CB30CH22-Heard

ARI

ANNUAL REVIEWS

4 September 2014

8:31

Further

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Click here for quick links to Annual Reviews content online, including: • Other articles in this volume • Top cited articles • Top downloaded articles • Our comprehensive search

Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation Anne-Valerie Gendrel and Edith Heard Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, 75248 Paris, France; email: [email protected]

Annu. Rev. Cell Dev. Biol. 2014. 30:561–80

Keywords

First published online as a Review in Advance on June 27, 2014

Xist, chromatin, dosage compensation, monoallelic expression

The Annual Review of Cell and Developmental Biology is online at cellbio.annualreviews.org

Abstract

This article’s doi: 10.1146/annurev-cellbio-101512-122415 c 2014 by Annual Reviews. Copyright  All rights reserved

In mammals, the process of X-chromosome inactivation ensures equivalent levels of X-linked gene expression between males and females through the silencing of one of the two X chromosomes in female cells. The process is established early in development and is initiated by a unique locus, which produces a long noncoding RNA, Xist. The Xist transcript triggers gene silencing in cis by coating the future inactive X chromosome. It also induces a cascade of chromatin changes, including posttranslational histone modifications and DNA methylation, and leads to the stable repression of all X-linked genes throughout development and adult life. We review here recent progress in our understanding of the molecular mechanisms involved in the initiation of Xist expression, the propagation of the Xist RNA along the chromosome, and the cis-elements and trans-acting factors involved in the maintenance of the repressed state. We also describe the diverse strategies used by nonplacental mammals for X-chromosome dosage compensation and highlight the common features and differences between eutherians and metatherians, in particular regarding the involvement of long noncoding RNAs.

561

CB30CH22-Heard

ARI

4 September 2014

8:31

Contents

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . THE X-INACTIVATION CENTER: A HOTBED OF NONCODING RNAS . . . . LOCALIZATION AND SPREADING OF XIST RNA ALONG THE INACTIVE X CHROMOSOME . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . THE NATURE OF CHROMATIN CHANGES DURING X-CHROMOSOME INACTIVATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . NUCLEAR COMPARTMENTALIZATION AND ORGANIZATION. . . . . . . . . . . . CIS-ELEMENTS: THE ROLES OF CHROMOSOMAL REPEAT ELEMENTS IN XIST RNA-MEDIATED X INACTIVATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . TRANS-ACTING FACTORS IMPLICATED IN XIST RNA-MEDIATED FUNCTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . THE EVOLUTIONARY DIVERSITY OF X-INACTIVATION MECHANISMS AND THE NONCODING RNAS THAT CONTROL THEM . . . . . . . . . . . . . . . . CONCLUDING REMARKS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

562 563 566 567 569 570 571 573 575

INTRODUCTION In mammals, sex is determined by a pair of sex chromosomes, the X and the Y, that emerged from an ancestral pair of autosomes. Males (XY) are the heterogametic sex, whereas females (XX) are homogametic and have two functional copies of genes carried by the X chromosome. Throughout evolution, the X chromosome has conserved a relatively high gene density, whereas the Y chromosome has dramatically degenerated and lost most of its genes, so that today it is composed of very few protein-coding genes compared with other chromosomes (Graves 2006, Ohno 1967). This situation has therefore led to obvious potential differences in X-linked gene dosage between XX females and XY males that are compensated by the silencing of one X chromosome in females, a phenomenon known as X-chromosome inactivation (XCI) (Lyon 1961, 1962). This chromosomewide silencing process takes place early in development and ensures equivalent levels of expression from genes on the X chromosome between males and females throughout development and during adult life. In mammalian species, the strategies for achieving X inactivation appear to be rather diverse. Eutherian mammals are generally believed to display random X inactivation in somatic tissues, so that females are mosaic for cell populations with either the maternal X (Xm) or paternal X (Xp) chromosome silenced (Chow & Heard 2009). In marsupials, however, imprinted inactivation of the paternal X is found in all tissues (Sharman 1971). In fact, in the mouse, imprinted inactivation of the Xp also exists and is found during early embryo development (Okamoto et al. 2004). This is initiated during the first cleavage stages of preimplantation development and is reversed in the inner cell mass (ICM) of the blastocyst, which will give rise to the embryo proper and where random X inactivation then takes place (Mak et al. 2004, Okamoto et al. 2004). Inactivation of the paternal X is maintained in extraembryonic tissues (Takagi & Sasaki 1975). However, rodents may be an exception to the eutherian rule when it comes to imprinted XCI. Indeed, recent studies highlight some important differences between mammalian species in the timing and nature of XCI during early development and in the soma (Okamoto et al. 2011). One common feature, however, seems to be the involvement of long noncoding RNA (lncRNA) as key players for the regulation of the process. In eutherian mammals, XCI is mediated by a lncRNA called Xist (for 562

Gendrel

·

Heard

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

ARI

4 September 2014

8:31

X-inactive-specific-transcript), expressed from the inactive X (Xi) chromosome only in females. In metatherians, there is no Xist gene (Duret et al. 2006, Elisaphenko et al. 2008), but another lncRNA, Rsx (for RNA-on-the-silent-X), which is expressed only in female cells and displays features very similar to those of Xist, was recently discovered in the marsupial opossum (Grant et al. 2012). Interestingly, these two lncRNAs have evolved independently in the eutherian and metatherian lineages as central players of the XCI process. Among eutherians, the mouse has been the preferred model for the investigation of Xchromosome inactivation. This is particularly thanks to the use of murine embryonic stem (ES) cells that are derived from the ICM and represent a useful model, as random X inactivation can be recapitulated during in vitro differentiation (Chaumeil et al. 2004). In mouse undifferentiated ES cells, as in cells from the ICM, the two X chromosomes are active. The silencing of one X chromosome is triggered during differentiation of ES cells or during embryo development. This process is initiated by a unique locus, the X-inactivation center (Xic), which includes the Xist gene. The Xist transcript coats the future Xi chromosome in cis and triggers gene silencing. It also induces a cascade of changes that can occur in an early or initiation phase after Xist expression starts, such as the exclusion of RNA polymerase II (pol II) and various covalent histone tail modifications, as well as a late (also called maintenance) phase, such as a switch to late replication timing, histone variant exchange, and DNA methylation (Chow & Heard 2009). These changes are thought to ensure stable repression of nearly all genes on the Xi chromosome, although some genes can escape inactivation (Berletch et al. 2010). Once established, the inactive state is clonally propagated and maintained through cell divisions and is believed to be reversed only in primordial germ cells prior to meiosis (Ohhata & Wutz 2013). In this review, we discuss the process of random X inactivation in detail, with a particular focus on the role of noncoding RNAs. We cover current views on the control of the initiation of XCI via Xist RNA upregulation, the spread of silencing along the X chromosome, and the faithful maintenance of the inactive state through cell divisions. Imprinted X inactivation during embryogenesis and in marsupials is also discussed in the last part of this review.

THE X-INACTIVATION CENTER: A HOTBED OF NONCODING RNAS The Xic is defined as the minimal region of the X chromosome that contains all the sequences both necessary and sufficient for the initiation of XCI. The existence of a Xic region was first described thanks to the study of balanced X-autosomal translocations in mouse and man (see Rastan 1983, Russell & Montgomery 1970, and references within Augui et al. 2011). These seminal studies revealed that the Xic is required to allow XCI in cis and that the presence of at least two Xic regions is necessary for X inactivation to occur (Rastan 1983). The Xic may span up to 1 Mb and harbors several protein-coding, as well as several noncoding, RNA genes that can impact on XCI initiation (Figure 1). The candidate Xic region also overlaps with the Xce (X-controlling element) locus in mice, which is known to lead to skewing in the choice of the X chromosome to be inactivated (Cattanach & Williams 1972). At the heart of the Xic lies the noncoding Xist transcript gene and its antisense transcription unit, Tsix. Xist was first described in the early nineties in mice and humans and is the central player in the X-inactivation process (Borsani et al. 1991, Brockdorff et al. 1991, Brown et al. 1991). Tsix is transcribed antisense to Xist and can mediate its repression (Lee & Lu 1999). Heterozygous null mutations in the Xist or Tsix genes result in completely nonrandom X inactivation. The monoallelic upregulation of Xist from the future Xi chromosome is one of the earliest steps in XCI and precedes the initiation of silencing. As this is a critical step in XCI initiation, the mechanisms controlling Xist regulation have been the focus of intense scrutiny. Work so far indicates that this involves several molecular players that act as part of a sophisticated www.annualreviews.org • Noncoding RNAs

563

CB30CH22-Heard

ARI

4 September 2014

Ppnx

8:31

Xist

Linx

Ftx

Slc16a2/Xpct

Rnf12

Xic Xite

Cdx4

Chic1

Tsix

Tsx

Exon 1

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Xist

Repeat A

F

B

Gene silencing

Jarid2/PRC2 recruitment

Jpx

2

3

4

5

6

7

C

D

E

Localization of Xist to chromatin

?

?

8

Proposed role for Xist noncoding RNA: • Formation of a silent nuclear compartment • Gene silencing (via the A-repeat region) • Mediator of chromosome interactions • Recruiter of chromatin modifiers

Figure 1 The X-inactivation center (Xic) and the Xist gene. The Xic encompasses a large region that is composed of several noncoding RNA loci (Xist, Tsix, Jpx, and Ftx) as well as protein-coding genes, some of which are involved in X-chromosome inactivation (XCI) (e.g., Rnf12) and others of which are apparently not. Putative positive regulators of XCI (blue) and putative negative regulators ( green) are shown. The Xist gene depicted at the bottom, which includes eight exons, contains several tandem repeats, named A to F, for which the putative roles are indicated. The various roles for the Xist noncoding RNA discussed in this review are listed below the figure.

regulatory network to regulate Xist expression in cis and in trans. These different regulators are described only briefly here, as recent reviews on this aspect can be found elsewhere (Augui et al. 2011, Pollex & Heard 2012). The functional Xist transcript is a lncRNA measuring 17 kb in length. Genetic deletions in mice have shown that Xist is absolutely essential for the initiation of X inactivation (Marahrens et al. 1998, Penny et al. 1996). However, it appears to be largely dispensable for the maintenance of the inactive state in differentiated cells, and furthermore, it cannot trigger gene silencing if upregulated in this context (Brown & Willard 1994, Csankovszki et al. 2001, Kohlmaier et al. 2004, Wutz & Jaenisch 2000). The Xist transcript is spliced and polyadenylated in the nucleus, similarly to most other messenger RNAs. However, Xist, which does not appear to contain an open reading frame, is not exported to the cytoplasm but rather remains in the nucleus, where it will coat the future Xi chromosome. Several blocks of tandem repeats lie within Xist, and these appear to be the most highly conserved regions of an otherwise poorly conserved RNA (Figure 1). Deletion experiments have shown that the most highly conserved of these, the A repeats, are necessary for Xist RNA to establish gene silencing (Wutz et al. 2002). However, the Xist RNA deleted for the A-repeat region is still competent to induce several chromatin changes and to coat the X chromosome. Other sequences within Xist RNA appear to act cooperatively to mediate the localization of the Xist transcript to the X, but no single sequence is absolutely required (Wutz et al. 2002). More recently, the Xist repeat C region was proposed to mediate the binding of Xist RNA to chromatin, as locked nucleic acid targeting of this region, which presumably blocks its interactions, induces rapid displacement of Xist RNA from the Xi (Sarma et al. 2010). However, this does not exclude 564

Gendrel

·

Heard

CB30CH22-Heard

ARI

4 September 2014

8:31

The Xist regulatory network Rnf12 Oct4 Sox2 Nanog

Klf4 c-Myc Rex1

Tsix Jpx Ftx

Xist

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

X-chromosome inactivation

Figure 2 The Xist regulatory network. The regulatory network acting on Xist involves multiple molecular players acting either in cis or in trans to regulate Xist expression and X-chromosome inactivation (XCI) during development and differentiation. Arrows indicate positive regulation, and inhibition lines indicate negative regulation. Pluripotency factors ( purple) can act either positively or negatively on downstream regulators. Putative positive regulators of XCI (blue) and putative negative regulators ( green) are shown. Tsix, Linx, Jpx, and Ftx act as noncoding RNAs. In addition, once established, XCI downregulates Rnf12, and recently, XCI was shown to feed back on the pluripotency factor network (dashed inhibition lines) (Schulz et al. 2014).

the participation of other regions of Xist in coating. Indeed, the various conserved repeats of Xist may play different roles. For example, in addition to its gene-silencing and chromosome-coating functions, Xist may also recruit Polycomb group proteins that participate in the early maintenance of the inactive state (Zhao et al. 2008), and a recent study has shown that the Xist region including repeats B and F is critical for recruitment of Jarid2, a cofactor of Polycomb group complex 2 (PRC2) (da Rocha et al. 2014) (Figure 1). During differentiation of female cells, Xist is upregulated in a monoallelic fashion and then induces silencing of the chromosome, from which it is expressed in a cis-limited manner. This elaborate expression profile is tightly controlled and involves various players acting in the same regulatory pathway. The antisense RNA Tsix, which also becomes monoallelically expressed at the onset of XCI, represses Xist on the active X (Xa) (Lee & Lu 1999). On the Xi, recent findings support a role for activators of Xist expression that are encoded by the X chromosome itself and are located within the Xic. Two of these activators, Enox/Jpx and Ftx, are located in very close proximity to Xist in a distal position and also encode noncoding RNAs. They were shown to play a role in activating Xist both in cis and in trans (Chureau et al. 2011, Sun et al. 2013, Tian et al. 2010) (Figures 1 and 2). Indeed, deletion of Ftx in a male ES cell line results in decreased expression of Xist in cis, although this has not yet been investigated in XX cells (Chureau et al. 2011). However, Enox/Jpx or Ftx transgenes introduced into ES cells do not appear to activate Xist efficiently in trans, indicating that they may act predominantly in cis (Heard et al. 1999, Jonkers et al. 2009, Sun et al. 2013). Yet the protein coding Rnf12 (RING finger protein 12) gene, located approximately 500 kb upstream of Xist, encodes a potent dose-dependent trans-activator of Xist ( Jonkers et al. 2009) (Figures 1 and 2). Rnf12 transgenes inserted randomly into the genome can activate Xist from its endogenous locus in male XY ES cells, or in a biallelic fashion in female XX cells (Barakat et al. 2011, Jonkers et al. 2009). Initiation of random XCI is reduced in Rnf12 heterozygote or homozygote mutant ES cells but is not completely impaired, indicating that other Xist activators probably exist. The Rnf12 protein is an E3 ubiquitin ligase and has been shown to target the Rex1 pluripotency factor for degradation (Gontan et al. 2012). Rex1 binding sites are found in the regulatory regions of both Xist and Tsix www.annualreviews.org • Noncoding RNAs

565

ARI

4 September 2014

8:31

(Gontan et al. 2012, Navarro et al. 2010), indicating that Rex1 acts directly as a Xist repressor and may also act indirectly through the positive control of Tsix and thus the negative regulation of Xist (Gontan et al. 2012, Navarro et al. 2010). Moreover, the Rnf12 gene itself is negatively regulated by pluripotency factors, adding another level of control of Xist/Tsix in stem cells (Navarro et al. 2011) (Figure 2). The developmental dynamics of Xist expression have been characterized in detail during preimplantation development (Kay et al. 1993, Mak et al. 2002, Okamoto et al. 2004) and in ES cells and their differentiated derivatives (Panning & Jaenisch 1996, Penny et al. 1996). Xist is very lowly expressed in undifferentiated ES cells, when the two X chromosomes are still active. Although the mechanisms for Xist repression in undifferentiated cells are not fully understood, it appears to be tightly linked to highly expressed pluripotency factors in these cells, such as Oct4, Nanog, and Sox2, but it is still debated whether this repression is direct or indirect (Schulz & Heard 2013). In mouse ES cells, the depletion of Oct4 and Nanog leads to ectopic upregulation of Xist in male cells (Navarro et al. 2008). This control was thought to be direct because these factors bind a region located within the first intron of Xist (Navarro et al. 2008). However, deletion of these sites has no effect on Xist upregulation in mouse ES cells or in developing mouse embryos, suggesting that the control of Xist expression by pluripotency factors occurs indirectly (Barakat et al. 2011, Minkovsky et al. 2013, Nesterova et al. 2011), through the control of either trans-acting regulators of Xist, such as Rnf12, or cis-acting regulators, such as Tsix (Navarro et al. 2010). Indeed, Tsix, the antisense transcription unit of Xist, plays a role in Xist repression (Lee & Lu 1999) and is positively regulated by pluripotency factors, such as Rex1, Klf4, and C-myc, that bind its promoter region (Navarro et al. 2010), thereby contributing to Xist repression (Figure 2). However, Tsix expression alone cannot account for Xist repression (Morey et al. 2001), as deletion of Tsix does not lead to ectopic expression of Xist in undifferentiated cells but rather leads to nonrandom X inactivation during differentiation, when stem cell factors are downregulated (Clerc & Avner 1998). Therefore, a combination of mechanisms, including pluripotency factors and Tsix-mediated repression, takes place in a synergistic manner to ensure proper silencing of Xist in undifferentiated ES cells (Nesterova et al. 2011). Although pluripotency factors clearly impact on the onset of XCI via Xist repression, a recent study has also revealed that the presence of two Xa chromosomes can inhibit the onset of differentiation by modulating the signaling pathways that ensure exit from the pluripotent state. Premature expression of Xist and induction of XCI can override this inhibition (Schulz et al. 2014) (Figure 2). Although the nature of the X-linked factors that inhibit pluripotency factor downregulation during early XX ES cell differentiation is still unknown, this reveals the tight integration of the XCI process and the pluripotency factor network.

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

LOCALIZATION AND SPREADING OF XIST RNA ALONG THE INACTIVE X CHROMOSOME Early cytological observations in human cells revealed that the Xi chromosome (or Barr body) is a condensed DNA structure in the nucleus, predominantly located at the nuclear envelope or sometimes near the nucleolus (Barr & Bertram 1949, Barton et al. 1964, Borden & Manuelidis 1988, Bourgeois et al. 1985, Dyer et al. 1989). Detection of Xist RNA, either by RNA fluorescence in situ hybridization (FISH) or live-cell imaging, in human and mouse cells demonstrates that it is never found in the cytoplasm and that its localization is confined to the Xi territory in the nucleus, indicating that specific, but as yet unknown, mechanisms restrict the propagation and binding of Xist in cis to the chromosome from which it is expressed (Clemson et al. 1996, Ng et al. 2011). However, Xist RNA localization appears to be very dynamic (Ng et al. 2011), and its properties seem to change during the cell cycle and to differ between species. In human cells, Xist 566

Gendrel

·

Heard

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

ARI

4 September 2014

8:31

RNA dissociates from the Xi during mitosis, progressively dispersing in the cytoplasm (Clemson et al. 1996), whereas in mouse cells, Xist remains associated with the Xi throughout the cell cycle, although a weaker interaction has been observed during telophase (Duthie et al. 1999, Jonkers et al. 2008, Smith et al. 2004). On metaphase chromosomes, the localization of Xist on the Xi is not uniform and appears as a banded pattern (Duthie et al. 1999, Mak et al. 2002, Smith et al. 2004). RNA FISH analysis of Xist RNA on mouse or vole metaphase chromosomes revealed that Xist RNA is concentrated in gene-rich R-band regions and excluded from gene-poor/repeat-rich regions, suggesting that the transcript coats the chromosome in a rather discontinuous manner. How Xist RNA actually binds and spreads along the chromosome is a very intriguing question, and so far, no proteins strictly involved in the recruitment of Xist to chromatin have been identified. Nor have specific sequences on the X chromosome necessary for the binding and/or spreading of Xist to DNA been identified. Indeed, it should be noted that Xist RNA binding and XCI are not uniquely targeted to X-chromosomal sequences but can occur on any chromosome from which Xist is expressed (Heard et al. 1999, Herzing et al. 1997, Lee & Jaenisch 1997, Lyon 1998a, Tang et al. 2010). Two recent studies sought to characterize the binding patterns of Xist RNA to the X chromosome during the early and later stages of XCI. In one study, maps of Xist binding were generated by using allele-specific capture hybridization analysis of RNA targets (CHART)seq. This revealed that during the course of XCI, Xist targets primarily gene-rich regions before eventually spreading to gene-poor domains. This pattern apparently closely resembles PRC2 and trimethylation of lysine 27 on histone H3 (H3K27me3) enrichments, based on chromatin immunoprecipitation (ChIP) analyses (Simon et al. 2013). In another study, the localization of Xist RNA to chromatin was investigated by RNA antisense purification (RAP)-seq and suggests a model whereby Xist exploits the preexisting 3D architecture of the Xi in the nucleus to spread, very early at the onset of XCI, to a restricted number of more distal regions (entry points) that do not correspond to any obvious sequence signature but rather to loci that are localized close to the Xist gene in 3D (Engreitz et al. 2013). Subsequently, Xist may spread, thanks to its unexplained ability to modify chromatin, and localize broadly across the entire Xi, although preferentially at gene-rich regions, with a similar pattern to the H3K27me3 distribution (Figure 3) (Engreitz et al. 2013). Thus, the preexisting 3D organization of the Xi in the nucleus, possibly through its interaction with nuclear matrix proteins (see below), may be a key determinant contributing to or influencing its spread across the chromosome. Xist RNA is highly unusual, as it can trigger the silencing of an entire chromosome. Xist has also been shown to be able to silence autosomal regions. Recently, the potential use of the Xist lncRNA in therapy has been highlighted after targeted integration of a XIST transgene on chromosome 21 in Down’s syndrome induced pluripotent stem cells ( Jiang et al. 2013). The XIST transgene was shown to coat and trigger silencing of chromosome 21, thereby improving cell proliferation and differentiation toward neural progenitors. Although it will be very challenging to use Xist in Down’s syndrome therapy, this study may help to improve our understanding of the disease.

THE NATURE OF CHROMATIN CHANGES DURING X-CHROMOSOME INACTIVATION The chromatin changes observed on the X chromosome during XCI may or may not directly reflect Xist RNA propagation (Calabrese et al. 2012, Marks et al. 2009, Pinter et al. 2012) and gene silencing (Chow et al. 2010, Lin et al. 2007). Recently, several groups have investigated the distribution of the PRC2-mediated histone modification H3K27me3 along the Xi in differentiating ES cells (Marks et al. 2009, Pinter et al. 2012) and trophoblast stem cells (Calabrese et al. 2012) by performing allele-specific ChIP-seq analysis. The distribution of this modification on the Xi www.annualreviews.org • Noncoding RNAs

567

CB30CH22-Heard

ARI

4 September 2014

8:31

ChrX

Early XCI

Entry sites for Xist localisation

Xist

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Spatially proximal sites

3D-SIM microscopy

RAP- and CHART-seq Mid-XCI

PRC2/H3K27me3 enrichment domains Xist localization (gene-dense)

Xist

Post-XCI Xist RNA foci

Escape domain

PRC2 protein foci

PRC2/H3K27me3 enrichment domains Xist

Escape domain

Xist localization (gene-dense and gene-poor)

Figure 3 Xist RNA spreading during the early, intermediate, and late phase of X-chromosome inactivation (XCI). Early after the induction of X inactivation, Xist RNA ( green) spreads to sites (putative entry sites; orange) on the X chromosome that are located spatially close to the Xist locus in 3D in the nucleus (Engreitz et al. 2013). Xist might then spread from these sites to neighboring gene-dense regions ( green) that correspond to PRC2/H3K27me3 enrichment domains ( purple) (Simon et al. 2013), although this is not yet established. In the maintenance stage of XCI (post-XCI), Xist localizes broadly over the entire chromosome in gene-dense and gene-poor regions ( green) and still shows a strong correlation with PCR2/H3K27me3 enrichment sites based on ChIP-seq comparisons with RAP-seq (Engreitz et al. 2013) and CHART-seq (Simon et al. 2013). On the other hand, escape domains seem to be depleted of Xist binding. However, in another recent study using 3D structured illumination microscopy (SIM; OMX), no or very little overlap could be found between Xist RNA ( green) and PRC2 protein foci ( purple) in interphase nuclei of differentiating embryonic stem or somatic cells (Cerase et al. 2014). The reasons for these discrepancies are not clear.

was found to correlate very well with more recent Xist RNA mapping data, when ChIP-seq and RNA CHART-seq data were compared (Simon et al. 2013). As expected, a large-scale enrichment of H3K27me3 was found on the Xi compared with the Xa. During ES cell differentiation, this overall increase seems to be distributed rather equally over the chromosome, indicating that H3K27me3 accumulates uniformly at multiple locations on the chromosome at approximately the same time (Marks et al. 2009, Pinter et al. 2012). The measured H3K27me3 levels were found to be higher than average in gene-dense regions but not in repeat-rich regions, in accordance with immunofluorescence studies on metaphase spreads (Mak et al. 2002). At a higher resolution, the H3K27me3 increase was seen at promoters and gene body of Xi-linked genes, alongside H4K20me1 enrichment and increased DNase1 hypersensitivity (Calabrese et al. 2012, Marks et al. 2009, Pinter et al. 2012). These observations do not support a local spreading model, where 568

Gendrel

·

Heard

CB30CH22-Heard

ARI

4 September 2014

8:31

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

H3K27me3 and Xist spread progressively from the Xic toward both ends of the chromosome, but rather suggest that spreading is likely to be a 3D process, with simultaneous association at multiple sites owing to the conformation of the chromosome in the nucleus. Although in theory this might explain the rather variable kinetics of gene silencing along the X chromosome observed during ES cell differentiation, with some genes being silenced early and some much later (Chow et al. 2010, Lin et al. 2007), no clear correlation between the positions of early/late genes relative to the Xist locus or their association with Xist RNA has so far been found. Thus, the molecular mechanisms triggering gene silencing during XCI remain completely unknown. Indeed, it is still unclear whether this is achieved through chromatin changes occurring downstream of Xist RNA, or whether Xist RNA itself plays a direct role in gene silencing, though not necessarily at those sites where it appears most enriched.

NUCLEAR COMPARTMENTALIZATION AND ORGANIZATION An early event following Xist RNA upregulation at the onset of X inactivation during ES cell differentiation is the formation of a distinct 3D nuclear compartment that can be easily observed by microscopy in the interphase nucleus. Detection of Xist by RNA FISH revealed that mouse and human female nuclei display a clear domain or cloud of Xist RNA molecules, corresponding to at least part of the Xi chromosome territory. The accumulation of Xist RNA is associated with a depletion of RNA pol II and transcription factors (Chaumeil et al. 2006, Clemson et al. 2006). During ES cell differentiation, the formation of this silent nuclear compartment is one of the first events associated with Xist RNA coating. This Xist RNA compartment was subsequently shown to be composed mainly of silent X-linked repeat sequences rather than genic sequences (Chaumeil et al. 2006, Chow et al. 2010, Namekawa et al. 2010). In mouse ES cells, X-linked genes are initially located at the periphery of the compartment but progressively move into it as differentiation proceeds and as they become silenced. Interestingly, formation of this silent compartment was shown to be independent of the A-repeat region of Xist. However, gene silencing and relocation into the Xist RNA compartment require the A repeat (Chaumeil et al. 2006). Only genes that escape from X inactivation remain located outside the Xist RNA domain in mouse cells (Chaumeil et al. 2006, Chow et al. 2010). These observations suggest that Xist RNA binding overlaps with repetitive sequences on the X chromosome. However, as noted above, Xist RNA does not overlay with repeat-rich G-bands on metaphase chromosomes in somatic cells but rather with gene-rich R-bands (Duthie et al. 1999, Mak et al. 2002, Smith et al. 2004). In interphase nuclei, however, the repetitive core of the X that is initially coated and appears to be transcriptionally inactive corresponds mainly to short interspersed element and long interspersed element (LINE) repeats (Chow et al. 2010). However, some LINE-rich sequences, corresponding to evolutionarily younger elements, were shown not to be initially located in the Xist RNA compartment (see below). Furthermore, using Xist transgenes on autosomes that can induce autosomal gene inactivation to some extent, Chow et al. (2010) found that genes located in more LINE-poor regions tend to be more external to the Xist RNA domain, and to be less well silenced, than those in LINE-rich regions. This is consistent with previous hypotheses that LINEs may participate in the spread of X inactivation (see below). Importantly, Xist RNA coating does not encompass the entire X chromosome from the outset, based on RNA/DNA FISH (Chow et al. 2010, Clemson et al. 2006) and more recently on Xist RAP and CHART mapping (Engreitz et al. 2013, Simon et al. 2013), where Xist was shown to target preferentially gene-rich regions. To gain insight into the role that Xist RNA plays in chromosome organization, allele-specific chromosome conformation capture-on-chip technology was used to produce high-resolution structural maps of the Xi and Xa in female cells (Splinter et al. 2011). This revealed that deletion www.annualreviews.org • Noncoding RNAs

569

CB30CH22-Heard

ARI

4 September 2014

8:31

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

of Xist leads to refolding of the Xi chromosome into a structure resembling the Xa, without affecting gene silencing or DNA methylation. This points to a role for the Xist RNA in shaping the conformation of the Xi chromosome in cells at least partially independently of its silencing function. Based on all the above studies, we conclude that initial Xist RNA accumulation exploits the structure of the X chromosome to begin its coating, and this rapidly leads to the formation of a silent, repetitive compartment that may participate in the initiation of gene silencing, as well as to a global spatial reorganization of the X chromosome. Whether this contributes to the longterm maintenance of gene silencing on the Xi, in addition to epigenetic modifications such as DNA methylation, remains an open question. In the following sections, we describe the possible cis-elements and trans-acting factors that participate in the functions of the Xist transcript and facilitate the spread of X inactivation.

CIS-ELEMENTS: THE ROLES OF CHROMOSOMAL REPEAT ELEMENTS IN XIST RNA-MEDIATED X INACTIVATION Quantification of Xist RNA abundance has led to estimates of approximately 2,000 molecules present per nucleus, thus ruling out the possibility that the Xist RNA covers the whole length of X chromosome DNA at any one time (Buzin et al. 1994). This finding reinforced the already existing idea that chromosomal elements present on the X chromosome may exist to facilitate the propagation of the inactive state in some way. Such elements could either be sequences targeted by Xist RNA itself (Engreitz et al. 2013), or else they could be independent sequences that enable propagation of a chromatin signal from Xist RNA-targeted entry points. What could such elements be? The mouse and human X chromosomes have a repeat density that is comparable to the average of the genome, except for the LINE-1 (or L1) family, which are found to be at least twofold enriched on the X chromosome when compared to autosomes (Boyle et al. 1990, Ross et al. 2005, Waterston et al. 2002). Given their overrepresentation on the X chromosome, L1 elements are potential candidates either for Xist RNA binding (or entry) sites and/or to help spread the inactive state. Mary Lyon (1998b) initially proposed the potential role of L1s more than 15 years ago (the repeat hypothesis), as the specific way station elements of Gartler & Riggs (1983) that enable efficient propagation of silencing along the X chromosome. This was based on several lines of evidence, including the X-chromosomal enrichment of L1 sequences in mouse and human. Furthermore, the density of L1s is greatest in the region surrounding the Xic, and an inverse correlation was found around genes that escape X inactivation (Bailey et al. 2000). However, the recent generation of Xist RNA binding maps, defining the first regions of the X chromosome targeted by Xist RNA, revealed that L1s are unlikely to act as direct landing sites. Indeed, Xist RNA coating and LINE repeats show rather mutually exclusive patterns (Duthie et al. 1999, Engreitz et al. 2013). However, studies of X:autosome translocations have revealed a good correlation in the efficiency of XCI spread along the translocated chromosome and the LINE content of the autosome in question (Lyon 1998b, Popova et al. 2006, Sharp et al. 2002). Similar findings have been reported using Xist transgenes on autosomes (Chow et al. 2010, Tang et al. 2010). On the X chromosome, the greatest LINE enrichment concerns the younger, full-length L1s, supporting the idea that such elements may have been selectively retained in the course of evolution to facilitate XCI (Bailey et al. 2000). More recently, Chow et al. (2010) proposed a potential role for both younger and older LINE repeats in XCI. First, truncated, inactive LINEs participate in the formation of the repetitive nuclear compartment formed by Xist RNA at the onset of XCI (Chaumeil et al. 2006, Chow et al. 2010, Clemson et al. 2006). Additionally, general L1 density (both full-length and truncated L1 elements) appears to facilitate Xist RNA-mediated 570

Gendrel

·

Heard

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

ARI

4 September 2014

8:31

silencing efficiency, as was shown using Xist transgenic autosomal cell lines (Chow et al. 2010, Tang et al. 2010). Finally, certain families of young, active L1 elements appear to be expressed from the Xi chromosome during the onset of XCI, which may facilitate gene silencing in certain regions of the X chromosome that are prone to escape from XCI (Chow et al. 2010). Remarkably, the marsupial X chromosome does not have a similar enrichment in L1 sequences (Mikkelsen et al. 2007), suggesting that the accumulation of X-linked L1s may have been selected for during eutherian X-chromosome evolution (Abrusan et al. 2008). Indeed, the fact that in marsupials XCI occurs in the absence of Xist (see section on evolutionary diversity) indicates that eutherian Xist-mediated XCI may have evolved to depend on the presence of L1 sequences as potential facilitators of the process. Importantly, the absence of L1 enrichment on the marsupial X argued against a long-standing hypothesis that the accumulation of L1s on the mammalian X could simply be the result of the X chromosome’s special status owing to the absence of recombination when it passes through the male germ line. In conclusion, although L1 elements are unlikely to act as Xist RNA entry points or binding elements, they do represent strong candidates as potential way stations for the spread of gene silencing during eutherian XCI. However, functional tests to address their roles are lacking. Furthermore, although L1 elements are the most overrepresented type of repeats on the X chromosome in eutherians, other types of sequences also appear to be more enriched on the X chromosome compared with autosomes, including inverted repeats (Warburton et al. 2004), long terminal repeats (Chow et al. 2005), and predicted scaffold/matrix attachment regions (Girod et al. 2007), and could also play a role as relay elements facilitating Xist spreading. To date, no studies have explored the role of these sequences in XCI.

TRANS-ACTING FACTORS IMPLICATED IN XIST RNA-MEDIATED FUNCTIONS Multiple protein factors likely mediate XCI, both at the level of Xist RNA coating and during downstream events. Nuclear fractionation experiments have revealed that Xist RNA is associated with the nuclear scaffold or matrix, suggesting that components of this structure may interact directly or indirectly with Xist RNA and perhaps participate in restricting its localization to the Xi territory (Clemson et al. 1996). The nuclear matrix is a filamentous protein network containing factors essential for various nuclear functions, including DNA replication and gene expression. It is believed to participate in such processes by providing a structural higher-order organization within the nucleus. Interestingly, Satb1 (special AT-rich binding 1) and hnRNP U (heterogeneous nuclear ribonucleoprotein U), two factors that were recently shown to play a role in the regulation of the X inactivation process (Agrelo et al. 2009, Hasegawa et al. 2010), are components of the nuclear matrix that are known to bind DNA regions corresponding to scaffold/matrix attachment regions (Kipp et al. 2000). These regions are highly polymorphic but have an AT-rich base composition (Laemmli et al. 1992) and were predicted to be present at high density on the X chromosome relative to autosomes (Girod et al. 2007). Using immunofluorescence staining, Helbig & Fackelmayer (2003) first showed that the hnRNP U factor, or Saf-A (scaffold attachment factor A), colocalizes with the Xi in human female somatic cells. Evidence for a potential role in X inactivation came from a study showing that Xist RNA is displaced from the Xi to the nucleoplasm upon knockdown of hnRNP U/Saf-A in somatic cells and differentiating ES cells. UV crosslinking experiments further suggested that hnRNP U/Saf-A interacts with the Xist transcript through its RNA binding domain (Hasegawa et al. 2010). Finally, the localization of Saf-A to the Xi was found to depend on Xist and to require both the RNA and the DNA binding domains of Saf-A. Thus, hnRNP U/Saf-A appears to be a www.annualreviews.org • Noncoding RNAs

571

ARI

4 September 2014

8:31

good candidate bridging factor between Xist RNA and chromatin. However, hnRNP U/Saf-A is recruited to the Xi only during the later phase of X inactivation, indicating that it may be necessary only for the stable maintenance of Xist RNA localization to the Xi territory (Pullirsch et al. 2010) and that it is unlikely to be involved in the initial coating of the chromosome by Xist RNA. Another protein, Satb1, was proposed to play a role in the silencing function of Xist RNA in different cell types (T cell lymphomas, thymocytes, mouse embryonic fibroblasts) where the silencing competence of Xist RNA is no longer effective (Agrelo et al. 2009). In thymocyte nuclei, Satb1 is observed in a ringlike structure (Cai et al. 2003), and Xist RNA does not form a cloud but appears as a diffuse pattern localized along the Satb1 ring in more than 50% of cells. The delocalization of Xist into a ringlike pattern appears to depend on Satb1, as it is not observed in thymocytes isolated from Satb1-deficient mice (Agrelo et al. 2009). Furthermore, ES cells depleted for Satb1 and Satb2 are impaired in their ability to trigger Xist-mediated gene silencing (Agrelo et al. 2009), and Satb1 has been shown to organize transcriptionally active chromatin into chromatin loops (Cai et al. 2006, Galande et al. 2007). Thus, Satb1 was also proposed to assist in the chromosomal organization that accompanies the initiation of silencing by Xist (Agrelo et al. 2009) and, in particular, the Xist RNA repeat-rich silent compartment into which silent genes are relocated (Chaumeil et al. 2006, Clemson et al. 2006). However, a recent study demonstrated that Satb1 and Satb2 are dispensable for XCI during mouse development, as X inactivation is not impaired in mouse embryonic fibroblasts derived from double Satb1, Satb2 mutant embryos (Nechanitzky et al. 2012). These conflicting results point toward additional factors that may act redundantly but do not rule out a role of Satb1 in XCI (Wutz & Agrelo 2012). Intriguingly, Satb1 binding sites are also found in L1 elements (de Belle et al. 1998), providing yet another potential link between LINEs and XCI, although this binding was not described specifically for the Xi. Following Xist RNA accumulation, several chromatin changes occur on the Xi, in particular, the recruitment of the PRC1 and PRC2 complexes, with PRC2 inducing chromosome-wide H3K27me3 (Plath et al. 2003, Silva et al. 2003) and PRC1 mediating ubiquitination of lysine 119 on histone H2A (H2AK119u) (de Napoles et al. 2004, Fang et al. 2004). The mechanisms for Polycomb complex recruitment to the Xi are unclear. Both PRC1 and PRC2 could be recruited to the Xi via Xist RNA. Indeed, Cbx7 (a PRC1 member) association with the Xi was shown to be disrupted following RNase treatment (Bernstein et al. 2006), and two core subunits of the PRC2 complex, Ezh2 and Suz12, have been shown to bind a short RNA containing the A-repeat region of the Xist transcript in ES cells (Maenner et al. 2010, Zhao et al. 2008). In support of this, Xist and PRC2 display similar localization-banding patterns on metaphase chromosomes (Duthie et al. 1999, Mak et al. 2002), and the comparison of Xist RNA binding patterns with that of ChIP-seq for Ezh2 revealed a faithful overlap between both (Simon et al. 2013) (Figure 3). However, very recent super-resolution 3D structured illumination (3D-SIM) microscopy analysis revealed a clear spatial separation of Xist RNA foci and PRC2 proteins in interphase nuclei (Cerase et al. 2014) (Figure 3). Moreover, during mouse early embryo development, although PRC2 components are present early on, their recruitment to the paternal X occurs only at the 16-cell stage, even though Xist coating begins as early as the 4-cell stage (Okamoto et al. 2004). Thus, PRC2 recruitment to the X chromosome, which requires the Jarid2 and Pcl2 cofactors (Casanova et al. 2011, da Rocha et al. 2014), apparently is not directly mediated by Xist RNA coating but requires some as-yet-unknown downstream event. The histone variant macroH2A is also incorporated into the chromatin of the Xi in a Xist-dependent manner, though this occurs at a rather late stage in differentiation (Csankovszki et al. 1999). However, similarly to the other factors mentioned above, there is so far no evidence of a direct interaction between Xist RNA and any of the chromatin modifiers recruited to the Xi during XCI. It is still not clear whether any of the protein factors

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

572

Gendrel

·

Heard

CB30CH22-Heard

ARI

4 September 2014

8:31

so far described to associate with the Xi in a Xist-induced fashion are recruited directly by Xist RNA, or whether Xist induces some change in Xi chromatin that makes it receptive to their binding.

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

THE EVOLUTIONARY DIVERSITY OF X-INACTIVATION MECHANISMS AND THE NONCODING RNAS THAT CONTROL THEM X-chromosome dosage compensation is found in most mammals, but the mechanisms vary considerably between species. Although Xist appears to be well conserved among eutherians, including mouse, human, cow, dog, and elephant (Chaumeil et al. 2011, Duret et al. 2006, Yen et al. 2007), it is absent in noneutherian vertebrates, including mammals such as marsupials, which nevertheless display XCI (Duret et al. 2006, Elisaphenko et al. 2008). Further sequence analysis of the Xic homologous region in various species revealed that Xist actually shares fragmented exonic sequence homology with the protein-coding Lnx3 gene found in marsupials, chickens, and fish (Duret et al. 2006, Elisaphenko et al. 2008). Xist must therefore have emerged de novo in the eutherian coancestor through pseudogenization of the Lnx3 gene. New Xist exons were formed with the insertion of mobile elements of various classes, which also gave rise to the blocks of tandem repeats found within the first exon of the gene. These events contributed to the creation of a novel ncRNA gene (Duret et al. 2006, Elisaphenko et al. 2008). Interestingly, other ncRNA loci, such as the Enox/Jpx ncRNA gene, may have evolved similarly in the Xic region (Elisaphenko et al. 2008). The Lnx3 gene is still functional in marsupials. In opossums, it is expressed in both males and females, a situation very different from Xist’s exclusively female expression in eutherians. Thus, XCI appears to be triggered independently of Xist in marsupials. Another interesting aspect of the study from Elisaphenko et al. (2008) is the analysis of the rapid evolution of the Xist gene within the eutherian lineage across different species. They show that the length and structure of the Xist gene differ substantially between species, notably in terms of exon-intron junctions and the presence of tandem repeats that may contribute to the RNA secondary structure (Elisaphenko et al. 2008). These tandem repeats originate from the insertion of mobile elements, some being young and species-specific insertions, which could contribute to the creation of new functional domains on the XIST/Xist gene and to some species-specific mode of Xist regulation (see below). Interestingly, this could be a general mechanism for the evolution of large regulatory RNAs. ncRNAs may thus evolve more rapidly than protein-coding genes, with repeat elements participating in this rapid evolution. In rodents, XCI initially affects only the paternal X chromosome, thanks largely to an imprint that prevents maternal Xist expression during early preimplantation development (Okamoto et al. 2005). Imprinted XCI is maintained in the trophectoderm lineage that will form part of the placenta and in the primitive endoderm, which gives rise to the visceral endoderm and the yolk sac in the mouse (Okamoto & Heard 2009). Studies of extraembryonic tissues and early embryos in eutherian species other than mouse have shown that XCI is usually random rather than imprinted, contrasting with the situation in the mouse (Moreira de Mello et al. 2010, Okamoto et al. 2011, Wang et al. 2012). Furthermore, the timing and nature of early XCI events and Xist regulation in human and rabbit embryos are rather different (Okamoto et al. 2011). These differences may be explained by differences in the cis and trans regulators of Xist. For example, pluripotency factor expression varies considerably between mammals in preimplantation embryos and may feed into Xist regulation at different stages, whereas cis-regulators of Xist, like the Tsix locus, are mouse specific (Table 1). Another interesting difference between eutherians that has emerged recently is the existence of a noncoding RNA, XACT, that specifically associates with the Xa chromosome, or with both Xs in www.annualreviews.org • Noncoding RNAs

573

CB30CH22-Heard

ARI

4 September 2014

8:31

Table 1 Conservation of the various players of X-chromosome inactivation between mouse, human, and marsupiala Mouse

Human

Marsupial

Xist







Tsix







Linx







Jpx



?



Ftx



?



Rsx







a

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Ticks indicate presence of the gene in a given species, crosses indicate absence, and question marks indicate unknown status.

the absence of XIST, in human ES and pluripotent cells and is present only in primates (Vallot et al. 2013). Whether XACT plays any functional role or whether it is just a highly expressed ncRNA species in human stem cells requires further investigation. In metatherians (or marsupials), Xchromosome dosage compensation also occurs, but in this case, X inactivation is imprinted, with the paternal X chromosome being affected in all tissues. As mentioned previously, marsupial XCI is not Xist dependent. Furthermore, unlike in eutherians, XCI is rather incomplete, tissue-specific, and unstable in marsupials, with a high percentage of genes showing some degree of escape from gene silencing in somatic tissues (Deakin et al. 2009, Kaslow & Migeon 1987). Despite these obvious differences in the molecular mechanisms that trigger XCI, marsupial and eutherian XCI share many common downstream features of the Xi, such as the depletion of active chromatin marks from the Xi and enrichment of the repressive marks (Chaumeil et al. 2011, Mahadevaiah et al. 2009, Rens et al. 2010). The question of how XCI is initiated in marsupials in the absence of a Xist gene was the subject of much speculation until the recent discovery of a lncRNA called Rsx in the marsupial species Monodelphis domestica (Grant et al. 2012). Rsx has several properties that resemble Xist, suggesting that it may have a role in XCI. RNA FISH showed that the Rsx RNA signal in the nucleus resembles a cloud, reminiscent of Xist, which colocalizes with enrichment of the Xi marker H3K27me3. The Rsx gene was shown to encode a large spliced RNA of approximately 27 kb (longer than the 17-kb Xist), expressed solely in female and not male cells in all tissues tested. Rsx and Xist do not share any homologous sequences, but Rsx contains several tandem repeat sequences at its 5 end, resembling the Xist A-repeat region. Moreover, Rsx can induce gene silencing in cis when inserted at a random position on a mouse autosome in ES cells (Grant et al. 2012). The fact that both Xist and Rsx are large nuclear regulatory RNAs with no sequence homology, which have evolved independently in eutherian and metatherian mammalian lineages, presumably for the same goal of silencing an entire chromosome, is a striking illustration of the evolutionary plasticity of noncoding RNAs compared to their more constrained protein-coding counterparts. These findings raise many questions about the evolution of the X-inactivation process. In particular, it is still not clear whether an Rsx orthologous genomic sequence might exist in eutherians and, if so, whether it could contribute to imprinted XCI. Also, whether marsupial and eutherian XCI differ in terms of their degree of stability as a result of differences in Rsx and Xist RNA structure/function, or owing to some other differences, such as the lack of locus-specific DNA methylation (Loebel & Johnston 1996, Piper et al. 1993) on the Xi, remains to be investigated. Moreover, these studies in different mammals indicate that imprinted paternal XCI must have evolved at least twice during evolution: once in metatherians via Rsx and a second time in rodents via an imprint on the maternal Xist gene. 574

Gendrel

·

Heard

CB30CH22-Heard

ARI

4 September 2014

8:31

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CONCLUDING REMARKS The ENCODE project revealed that almost every human coding gene overlaps with the transcription of approximately ten lncRNA isoforms on average (Djebali et al. 2012). Many of those arise from pervasive transcription, but several may also play regulatory roles in important cellular processes. Indeed, it is becoming increasingly apparent that regulatory ncRNAs play crucial roles in XCI as well as in other epigenetic processes, such as genomic imprinting. There is also much interest in their potential roles in broader cellular processes, for example, during development (Fatica & Bozzoni 2014). Although ncRNAs can act in many different ways, both in cis and in trans, in the context of XCI, the roles of Xist and Rsx illustrate how such ncRNAs can have multiple possible cis-limiting roles, as recruiters of epigenetic factors and mediators of chromosome interactions as well as nuclear compartment formation. The mechanisms underlying their capacity to bind and spread along a chromosome in cis still remain among the most puzzling questions in the field. Although recent findings suggest that Xist RNA can both exploit and alter the architecture of the chromosome from which it is expressed, the molecular basis for Xist’s capacity to coat chromatin and to silence genes still remains a mystery. Our rapidly expanding understanding of Xist RNA functions will undoubtedly have important implications for other ncRNAs.

DISCLOSURE STATEMENT The authors are not aware of any affiliations, memberships, funding, or financial holdings that might be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS We are grateful to members of the Heard group for helpful discussions and would like to apologize to colleagues whose work could not be cited owing to space constraints. Work in E.H.’s group is supported by the Ligue Nationale contre le cancer, Labex DEEP (ANR-11-LBX-0044), part of the IDEX Idex PSL (ANR-10-IDEX-0001-02 PSL), the EU EpiGeneSys FP7 257082 Network of Excellence, ERC Advanced Investigator award 250367, and EU FP7 MODHEP (259743) and SYBOSS (242129) grants (E.H.). LITERATURE CITED Abrusan G, Giordano J, Warburton PE. 2008. Analysis of transposon interruptions suggests selection for L1 elements on the X chromosome. PLOS Genet. 4:e1000172 Agrelo R, Souabni A, Novatchkova M, Haslinger C, Leeb M, et al. 2009. SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells. Dev. Cell 16:507–16 Augui S, Nora EP, Heard E. 2011. Regulation of X-chromosome inactivation by the X-inactivation centre. Nat. Rev. Genet. 12:429–42 Bailey JA, Carrel L, Chakravarti A, Eichler EE. 2000. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis. Proc. Natl. Acad. Sci. USA 97:6634– 39 Barakat TS, Gunhanlar N, Pardo CG, Achame EM, Ghazvini M, et al. 2011. RNF12 activates Xist and is essential for X chromosome inactivation. PLOS Genet. 7:e1002001 Barr ML, Bertram EG. 1949. A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis. Nature 163:676–77 Barton DE, David FN, Merrington M. 1964. The positions of the sex chromosomes in the human cell in mitosis. Ann. Hum. Genet. 28:123–28 Berletch JB, Yang F, Disteche CM. 2010. Escape from X inactivation in mice and humans. Genome Biol. 11:213 www.annualreviews.org • Noncoding RNAs

575

ARI

4 September 2014

8:31

Bernstein E, Duncan EM, Masui O, Gil J, Heard E, Allis CD. 2006. Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol. Cell. Biol. 26:2560–69 Borden J, Manuelidis L. 1988. Movement of the X chromosome in epilepsy. Science 242:1687–91 Borsani G, Tonlorenzi R, Simmler MC, Dandolo L, Arnaud D, et al. 1991. Characterization of a murine gene expressed from the inactive X chromosome. Nature 351:325–29 Bourgeois CA, Laquerriere F, Hemon D, Hubert J, Bouteille M. 1985. New data on the in-situ position of the inactive X chromosome in the interphase nucleus of human fibroblasts. Hum. Genet. 69:122–29 Boyle AL, Ballard SG, Ward DC. 1990. Differential distribution of long and short interspersed element sequences in the mouse genome: chromosome karyotyping by fluorescence in situ hybridization. Proc. Natl. Acad. Sci. USA 87:7757–61 Brockdorff N, Ashworth A, Kay GF, Cooper P, Smith S, et al. 1991. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature 351:329–31 Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, et al. 1991. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349:38–44 Brown CJ, Willard HF. 1994. The human X-inactivation centre is not required for maintenance of Xchromosome inactivation. Nature 368:154–56 Buzin CH, Mann JR, Singer-Sam J. 1994. Quantitative RT-PCR assays show Xist RNA levels are low in mouse female adult tissue, embryos and embryoid bodies. Development 120:3529–36 Cai S, Han HJ, Kohwi-Shigematsu T. 2003. Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat. Genet. 34:42–51 Cai S, Lee CC, Kohwi-Shigematsu T. 2006. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat. Genet. 38:1278–88 Calabrese JM, Sun W, Song L, Mugford JW, Williams L, et al. 2012. Site-specific silencing of regulatory elements as a mechanism of X inactivation. Cell 151:951–63 Casanova M, Preissner T, Cerase A, Poot R, Yamada D, et al. 2011. Polycomblike 2 facilitates the recruitment of PRC2 Polycomb group complexes to the inactive X chromosome and to target loci in embryonic stem cells. Development 138:1471–82 Cattanach BM, Williams CE. 1972. Evidence of non-random X chromosome activity in the mouse. Genet. Res. 19:229–40 Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, et al. 2014. Spatial separation of Xist RNA and polycomb proteins revealed by super-resolution microscopy. Proc. Natl. Acad. Sci. USA 111:2235–40 Chaumeil J, Le Baccon P, Wutz A, Heard E. 2006. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev. 20:2223–37 Chaumeil J, Okamoto I, Heard E. 2004. X-chromosome inactivation in mouse embryonic stem cells: analysis of histone modifications and transcriptional activity using immunofluorescence and FISH. Methods Enzymol. 376:405–19 Chaumeil J, Waters PD, Koina E, Gilbert C, Robinson TJ, Graves JA. 2011. Evolution from XISTindependent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals. PLOS ONE 6:e19040 Chow J, Heard E. 2009. X inactivation and the complexities of silencing a sex chromosome. Curr. Opin. Cell Biol. 21:359–66 Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, et al. 2010. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141:956–69 Chow JC, Yen Z, Ziesche SM, Brown CJ. 2005. Silencing of the mammalian X chromosome. Annu. Rev. Genomics Hum. Genet. 6:69–92 Chureau C, Chantalat S, Romito A, Galvani A, Duret L, et al. 2011. Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum. Mol. Genet. 20:705–18 Clemson CM, Hall LL, Byron M, McNeil J, Lawrence JB. 2006. The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc. Natl. Acad. Sci. USA 103:7688–93 Clemson CM, McNeil JA, Willard HF, Lawrence JB. 1996. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J. Cell Biol. 132:259–75

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

576

Gendrel

·

Heard

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

ARI

4 September 2014

8:31

Clerc P, Avner P. 1998. Role of the region 3 to Xist exon 6 in the counting process of X-chromosome inactivation. Nat. Genet. 19:249–53 Csankovszki G, Nagy A, Jaenisch R. 2001. Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. J. Cell Biol. 153:773–84 Csankovszki G, Panning B, Bates B, Pehrson JR, Jaenisch R. 1999. Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation. Nat. Genet. 22:323–24 da Rocha ST, Boeva V, Escamilla-Del-Arenal M, Ancelin K, Granier C, et al. 2014. Jarid2 is implicated in the initial Xist-induced targeting of PRC2 to the inactive X chromosome. Mol. Cell 53:301–16 de Belle I, Cai S, Kohwi-Shigematsu T. 1998. The genomic sequences bound to special AT-rich sequencebinding protein 1 (SATB1) in vivo in Jurkat T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops. J. Cell Biol. 141:335–48 de Napoles M, Mermoud JE, Wakao R, Tang YA, Endoh M, et al. 2004. Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev. Cell 7:663–76 Deakin JE, Chaumeil J, Hore TA, Marshall Graves JA. 2009. Unravelling the evolutionary origins of X chromosome inactivation in mammals: insights from marsupials and monotremes. Chromosome Res. 17:671–85 Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et al. 2012. Landscape of transcription in human cells. Nature 489:101–8 Duret L, Chureau C, Samain S, Weissenbach J, Avner P. 2006. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312:1653–55 Duthie SM, Nesterova TB, Formstone EJ, Keohane AM, Turner BM, et al. 1999. Xist RNA exhibits a banded localization on the inactive X chromosome and is excluded from autosomal material in cis. Hum. Mol. Genet. 8:195–204 Dyer KA, Canfield TK, Gartler SM. 1989. Molecular cytological differentiation of active from inactive X domains in interphase: implications for X chromosome inactivation. Cytogenet. Cell Genet. 50:116–20 Elisaphenko EA, Kolesnikov NN, Shevchenko AI, Rogozin IB, Nesterova TB, et al. 2008. A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLOS ONE 3:e2521 Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, et al. 2013. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341:1237973 Fang J, Chen T, Chadwick B, Li E, Zhang Y. 2004. Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J. Biol. Chem. 279:52812–15 Fatica A, Bozzoni I. 2014. Long non-coding RNAs: new players in cell differentiation and development. Nat. Rev. Genet. 15:7–21 Galande S, Purbey PK, Notani D, Kumar PP. 2007. The third dimension of gene regulation: organization of dynamic chromatin loopscape by SATB1. Curr. Opin. Genet. Dev. 17:408–14 Gartler SM, Riggs AD. 1983. Mammalian X-chromosome inactivation. Annu. Rev. Genet. 17:155–90 Girod PA, Nguyen DQ, Calabrese D, Puttini S, Grandjean M, et al. 2007. Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells. Nat. Methods 4:747–53 Gontan C, Achame EM, Demmers J, Barakat TS, Rentmeester E, et al. 2012. RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation. Nature 485:386–90 Grant J, Mahadevaiah SK, Khil P, Sangrithi MN, Royo H, et al. 2012. Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. Nature 487:254–58 Graves JA. 2006. Sex chromosome specialization and degeneration in mammals. Cell 124:901–14 Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Nakagawa S. 2010. The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. Dev. Cell 19:469–76 Heard E, Mongelard F, Arnaud D, Avner P. 1999. Xist yeast artificial chromosome transgenes function as X-inactivation centers only in multicopy arrays and not as single copies. Mol. Cell. Biol. 19:3156–66 Helbig R, Fackelmayer FO. 2003. Scaffold attachment factor A (SAF-A) is concentrated in inactive X chromosome territories through its RGG domain. Chromosoma 112:173–82 Herzing LB, Romer JT, Horn JM, Ashworth A. 1997. Xist has properties of the X-chromosome inactivation centre. Nature 386:272–75 Jiang J, Jing Y, Cost GJ, Chiang JC, Kolpa HJ, et al. 2013. Translating dosage compensation to trisomy 21. Nature 500:296–300 www.annualreviews.org • Noncoding RNAs

577

ARI

4 September 2014

8:31

Jonkers I, Barakat TS, Achame EM, Monkhorst K, Kenter A, et al. 2009. RNF12 is an X-encoded dosedependent activator of X chromosome inactivation. Cell 139:999–1011 Jonkers I, Monkhorst K, Rentmeester E, Grootegoed JA, Grosveld F, Gribnau J. 2008. Xist RNA is confined to the nuclear territory of the silenced X chromosome throughout the cell cycle. Mol. Cell. Biol. 28:5583–94 Kaslow DC, Migeon BR. 1987. 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 84:6210–14 Kay GF, Penny GD, Patel D, Ashworth A, Brockdorff N, Rastan S. 1993. Expression of Xist during mouse development suggests a role in the initiation of X chromosome inactivation. Cell 72:171–82 Kipp M, Gohring F, Ostendorp T, van Drunen CM, van Driel R, et al. 2000. SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA. Mol. Cell. Biol. 20:7480–89 Kohlmaier A, Savarese F, Lachner M, Martens J, Jenuwein T, Wutz A. 2004. A chromosomal memory triggered by Xist regulates histone methylation in X inactivation. PLOS Biol. 2:E171 Laemmli UK, Kas E, Poljak L, Adachi Y. 1992. Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains. Curr. Opin. Genet. Dev. 2:275–85 Lee JT, Jaenisch R. 1997. Long-range cis effects of ectopic X-inactivation centres on a mouse autosome. Nature 386:275–79 Lee JT, Lu N. 1999. Targeted mutagenesis of Tsix leads to nonrandom X inactivation. Cell 99:47–57 Lin H, Gupta V, Vermilyea MD, Falciani F, Lee JT, et al. 2007. Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLOS Biol. 5:e326 Loebel DA, Johnston PG. 1996. Methylation analysis of a marsupial X-linked CpG island by bisulfite genomic sequencing. Genome Res. 6:114–23 Lyon MF. 1961. Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 190:372–73 Lyon MF. 1962. Sex chromatin and gene action in the mammalian X-chromosome. Am. J. Hum. Genet. 14:135–48 Lyon MF. 1998a. X-chromosome inactivation spreads itself: effects in autosomes. Am. J. Hum. Genet. 63:17–19 Lyon MF. 1998b. X-chromosome inactivation: a repeat hypothesis. Cytogenet. Cell Genet. 80:133–37 Maenner S, Blaud M, Fouillen L, Savoye A, Marchand V, et al. 2010. 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLOS Biol. 8:e1000276 Mahadevaiah SK, Royo H, VandeBerg JL, McCarrey JR, Mackay S, Turner JM. 2009. Key features of the X inactivation process are conserved between marsupials and eutherians. Curr. Biol. 19:1478–84 Mak W, Baxter J, Silva J, Newall AE, Otte AP, Brockdorff N. 2002. Mitotically stable association of polycomb group proteins eed and enx1 with the inactive x chromosome in trophoblast stem cells. Curr. Biol. 12:1016– 20 Mak W, Nesterova TB, de Napoles M, Appanah R, Yamanaka S, et al. 2004. Reactivation of the paternal X chromosome in early mouse embryos. Science 303:666–69 Marahrens Y, Loring J, Jaenisch R. 1998. Role of the Xist gene in X chromosome choosing. Cell 92:657–64 Marks H, Chow JC, Denissov S, Francoijs KJ, Brockdorff N, et al. 2009. High-resolution analysis of epigenetic changes associated with X inactivation. Genome Res. 19:1361–73 Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167–77 Minkovsky A, Barakat TS, Sellami N, Chin MH, Gunhanlar N, et al. 2013. The pluripotency factor-bound intron 1 of Xist is dispensable for X chromosome inactivation and reactivation in vitro and in vivo. Cell Rep. 3:905–18 Moreira de Mello JC, de Araujo ES, Stabellini R, Fraga AM, de Souza JE, et al. 2010. Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome. PLOS ONE 5:e10947 Morey C, Arnaud D, Avner P, Clerc P. 2001. Tsix-mediated repression of Xist accumulation is not sufficient for normal random X inactivation. Hum. Mol. Genet. 10:1403–11 Namekawa SH, Payer B, Huynh KD, Jaenisch R, Lee JT. 2010. Two-step imprinted X inactivation: repeat versus genic silencing in the mouse. Mol. Cell. Biol. 30:3187–205 Navarro P, Chambers I, Karwacki-Neisius V, Chureau C, Morey C, et al. 2008. Molecular coupling of Xist regulation and pluripotency. Science 321:1693–95

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

578

Gendrel

·

Heard

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

ARI

4 September 2014

8:31

Navarro P, Moffat M, Mullin NP, Chambers I. 2011. The X-inactivation trans-activator Rnf12 is negatively regulated by pluripotency factors in embryonic stem cells. Hum. Genet. 130:255–64 Navarro P, Oldfield A, Legoupi J, Festuccia N, Dubois A, et al. 2010. Molecular coupling of Tsix regulation and pluripotency. Nature 468:457–60 Nechanitzky R, D´avila A, Savarese F, Fietze S, Grosschedl R. 2012. Satb1 and Satb2 are dispensable for X chromosome inactivation in mice. Dev. Cell 23:866–71 Nesterova TB, Senner CE, Schneider J, Alcayna-Stevens T, Tattermusch A, et al. 2011. Pluripotency factor binding and Tsix expression act synergistically to repress Xist in undifferentiated embryonic stem cells. Epigenetics Chromatin 4:17 Ng K, Daigle N, Bancaud A, Ohhata T, Humphreys P, et al. 2011. A system for imaging the regulatory noncoding Xist RNA in living mouse embryonic stem cells. Mol. Biol. Cell 22:2634–45 Ohhata T, Wutz A. 2013. Reactivation of the inactive X chromosome in development and reprogramming. Cell. Mol. Life Sci. 70:2443–61 Ohno S. 1967. Sex Chromosomes and Sex Linked Genes. Berlin: Springer Verlag Okamoto I, Arnaud D, Le Baccon P, Otte AP, Disteche CM, et al. 2005. Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice. Nature 438:369–73 Okamoto I, Heard E. 2009. Lessons from comparative analysis of X-chromosome inactivation in mammals. Chromosome Res. 17:659–69 Okamoto I, Otte AP, Allis CD, Reinberg D, Heard E. 2004. Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303:644–49 Okamoto I, Patrat C, Thepot D, Peynot N, Fauque P, et al. 2011. Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development. Nature 472:370–74 Panning B, Jaenisch R. 1996. DNA hypomethylation can activate Xist expression and silence X-linked genes. Genes Dev. 10:1991–2002 Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N. 1996. Requirement for Xist in X chromosome inactivation. Nature 379:131–37 Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, et al. 2012. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Res. 22:1864–76 Piper AA, Bennett AM, Noyce L, Swanton MK, Cooper DW. 1993. Isolation of a clone partially encoding hill kangaroo X-linked hypoxanthine phosphoribosyltransferase: sex differences in methylation in the body of the gene. Somat. Cell Mol. Genet. 19:141–59 Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, et al. 2003. Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–35 Pollex T, Heard E. 2012. Recent advances in X-chromosome inactivation research. Curr. Opin. Cell Biol. 24:825–32 Popova BC, Tada T, Takagi N, Brockdorff N, Nesterova TB. 2006. Attenuated spread of X-inactivation in an X;autosome translocation. Proc. Natl. Acad. Sci. USA 103:7706–11 Pullirsch D, Hartel R, Kishimoto H, Leeb M, Steiner G, Wutz A. 2010. The Trithorax group protein Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation. Development 137:935–43 Rastan S. 1983. Non-random X-chromosome inactivation in mouse X-autosome translocation embryos— location of the inactivation centre. J. Embryol. Exp. Morphol. 78:1–22 Rens W, Wallduck MS, Lovell FL, Ferguson-Smith MA, Ferguson-Smith AC. 2010. Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation. Proc. Natl. Acad. Sci. USA 107:17657–62 Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, et al. 2005. The DNA sequence of the human X chromosome. Nature 434:325–37 Russell LB, Montgomery CS. 1970. Comparative studies on X-autosome translocations in the mouse. II. Inactivation of autosomal loci, segregation, and mapping of autosomal breakpoints in five T(x;1)’s. Genetics 64:281–312 Sarma K, Levasseur P, Aristarkhov A, Lee JT. 2010. Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome. Proc. Natl. Acad. Sci. USA 107:22196–201 www.annualreviews.org • Noncoding RNAs

579

ARI

4 September 2014

8:31

Schulz EG, Meisig J, Nakamura T, Okamoto I, Sieber A, et al. 2014. The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network. Cell Stem Cell 14:203–16 Schulz EG, Heard E. 2013. Role and control of X chromosome dosage in mammalian development. Curr. Opin. Genet. Dev. 23:109–15 Sharman GB. 1971. Late DNA replication in the paternally derived X chromosome of female kangaroos. Nature 230:231–32 Sharp AJ, Spotswood HT, Robinson DO, Turner BM, Jacobs PA. 2002. Molecular and cytogenetic analysis of the spreading of X inactivation in X;autosome translocations. Hum. Mol. Genet. 11:3145–56 Silva J, Mak W, Zvetkova I, Appanah R, Nesterova TB, et al. 2003. Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev. Cell 4:481–95 Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, et al. 2013. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504:465–69 Smith KP, Byron M, Clemson CM, Lawrence JB. 2004. Ubiquitinated proteins including uH2A on the human and mouse inactive X chromosome: enrichment in gene rich bands. Chromosoma 113:324–35 Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJ, et al. 2011. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev. 25:1371–83 Sun S, Del Rosario BC, Szanto A, Ogawa Y, Jeon Y, Lee JT. 2013. Jpx RNA activates Xist by evicting CTCF. Cell 153:1537–51 Takagi N, Sasaki M. 1975. Preferential inactivation of the paternally derived X chromosome in the extraembryonic membranes of the mouse. Nature 256:640–42 Tang YA, Huntley D, Montana G, Cerase A, Nesterova TB, Brockdorff N. 2010. Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation. Epigenetics Chromatin 3:10 Tian D, Sun S, Lee JT. 2010. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143:390–403 Vallot C, Huret C, Lesecque Y, Resch A, Oudrhiri N, et al. 2013. XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells. Nat. Genet. 45:239–41 Wang X, Miller DC, Clark AG, Antczak DF. 2012. Random X inactivation in the mule and horse placenta. Genome Res. 22:1855–63 Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G. 2004. Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res. 14:1861–69 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–62 Wutz A, Agrelo R. 2012. Response: the diversity of proteins linking Xist to gene silencing. Dev. Cell 23:680 Wutz A, Jaenisch R. 2000. A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. Mol. Cell 5:695–705 Wutz A, Rasmussen TP, Jaenisch R. 2002. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat. Genet. 30:167–74 Yen ZC, Meyer IM, Karalic S, Brown CJ. 2007. A cross-species comparison of X-chromosome inactivation in Eutheria. Genomics 90:453–63 Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. 2008. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322:750–56

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

CB30CH22-Heard

580

Gendrel

·

Heard

ANNUAL REVIEWS Connect With Our Experts

New From Annual Reviews:

ONLINE NOW!

Annual Review of Cancer Biology

cancerbio.annualreviews.org • Volume 1 • March 2017

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Co-Editors: Tyler Jacks, Massachusetts Institute of Technology Charles L. Sawyers, Memorial Sloan Kettering Cancer Center The Annual Review of Cancer Biology reviews a range of subjects representing important and emerging areas in the field of cancer research. The Annual Review of Cancer Biology includes three broad themes: Cancer Cell Biology, Tumorigenesis and Cancer Progression, and Translational Cancer Science.

TABLE OF CONTENTS FOR VOLUME 1:

• How Tumor Virology Evolved into Cancer Biology and Transformed Oncology, Harold Varmus • The Role of Autophagy in Cancer, Naiara Santana-Codina, Joseph D. Mancias, Alec C. Kimmelman • Cell Cycle–Targeted Cancer Therapies, Charles J. Sherr, Jiri Bartek • Ubiquitin in Cell-Cycle Regulation and Dysregulation in Cancer, Natalie A. Borg, Vishva M. Dixit • The Two Faces of Reactive Oxygen Species in Cancer, Colleen R. Reczek, Navdeep S. Chandel • Analyzing Tumor Metabolism In Vivo, Brandon Faubert, Ralph J. DeBerardinis • Stress-Induced Mutagenesis: Implications in Cancer and Drug Resistance, Devon M. Fitzgerald, P.J. Hastings, Susan M. Rosenberg • Synthetic Lethality in Cancer Therapeutics, Roderick L. Beijersbergen, Lodewyk F.A. Wessels, René Bernards • Noncoding RNAs in Cancer Development, Chao-Po Lin, Lin He • p53: Multiple Facets of a Rubik’s Cube, Yun Zhang, Guillermina Lozano • Resisting Resistance, Ivana Bozic, Martin A. Nowak • Deciphering Genetic Intratumor Heterogeneity and Its Impact on Cancer Evolution, Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Charles Swanton

• Immune-Suppressing Cellular Elements of the Tumor Microenvironment, Douglas T. Fearon • Overcoming On-Target Resistance to Tyrosine Kinase Inhibitors in Lung Cancer, Ibiayi Dagogo-Jack, Jeffrey A. Engelman, Alice T. Shaw • Apoptosis and Cancer, Anthony Letai • Chemical Carcinogenesis Models of Cancer: Back to the Future, Melissa Q. McCreery, Allan Balmain • Extracellular Matrix Remodeling and Stiffening Modulate Tumor Phenotype and Treatment Response, Jennifer L. Leight, Allison P. Drain, Valerie M. Weaver • Aneuploidy in Cancer: Seq-ing Answers to Old Questions, Kristin A. Knouse, Teresa Davoli, Stephen J. Elledge, Angelika Amon • The Role of Chromatin-Associated Proteins in Cancer, Kristian Helin, Saverio Minucci • Targeted Differentiation Therapy with Mutant IDH Inhibitors: Early Experiences and Parallels with Other Differentiation Agents, Eytan Stein, Katharine Yen • Determinants of Organotropic Metastasis, Heath A. Smith, Yibin Kang • Multiple Roles for the MLL/COMPASS Family in the Epigenetic Regulation of Gene Expression and in Cancer, Joshua J. Meeks, Ali Shilatifard • Chimeric Antigen Receptors: A Paradigm Shift in Immunotherapy, Michel Sadelain

ANNUAL REVIEWS | CONNECT WITH OUR EXPERTS 650.493.4400/800.523.8635 (us/can) www.annualreviews.org | [email protected]

CB30-FrontMatter

ARI

2 September 2014

12:28

Annual Review of Cell and Developmental Biology

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Contents

Volume 30, 2014

Twists and Turns: A Scientific Journey Shirley M. Tilghman p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 1 Basic Statistics in Cell Biology David L. Vaux p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p23 Liquid-Liquid Phase Separation in Biology Anthony A. Hyman, Christoph A. Weber, and Frank Julicher ¨ p p p p p p p p p p p p p p p p p p p p p p p p p p p p p39 Physical Models of Plant Development Olivier Ali, Vincent Mirabet, Christophe Godin, and Jan Traas p p p p p p p p p p p p p p p p p p p p p p p p p p p59 Bacterial Pathogen Manipulation of Host Membrane Trafficking Seblewongel Asrat, Dennise A. de Jesus, ´ Andrew D. Hempstead, Vinay Ramabhadran, and Ralph R. Isberg p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p79 Virus and Cell Fusion Mechanisms Benjamin Podbilewicz p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 111 Spatiotemporal Basis of Innate and Adaptive Immunity in Secondary Lymphoid Tissue Hai Qi, Wolfgang Kastenmuller, ¨ and Ronald N. Germain p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 141 Protein Sorting at the trans-Golgi Network Yusong Guo, Daniel W. Sirkis, and Randy Schekman p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 169 Intercellular Protein Movement: Deciphering the Language of Development Kimberly L. Gallagher, Rosangela Sozzani, and Chin-Mei Lee p p p p p p p p p p p p p p p p p p p p p p p p p p 207 The Rhomboid-Like Superfamily: Molecular Mechanisms and Biological Roles Matthew Freeman p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 235 Biogenesis, Secretion, and Intercellular Interactions of Exosomes and Other Extracellular Vesicles Marina Colombo, Gra¸ca Raposo, and Clotilde Th´ery p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 255

vii

CB30-FrontMatter

ARI

2 September 2014

12:28

Cadherin Adhesion and Mechanotransduction D.E. Leckband and J. de Rooij p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 291 Electrochemical Control of Cell and Tissue Polarity Fred Chang and Nicolas Minc p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 317 Regulated Cell Death: Signaling and Mechanisms Avi Ashkenazi and Guy Salvesen p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 337 Determinants and Functions of Mitochondrial Behavior Katherine Labb´e, Andrew Murley, and Jodi Nunnari p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 357 Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Cytoplasmic Polyadenylation Element Binding Proteins in Development, Health, and Disease Maria Ivshina, Paul Lasko, and Joel D. Richter p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 393 Cellular and Molecular Mechanisms of Synaptic Specificity Shaul Yogev and Kang Shen p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 417 Astrocyte Regulation of Synaptic Behavior Nicola J. Allen p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 439 The Cell Biology of Neurogenesis: Toward an Understanding of the Development and Evolution of the Neocortex Elena Taverna, Magdalena G¨otz, and Wieland B. Huttner p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 465 Myelination of the Nervous System: Mechanisms and Functions Klaus-Armin Nave and Hauke B. Werner p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 503 Insights into Morphology and Disease from the Dog Genome Project Jeffrey J. Schoenebeck and Elaine A. Ostrander p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 535 Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation Anne-Valerie Gendrel and Edith Heard p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 561 Zygotic Genome Activation During the Maternal-to-Zygotic Transition Miler T. Lee, Ashley R. Bonneau, and Antonio J. Giraldez p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 581 Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control Dan Filipescu, Sebastian Muller, ¨ and Genevi`eve Almouzni p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 615 The Nature of Embryonic Stem Cells Graziano Martello and Austin Smith p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 647 “Mesenchymal” Stem Cells Paolo Bianco p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 677

viii

Contents

CB30-FrontMatter

ARI

2 September 2014

12:28

Haploid Mouse Embryonic Stem Cells: Rapid Genetic Screening and Germline Transmission Anton Wutz p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 705 Indexes Cumulative Index of Contributing Authors, Volumes 26–30 p p p p p p p p p p p p p p p p p p p p p p p p p p p 723 Cumulative Index of Article Titles, Volumes 26–30 p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 726

Annu. Rev. Cell Dev. Biol. 2014.30:561-580. Downloaded from www.annualreviews.org Access provided by University of Reading on 12/06/17. For personal use only.

Errata An online log of corrections to Annual Review of Cell and Developmental Biology articles may be found at http://www.annualreviews.org/errata/cellbio

Contents

ix

Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation.

In mammals, the process of X-chromosome inactivation ensures equivalent levels of X-linked gene expression between males and females through the silen...
635KB Sizes 1 Downloads 4 Views