Xist

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Entry NameAlias
Xist ENSG00000229807
Name
Xist: X inactive-specific transcript
Characteristics
Spliced, polyadenylated, ~17kb in mice, ~19kb in humans.

Contains repeated sequence motifs A-F that are critical for its function.

Xist is located on the X chromosome in the X-inactivation center (Xic), an approximately 100-kb region in the mouse containing (as of June 2012) five other lncRNAs, many of which play crucial roles in X-chromosome inactivation (XCI).

Xist expression initiates the process of XCI in mammals.
Expression
Xist is expressed in all somatic cells in female eutherian mammals, monoallelically from the inactive X-chromosome (Xi) ((Brown 1991)). Xist is not expressed in males

Xist is a nuclear RNA that coats the Xi ((Brown 1992), (Clemson 1996)).

In the mouse, Xist expression is imprinted at specific times and places in development: Xist is transcribed exclusively from the paternally-inherited X (and thus the paternal X is always the Xi) only in the early pre-implantation blastocyst, and later in development only in extra-embryonic tissues such as the placenta.

Imprinted XCI in humans has not been demonstrated and may not exist ((Moreira de Mello 2010)).

In somatic tissues in mouse and human, XCI is random, not imprinted: either the paternal or maternal X can express Xist and become the Xi. This decision is made in each cell of the epiblast in the mouse, and the same X is inactivated in subsequent generations of daughter cells. Thus expression of Xist (and of nearly all X-linked genes) is mosaic, in the sense that each of the two alleles is active in different populations of cells.

Stage specific expression in different regions of developing mouse retina, with Tsix displaying a similar but weaker profile ((Blackshaw 2004)).

In female undifferentiated mouse ES (embryonic stem) and iPS (induced pluripotent stem) cells, Xist is not expressed and both X chromosomes are active. Differentiation of mouse ES cells results in the onset of Xist expression and XCI, and thus these cells are an important model system for the study of XCI.

In contrast, Xist expression and XCI are variable in female undifferentiated human ES cells ((Shen 2008), (Silva 2008), (Hall 2008), (Lengner 2010)) and iPS cells ((Bruck 2011), (Hanna 2009), (Marchetto 2010), (Tchieu 2010)), which may reflect variability in the broader epigenetic states and developmental potential of these cells.
Function
Xist is the master regulator of mammalian XCI, the mechanism of dosage compensation that balances X-linked gene expression between males and females.

Xist function is required to initiate XCI ((Penny 1996), (Marahrens 1997)). Ectopic Xist expression from an autosomal transgene causes long-range gene repression in cis ((Wutz 2000)).

Xist and RepA (see associated components below) RNAs bind to and recruit PRC2, which catalyzes the deposition of the repressive chromatin mark H3K27me3 on the Xi ((Zhao 2008), (Kaneko 2010), (Kanhere 2010), (Zhao 2010), (Guil 2012)).

Small RNAs formed from Xist/Tsix duplexes may play a role in regulating Xist expression and XCI ((Ogawa 2008)). However, loss of Dicer has only a modest effect on Xist expression ((Kanellopoulou 2009)), contrary to what would be expected if RNAi is a major regulator of XCI.

hnRNP U (also known as SP120 or SAF-A) binds Xist through its RGG domain while the SAF domain is also required for localisation to the Xi. hnRNP U is required for both Xist localisation to the Xi and the initation of X-inactivation ((Hasegawa 2010).

Xist Repeat C sequences are required for Xist localization to the Xi ((Beletskii 2001), (Sarma 2010)).

YY1 can interact with several DNA binding sites within exon 1 of Xist, and also to the repeat C (and perhaps repeat B) RNA sequences of the Xist transcript. Thus YY1 tethers Xist RNAs to the Xi and nucleates the Xist cloud that coats the Xi ((Jeon 2011)).

Xist forms a transcriptionally silenced sub-nuclear domain ((Chaumeil 2006)) and perinucleolar localisation of the silent Xist coated chromosome has been observed ((Zhang 2007)). The A region repeats are essential for the recruitment of late inactivated X genes to the silencing compartment and for the recruitment of the silencing complex PRC2 ((Maenner 2010)).

After the initiation of XCI, Xist function is not absolutely required to maintain XCI in fibroblasts ((Csankovszki 1999)). Nor is continued Xist expression required to maintain XCI-like repression around an autosomal Xist transgene in male, differentiated ES cells ((Wutz 2000)). However, lack of Xist function in differentiated cells can lead to partial reactivation of select X-linked genes ((Csankovszki 2001)).
Conservation
Xist is present in all eutherian (placental) mammals examined to date, but it is not present in marsupials or monotremes ((Duret 2006), (Davidow 2007), (Hore 2007), (Shevchenko 2007)). An unrelated ncRNA in marsupials, Rsx, is likely to play a role similar to that of Xist in XCI ((Grant 2012)).

The most conserved Xist RNA region, the A region, contains eight or nine repeats separated by U-rich spacers.
Acknowledgement
Thanks to Derek Lessing and other members of the Lee lab for writing the majority of this entry.
Human Body Atlas
Sort values
Species
Species UCSC Genome Browser Link
Rattus norvegicus (Rat) rn4 chrX:91,445,506-91,468,415
Ovis aries (Sheep) NULL
Canis familiaris (Dog) NULL
Bos taurus (Cattle) bosTau4 chrX:47,180,022-47,216,556
Pongo abelii (Sumatran orangutan) ponAbe2 chrX:71,263,806-71,295,068
Pan troglodytes (Chimpanzee) panTro3 chrX:73,614,734-73,636,256
Mus musculus (Mouse) mm9 chrX:100,655,712-100,678,572
Oryctolagus cuniculus (Rabbit) NULL
Loxodonta africana (African elephant) NULL
Homo sapiens (Human) hg19 chrX:73,040,495-73,072,588
Literature
Pub Med ID Author Title Year
1423611 Brown The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. 1992
16912274 Chaumeil A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. 2006
19802707 Deakin Unravelling the evolutionary origins of X chromosome inactivation in mammals: insights from marsupials and monotremes. 2009
17512404 Zhang Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. 2007
18535243 Ogawa Intersection of the RNA interference and X-inactivation pathways. 2008
18974356 Zhao Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. 2008
20052282 Maenner 2-D structure of the A region of Xist RNA and its implication for PRC2 association. 2010
8636206 Clemson XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. 1996
21172659 Zhao Genome-wide identification of polycomb-associated RNAs by RIP-seq. 2010
21729784 Jeon YY1 tethers Xist RNA to the inactive X nucleation center. 2011
20833368 Hasegawa The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. 2010
11780141 Wutz Chromosomal silencing and localization are mediated by different domains of Xist RNA. 2002
2034278 Borsani Characterization of a murine gene expressed from the inactive X chromosome. 1991
2034279 Brockdorff Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. 1991
1985261 Brown A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. 1991
1423610 Brockdorff The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. 1992
18575625 Elisaphenko A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. 2008
9335338 Sheardown Stabilization of Xist RNA mediates initiation of X chromosome inactivation. 1997
15226823 Blackshaw Genomic analysis of mouse retinal development. 2004
11481485 Beletskii PNA interference mapping demonstrates functional domains in the noncoding RNA Xist. 2001
21276761 Bruck Meta-analysis of the heterogeneity of X chromosome inactivation in human pluripotent stem cells. 2011
21541345 Chaumeil Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals. 2011
11352938 Csankovszki Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. 2001
10431231 Csankovszki Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation. 1999
17333538 Davidow The search for a marsupial XIC reveals a break with vertebrate synteny. 2007
16778056 Duret The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. 2006
18340642 Hall X-inactivation reveals epigenetic anomalies in most hESC but identifies sublines that initiate as expected. 2008
19898493 Hanna Direct cell reprogramming is a stochastic process amenable to acceleration. 2009
17333539 Hore The region homologous to the X-chromosome inactivation centre has been disrupted in marsupial and monotreme mammals. 2007
21123648 Kaneko Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. 2010
19164542 Kanellopoulou X chromosome inactivation in the absence of Dicer. 2009
20542000 Kanhere Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. 2010
20471072 Lengner Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. 2010
9009199 Marahrens Xist-deficient mice are defective in dosage compensation but not spermatogenesis. 1997
20532033 Moreira de Mello Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome. 2010
18339804 Shen X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. 2008
18339803 Silva X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells. 2008
20727844 Tchieu Female human iPSCs retain an inactive X chromosome. 2010
21074045 Marchetto A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. 2010
8538762 Penny Requirement for Xist in X chromosome inactivation. 1996
10882105 Wutz A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. 2000
21135235 Sarma Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome. 2010
17333537 Shevchenko Genes flanking Xist in mouse and human are separated on the X chromosome in American marsupials. 2007
21113679 Zhao Molecular and DNA methylation analysis of Peg10 and Xist gene in sheep. 2010
21471966 Okamoto Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development. 2011
22722828 Grant Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. 2012
22659877 Guil Intronic RNAs mediate EZH2 regulation of epigenetic targets. 2012

showing of total 48 results

Associated Components
Component Type Component ID Description Pub Med ID
Protein hnRNP U hnRNP U (also known as SP120 or SAF-A) binds Xist through its RGG domain. Interaction required for Xist to localise to the Xi 20833368
Protein Ezh2 Ezh2 – PRC2 subunit that makes direct contact with Xist in vitro. 21172659
Protein YY1 Xist RNA can bind to the YY1 protein, which acts as a tether nucleate Xist binding to the Xi 21729784
Protein Suz12 Suz12 – PRC2 subunit that makes direct contact with Xist in vitro 20542000
Transcript RepA A short 1.6-kb RNA identified in mouse that is transcribed from within Xist and includes the Xist Repeat A motifs. Binds PRC2 18974356
Sequences
Sequence Name Sequence Accessions Species Fasta Sequence
Xist_hg_1 NR_001564. Human ccttcagttcttaaagcgctgcaattcgctgctgcagccatatttcttactctctcggggctggaagcttcctgactgaagatctctctgcacttggggttctttctagaacattttctagtcccccaacaccctttatggcgtatttctttaaaaaaatcacctaaattccataaaatatttttttaaattctatactttctcctagtgtcttcttgacacgtcctccatatttttttaaagaaagtatttggaatattttgaggcaatttttaatatttaaggaatttttctttggaatcatttttggttgacatctctgttttttgtggatcagttttttactcttccactctcttttctatattttgcccatcggggctgcggatacctggttttattattttttctttgcccaacggggccgtggatacctgccttttaattcttttttattcgcccatcggggccgcggatacctgctttttatttttttttccttagcccatcggggtatcggatacctgctgattcccttcccctctgaacccccaacactctggcccatcggggtgacggatatctgctttttaaaaattttctttttttggcccatcggggcttcggatacctgctttttttttttttatttttccttgcccatcggggcctcggatacctgctttaatttttgtttttctggcccatcggggccgcggatacctgctttgatttttttttttcatcgcccatcggtgctttttatggatgaaaaaatgttggttttgtgggttgttgcactctctggaatatctacacttttttttgctgctgatcatttggtggtgtgtgagtgtacctaccgctttggcagagaatgactctgcagttaagctaagggcgtgttcagattgtggaggaaaagtggccgccattttagacttgccgcataactcggcttagggctagtcgtttgtgctaagttaaactagggaggcaagatggatgatagcaggtcaggcagaggaagtcatgtgcattgcatgagctaaacctatctgaatgaattgatttggggcttgttaggagctttgcgtgattgttgtatcgggaggcagtaagaatcatcttttatcagtacaagggactagttaaaaatggaaggttaggaaagactaaggtgcagggcttaaaatggcgattttgacattgcggcattgctcagcatggcgggctgtgctttgttaggttgtccaaaatggcggatccagttctgtcgcagtgttcaagtggcgggaaggccacatcatgatgggcgaggctttgttaagtggttagcatggtggtggacatgtgcggtcacacaggaaaagatggcggctgaaggtcttgccgcagtgtaaaacatggcgggcctctttgtctttgctgtgtgcttttcgtgttgggttttgccgcagggacaatatggcaggcgttgtcatatgtatatcatggcttttgtcacgtggacatcatggcgggcttgccgcattgttaaagatggcgggttttgccgcctagtgccacgcagagcgggagaaaaggtgggatggacagtgctggattgctgcataacccaaccaattagaaatgggggtggaattgatcacagccaattagagcagaagatggaattagactgatgacacactgtccagctactcagcgaagacctgggtgaattagcatggcacttcgcagctgtctttagccagtcaggagaaagaagtggaggggccacgtgtatgtctcccagtgggcggtacaccaggtgttttcaaggtcttttcaaggacatttagcctttccacctctgtcccctcttatttgtcccctcctgtccagtgctgcctcttgcagtgctggatatctggctgtgtggtctgaacctccctccattcctctgtattggtgcctcacctaaggctaagtatacctccccccccaccccccaacccccccaactccccacccccaccccccaccccccacctccccacccccctacccccctacccccctacccccctctggtctgccctgcactgcactgttgccatgggcagtgctccaggcctgcttggtgtggacatggtggtgagccgtggcaaggaccagaatggatcacagatgatcgttggccaacaggtggcagaagaggaattcctgccttcctcaagaggaacacctaccccttggctaatgctggggtcggattttgatttatatttatcttttggatgtcagtcatacagtctgattttgtggtttgctagtgtttgaatttaagtcttaagtgactattatagaaatgtattaagaggctttatttgtagaattcactttaattacatttaatgagtttttgttttgagttccttaaaattccttaaagtttttagcttctcattacaaattccttaacctttttttggcagtagatagtcaaagtcaaatcatttctaatgttttaaaaatgtgctggtcattttctttgaaattgacttaactattttcctttgaagagtctgtagcacagaaacagtaaaaaatttaacttcatgacctaatgtaaaaaagagtgtttgaaggtttacacaggtccaggccttgctttgttcccatccttgatgctgcactaattgactaatcacctacttatcagacaggaaacttgaattgctgtggtctggtgtcctctattcagacttattatattggagtatttcaatttttcgttgtatcctgcctgcctagcatccagttcctccccagccctgctcccagcaaacccctagtctagccccagccctactcccaccccgccccagccctgccccagccccagtcccctaaccccccagccctagccccagtcccagtcctagttcctcagtcccgcccagcttctctcgaaagtcactctaattttcattgattcagtgctcaaaataagttgtccattgcttatcctattatactgggatattccgtttacccttggcattgctgatcttcagtactgactccttgaccattttcagttaatgcatacaatcccatttgtctgtgatctcaggacaaagaatttccttactcggtacgttgaagttagggaatgtcaattgagagctttctatcagagcattattgcccacaatttgagttacttatcattttctcgatcccctgcccttaaaggagaaaccatttctctgtcattgcttctgtagtcacagtcccaattttgagtagtgatcttttcttgtgtactgtgttggccacctaaaactctttgcattgagtaaaattctaattgccaataatcctacccattggattagacagcactctgaaccccatttgcattcagcagggggtcgcagacaacccgtcttttgttggacagttaaaatgctcagtcccaattgtcatagctttgcctattaaacaaaggcaccctactgcgctttttgctgtgcttctggagaatcctgctgttcttggacaattaaagaacaaagtagtaattgctaattgtctcacccattaatcatgaagactaccagtcgcccttgcatttgccttgaggcagcgctgactacctgagatttaagagtttcttaaattattgagtaaaatcccaattatccatagttctgttagttacactatggcctttgcaaacatctttgcataacagcagtgggactgactcattcttagagccccttcccttggaatattaatggatacaatagtaattattcatggttctgcgtaacagagaagacccacttatgtgtatgcctttatcattgctcctagatagtgtgaactacctaccaccttgcattaatatgtaaaacactaattgcccatagtcccactcattagtctaggatgtcctctttgccattgctgctgagttctgactacccaagtttccttctcttaaacagttgatatgcataattgcatatattcatggttctgtgcaataaaaatggattctcaccccatcccaccttctgtgggatgttgctaacgagtgcagattattcaataacagctcttgaacagttaatttgcacagttgcaattgtccagagtcctgtccattagaaagggactctgtatcctatttgcacgctacaatgtgggctgatcacccaaggactcttcttgtgcattgatgttcataattgtatttgtccacgatcttgtgcactaacccttccactccctttgtattccagcaggggacccttactactcaagacctctgtactaggacagtttatgtgcacaatcctaattgattagaactgagtcttttatatcaaggtccctgcatcatctttgctttacatcaagagggtgctggttacctaatgcccctcctccagaaattattgatgtgcaaaatgcaatttccctatctgctgttagtctggggtctcatcccctcatattccttttgtcttacagcagggggtacttgggactgttaatgcgcataattgcaattatggtcttttccattaaattaagatcccaactgctcacaccctcttagcattacagtagagggtgctaatcacaaggacatttcttttgtactgttaatgtgctacttgcatttgtccctcttcctgtgcactaaagaccccactcacttccctagtgttcagcagtggatgacctctagtcaagacctttgcactaggatagttaatgtgaaccatggcaactgatcacaacaatgtctttcagatcagatccattttatcctccttgttttacagcaagggatattaattacctatgttacctttccctgggactatgaatgtgcaaaattccaatgttcatggtctctccctttaaacctatattctaccccttttacattatagaaagggatgctggaaacccagagtccttctcttgggact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lncrnadb version 2.0. lastupdate : 03 Sep 2015