in turn, may facilitate propagation of the H3K9me2
mark by anchoring G9a.
... Multiple lncRNAs participate in the inactivation of one of the two X-chromosomes in female mammals. [44][45][46] XIST/Xist (X-inactive specific transcript) (~17 kb) is the best-studied long nuclear RNA that is primarily transcribed from the female inactive X-chromosome in mammals and is involved in X-chromosome inactivation (XCI). Xist and the recently identified RepA transcripts facilitate the recruitment of chromatin-remodeling complexes to silence the future inactive X-chromosome (Xi). ...
The mammalian genome harbors a large number of long non-coding RNAs (lncRNAs) that do not code for proteins, but rather they exert their function directly as RNA molecules. LncRNAs are involved in executing several vital cellular functions. They facilitate the recruitment of proteins to specific chromatin sites, ultimately regulating processes like dosage compensation and genome imprinting. LncRNAs are also known to regulate nucleocytoplasmic transport of macromolecules. A large number of the regulatory lncRNAs are retained within the cell nucleus and constitute a subclass termed nuclear-retained RNAs (nrRNAs). NrRNAs are speculated to be involved in crucial gene regulatory networks, acting as structural scaffolds of subnuclear domains. NrRNAs modulate gene expression by influencing chromatin modification, transcription and post-transcriptional gene processing. The cancer-associated Metastasis-associated lung adenocarcinoma transcript1 (MALAT1) is one such long nrRNA that regulates pre-mRNA processing in mammalian cells. Thus far, our understanding about the roles played by nrRNAs and their relevance in disease pathways is only 'a tip of an iceberg'. It will therefore be crucial to unravel the functions for the vast number of long nrRNAs, buried within the complex mine of the human genome.
... The first ncRNA was discovered in the 1960s in studies on tRNA; however, its function was restricted to conveying genetic information, rather than regulating gene expression. In the early 1990s, several groups reported a long ncRNA, called X-inactive specific transcript (Xist), which is specifically transcribed in the inactive X chromosome and directly regulates X-chromosome inactivation (Brockdorff et al., 1991;McCarrey and Dilworth, 1992;Masui and Heard, 2006). In addition to XIST, the roX genes mediate X-chromosome hyperactivation in Drosophila and several long ncRNAs, including Air, have been implicated in genomic imprinting (Braidotti et al., 2004). ...
For eukaryotes, fine tuning of gene expression is necessary to coordinate complex genetic information. Recent studies have shown that noncoding RNAs (ncRNAs) play central roles in this process. For example, ncRNAs participate in multiple diverse functions such as mRNA degradation, epigenetic regulation and alternative splicing. The findings regarding this new player in gene regulation suggest that the mechanism of gene regulation is much more complicated and subtle than previously thought. In this review, new findings concerning the role of ncRNAs in gene regulation are discussed.
... Since it was first proposed by Lyon in 1961(Lyon, 1961, X chromosome inactivation has provided an excellent model system to study the epigenetic regulation of gene expression (for review, see Brockdorff, 2002;Lee, 2003;Masui and Heard, 2006;Ng et al., 2007). In female mammals, one of the two X chromosomes is transcriptionally repressed during early development to equalize the expression of X-linked genes in females and males (Lyon, 1961). ...
... In addition, a variety of proteins are known to be localized to the Xi during and following the initiation of X inactivation; these include another polycomb complex, PRC1 (Plath et al., 2004); structural maintenance of chromosomes hinge domain-containing 1 protein (SmcHD1) (Blewitt et al., 2008); a histone variant called macro histone H2A1 (Costanzi and Pehrson, 1998); a trithorax group protein Ash2l (Pullirsch et al., 2010) and a nuclear matrix protein, heterogeneous nuclear ribonucleoprotein U (hnRNP U; also known as SP120 and SAF-A) (Helbig and Fackelmayer, 2003;Pullirsch et al., 2010). Although many of these proteins are functionally required for the establishment and maintenance of the Xi, none of them has been shown to regulate the unique localization of Xist RNA on the Xi itself (for review, see Brockdorff, 2002;Masui and Heard, 2006). BRCA1 has previously been proposed to regulate the chromosomal accumulation of Xist RNA (Ganesan et al., 2002;Silver et al., 2007). ...
... To test this, we carried out a coimmunoprecipitation experiment. Xist RNA is fractionated into the nuclear matrix (Clemson et al., 1996) and its insoluble nature has hampered biochemical analyses (for review, see Masui and Heard, 2006;Ng et al., 2007). We thus initially examined various conditions that enable efficient solubilization of Xist RNA. ...
In XX female mammals, one of the two X chromosomes is epigenetically inactivated to equalize gene expression with XY males. The formation of the inactive X chromosome (Xi) is regulated by an X-linked long noncoding RNA Xist, which accumulates on the entire length of the chromosome in cis and induces heterochromatin formation. However, the mechanism by which Xist RNA "paints" the Xi has long remained elusive. Here, we show that a matrix protein hnRNP U/SP120/SAF-A is required for the accumulation of Xist RNA on the Xi. Xist RNA and hnRNP U interact and upon depletion of hnRNP U, Xist RNA is detached from the Xi and diffusely localized into the nucleoplasm. In addition, ES cells lacking hnRNP U expression fail to form the Xi. We propose that the association with matrix proteins is an essential step in the epigenetic regulation of gene expression by Xist RNA.
... Epigeneticists have long been drawn to the mystique surrounding RNA behemoths, beginning with the discovery of the 2.6-kb H19 RNA in the field of genomic imprinting (Brannan et al. 1990; Bartolomei et al. 1991) and the 17-kb XIST RNA for X-chromosome inactivation (XCI) (Borsani et al. 1991; Brown et al. 1991a; Brockdorff et al. 1992; Brown et al. 1992 ). Genes subject to imprinting are expressed from only one of two alleles in a manner dependent on parent of origin, and such genes are almost always clustered within domains and coordinately regulated in cis by a single (sometimes two) " imprinting centers " (Edwards and Ferguson-Smith 2007; Wan and Bartolomei 2008 ). Likewise, XCI—the mechanism of dosage compensation in mammals—is a domain phenomenon that extends to include the entire X-chromosome (Lyon 1961; Wutz 2003; Lucchesi et al. 2005; Masui and Heard 2006; Wutz and Gribnau 2007; Payer and Lee 2008). During XCI, almost all of the 1000 protein-coding genes on one of two X-chromosomes become transcriptionally inactivated in cis by a single control region known as the " X-inactivation center " (Cattanach and Isaacson 1967; Rastan and Robertson 1985). ...
The X-linked region now known as the "X-inactivation center" (Xic) was once dominated by protein-coding genes but, with the rise of Eutherian mammals some 150-200 million years ago, became infiltrated by genes that produce long noncoding RNA (ncRNA). Some of the noncoding genes have been shown to play crucial roles during X-chromosome inactivation (XCI), including the targeting of chromatin modifiers to the X. The rapid establishment of ncRNA hints at a possible preference for long transcripts in some aspects of epigenetic regulation. This article discusses the role of RNA in XCI and considers the advantages RNA offers in delivering allelic, cis-limited, and locus-specific control. Unlike proteins and small RNAs, long ncRNAs are tethered to the site of transcription and effectively tag the allele of origin. Furthermore, long ncRNAs are drawn from larger sequence space than proteins and can mark a unique region in a complex genome. Thus, like their small RNA cousins, long ncRNAs may emerge as versatile and powerful regulators of the epigenome.
