A Tale of Two Cities: How Xist and its partners localize to and silence the bicompartmental X
Tài liệu tham khảo
Mank, 2013, Sex chromosome dosage compensation: definitely not for everyone, Trends Genet., 29, 677, 10.1016/j.tig.2013.07.005
Lucchesi, 2015, Dosage compensation in Drosophila, Cold Spring Harb. Perspect. Biol., 7, a019398, 10.1101/cshperspect.a019398
Strome, 2014, Regulation of the X chromosomes in Caenorhabditis elegans, Cold Spring Harb. Perspect. Biol., 6, 10.1101/cshperspect.a018366
Veitia, 2015, X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses, J. Mol. Cell Biol., 7, 2, 10.1093/jmcb/mjv001
Pessia, 2014, The evolution of X chromosome inactivation in mammals: the demise of Ohno’s hypothesis?, Cell. Mol. Life Sci., 71, 1383, 10.1007/s00018-013-1499-6
Ercan, 2015, Mechanisms of X chromosome dosage compensation, J. Genom., 3, 1, 10.7150/jgen.10404
Kay, 1993, Expression of Xist during mouse development suggests a role in the initiation of X chromosome inactivation, Cell, 72, 171, 10.1016/0092-8674(93)90658-D
Kay, 1994, Imprinting and X chromosome counting mechanisms determine Xist expression in early mouse development, Cell, 77, 639, 10.1016/0092-8674(94)90049-3
Brockdorff, 1992, The product of the mouse Xist gene is a 15kb inactive X-specific transcript containing no conserved ORF and located in the nucleus, Cell, 71, 515, 10.1016/0092-8674(92)90519-I
Brown, 1992, The human XIST gene: analysis of a 17kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus, Cell, 71, 527, 10.1016/0092-8674(92)90520-M
Clemson, 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, 10.1083/jcb.132.3.259
Penny, 1996, Requirement for Xist in X chromosome inactivation, Nature, 379, 131, 10.1038/379131a0
Marahrens, 1997, Xist-deficient mice are defective in dosage compensation but not spermatogenesis, Genes Dev., 11, 156, 10.1101/gad.11.2.156
Brown, 1994, The human X-inactivation centre is not required for maintenance of X-chromosome inactivation, Nature, 368, 154, 10.1038/368154a0
Csankovszki, 1999, Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation, Nat. Genet., 22, 323, 10.1038/11887
Dixon-McDougall, 2015, The making of a Barr body: the mosaic of factors that eXIST on the mammalian inactive X chromosome, Biochem. Cell Biol., 15, 1
Okamoto, 2004, Epigenetic dynamics of imprinted X inactivation during early mouse development, Science, 303, 644, 10.1126/science.1092727
Chaumeil, 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, 10.1101/gad.380906
Jeppesen, 1993, The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression, Cell, 74, 281, 10.1016/0092-8674(93)90419-Q
Belyaev, 1996, Differential underacetylation of histones H2A, H3 and H4 on the inactive X chromosome in human female cells, Hum. Genet., 97, 573, 10.1007/BF02281863
Keohane, 1996, X-Inactivation and histone H4 acetylation in embryonic stem cells, Dev. Biol., 180, 618, 10.1006/dbio.1996.0333
Boggs, 1996, Reduced levels of histone H3 acetylation on the inactive X chromosome in human females, Chromosoma, 105, 303, 10.1007/BF02524648
Heard, 2001, Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation, Cell, 107, 727, 10.1016/S0092-8674(01)00598-0
Boggs, 2002, Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes, Nat. Genet., 30, 73, 10.1038/ng787
Chaumeil, 2002, Integrated kinetics of X chromosome inactivation in differentiating embryonic stem cells, Cytogenet. Genome Res., 99, 75, 10.1159/000071577
Kohlmaier, 2004, A chromosomal memory triggered by Xist regulates histone methylation in X inactivation, PLoS Biol., 2, E171, 10.1371/journal.pbio.0020171
de Napoles, 2004, Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation, Dev. Cell, 7, 663, 10.1016/j.devcel.2004.10.005
Plath, 2004, Developmentally regulated alterations in polycomb repressive complex 1 proteins on the inactive X chromosome, J. Cell Biol., 167, 1025, 10.1083/jcb.200409026
Fang, 2004, Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation, J. Biol. Chem., 279, 52812, 10.1074/jbc.C400493200
Wang, 2001, Imprinted X inactivation maintained by a mouse Polycomb group gene, Nat. Genet., 28, 371, 10.1038/ng574
Mak, 2002, Mitotically stable association of polycomb group proteins Eed and Enx1 with the inactive X chromosome in trophoblast stem cells, Curr. Biol., 12, 1016, 10.1016/S0960-9822(02)00892-8
Plath, 2003, Role of histone H3 lysine 27 methylation in X inactivation, Science, 300, 131, 10.1126/science.1084274
Silva, 2003, Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes, Dev. Cell, 4, 481, 10.1016/S1534-5807(03)00068-6
Erhardt, 2003, Consequences of the depletion of zygotic and embryonic enhancer of zeste 2 during preimplantation mouse development, Development, 130, 4235, 10.1242/dev.00625
Takagi, 1982, Regional and temporal changes in the pattern of X-chromosome replication during the early post-implantation development of the female mouse, Chromosoma, 85, 275, 10.1007/BF00294971
Grumbach, 1963, Human sex chromosome abnormalities in relation to DNA replication and heterochromatinization, Proc. Natl. Acad. Sci. U. S. A., 49, 581, 10.1073/pnas.49.5.581
Eils, 1996, Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure, J. Cell Biol., 135, 1427, 10.1083/jcb.135.6.1427
Rego, 2008, The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure, J. Cell Sci., 121, 1119, 10.1242/jcs.026104
Barr, 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, 10.1038/163676a0
Rougeulle, 2004, Differential histone H3 Lys-9 and Lys-27 methylation profiles on the X chromosome, Mol. Cell. Biol., 24, 5475, 10.1128/MCB.24.12.5475-5484.2004
Chaumeil, 2011, Evolution from XIST-independent to XIST-controlled X-chromosome inactivation: epigenetic modifications in distantly related mammals, PLoS One, 6, 1, 10.1371/journal.pone.0019040
Chadwick, 2003, Chromatin of the Barr body: histone and non-histone proteins associated with or excluded from the inactive X chromosome, Hum. Mol. Genet., 12, 2167, 10.1093/hmg/ddg229
Chadwick, 2004, Multiple spatially distinct types of facultative heterochromatin on the human inactive X chromosome, Proc. Natl. Acad. Sci. U. S. A., 101, 17450, 10.1073/pnas.0408021101
C. Costanzi, J.R. Pehrson, Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals, 628 (1998) 1997–1999.
Mermoud, 1999, Histone macroH2A1.2 relocates to the inactive X chromosome after initiation and propagation of X-inactivation, J. Cell Biol., 147, 1399, 10.1083/jcb.147.7.1399
Rasmussen, 2000, Dynamic relocalization of histone macroH2A1 from centrosomes to inactive X chromosomes during X inactivation, J. Cell Biol., 150, 1189, 10.1083/jcb.150.5.1189
Chadwick, 2002, Cell cycle-dependent localization of macroH2A in chromatin of the inactive X chromosome, J. Cell Biol., 157, 1113, 10.1083/jcb.200112074
Rasmussen, 2001, Expression of Xist RNA is sufficient to initiate macrochromatin body formation, Chromosoma, 110, 411, 10.1007/s004120100158
Lock, 1987, Methylation of the Hprt gene on the inactive X occurs after chromosome inactivation, Cell, 48, 39, 10.1016/0092-8674(87)90353-9
Gilbert, 1999, Promoter-specific hypoacetylation of X-inactivated genes, Proc. Natl. Acad. Sci., 96, 13825, 10.1073/pnas.96.24.13825
Hellman, 2007, Gene body-specific methylation on the active X chromosome, Science, 315, 1141, 10.1126/science.1136352
Sado, 2000, X inactivation in the mouse embryo deficient for Dnmt1: distinct effect of hypomethylation on imprinted and random X inactivation, Dev. Biol., 225, 294, 10.1006/dbio.2000.9823
Brown, 1991, Localization of the X inactivation centre on the human X chromosome in Xq13, Nature, 349, 82, 10.1038/349082a0
Brown, 1991, A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome, Nature, 349, 38, 10.1038/349038a0
Brockdorff, 1991, Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome, Nature, 351, 329, 10.1038/351329a0
Martin, 1978, X-chromosome inactivation during differentiation of female teratocarcinoma stem cells in vitro, Nature, 271, 329, 10.1038/271329a0
Norris, 1994, Evidence that random and imprinted Xist expression is controlled by preemptive methylation, Cell, 77, 41, 10.1016/0092-8674(94)90233-X
Pintacuda, 2015, X inactivation lessons from differentiating mouse embryonic stem cells, Stem Cell Rev. Rep., 11, 699, 10.1007/s12015-015-9597-5
Monkhorst, 2008, X inactivation counting and choice is a stochastic process: evidence for involvement of an X-linked activator, Cell, 132, 410, 10.1016/j.cell.2007.12.036
Wutz, 2002, Chromosomal silencing and localization are mediated by different domains of Xist RNA, Nat. Genet., 30, 167, 10.1038/ng820
Wutz, 2000, A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation, Mol. Cell, 5, 695, 10.1016/S1097-2765(00)80248-8
McHugh, 2015, The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3, Nature, 1
Lee, 1996, A 450kb transgene displays properties of the mammalian X-inactivation center, Cell, 86, 83, 10.1016/S0092-8674(00)80079-3
Lee, 1997, Long-range cis effects of ectopic X-inactivation centres on a mouse autosome, Nature, 386, 275, 10.1038/386275a0
Lee, 1999, Genetic analysis of the mouse X inactivation center defines an 80-kb multifunction domain, Proc. Natl. Acad. Sci., 96, 3836, 10.1073/pnas.96.7.3836
Heard, 1999, Human XIST yeast artificial chromosome transgenes show partial X inactivation center function in mouse embryonic stem cells, Proc. Natl. Acad. Sci. U. S. A., 96, 6841, 10.1073/pnas.96.12.6841
Heard, 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, 10.1128/MCB.19.4.3156
G. Klein, I. Ernberg, Effects on apoptosis cell cycle and transformation and comparative aspects of EBV with other known DNA tumor viruses (2007).
Deeb, 2007, Identification of an integrated SV40 T/t-antigen cancer signature in aggressive human breast, prostate, and lung carcinomas with poor prognosis, Cancer Res., 67, 8065, 10.1158/0008-5472.CAN-07-1515
Chow, 2007, Inducible XIST-dependent X-chromosome inactivation in human somatic cells is reversible, Proc. Natl. Acad. Sci. U. S. A., 104, 10104, 10.1073/pnas.0610946104
Savarese, 2006, Hematopoietic precursor cells transiently reestablish permissiveness for X inactivation, Mol. Cell. Biol., 26, 7167, 10.1128/MCB.00810-06
Hong, 2000, A revision of the human XIST gene organization and structural comparison with mouse Xist, Mamm. Genome, 11, 220, 10.1007/s003350010040
Memili, 2001, Murine Xist RNA isoforms are different at their 3′ ends: a role for differential polyadenylation, Gene, 266, 131, 10.1016/S0378-1119(01)00353-5
Ma, 2005, Analysis of the Xist RNA isoforms suggests two distinctly different forms of regulation, Mamm. Genome, 16, 391, 10.1007/s00335-004-2464-3
Nesterova, 2001, Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence, Genome Res., 11, 833, 10.1101/gr.174901
Elisaphenko, 2008, A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements, PLoS One, 3, 1, 10.1371/journal.pone.0002521
Minks, 2013, XIST-induced silencing of flanking genes is achieved by additive action of repeat a monomers in human somatic cells, Epigenet. Chromatin, 6, 23, 10.1186/1756-8935-6-23
Lv, 2016, D-repeat in the XIST gene is required for X chromosome inactivation, RNA Biol., 13, 172, 10.1080/15476286.2015.1137420
Senner, 2011, Disruption of a conserved region of Xist exon 1 impairs Xist RNA localisation and X-linked gene silencing during random and imprinted X chromosome inactivation, Development, 138, 1541, 10.1242/dev.056812
Beletskii, 2001, PNA interference mapping demonstrates functional domains in the noncoding RNA Xist, Proc. Natl. Acad. Sci. U. S. A., 98, 9215, 10.1073/pnas.161173098
Sarma, 2010, Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome, Proc. Natl. Acad. Sci., 1
Fang, 2015, Probing Xist RNA structure in cells using targeted structure-seq, PLoS Genet., 11, e1005668, 10.1371/journal.pgen.1005668
Yamada, 2015, Xist exon 7 contributes to the stable localization of Xist RNA on the inactive X-chromosome, PLoS Genet., 11, e1005430, 10.1371/journal.pgen.1005430
Atchison, 2014, Function of YY1 in long-distance DNA interactions, Front. Immunol., 5, 1, 10.3389/fimmu.2014.00045
Lee, 2010, The X as model for RNA’ s niche in epigenomic regulation, Cold Spring Harb. Perspect. Biol., 2, 10.1101/cshperspect.a003749
Donohoe, 2007, Identification of a Ctcf cofactor Yy1, for the X chromosome binary switch, Mol. Cell, 25, 43, 10.1016/j.molcel.2006.11.017
Hendrich, 1997, Identification and characterization of the human XIST gene promoter: implications for models of X chromosome inactivation, Nucleic Acids Res., 25, 2661, 10.1093/nar/25.13.2661
Chapman, 2014, Differentially methylated CpG island within human XIST mediates alternative P2 transcription and YY1 binding, BMC Genet., 15, 89, 10.1186/s12863-014-0089-4
Makhlouf, 2014, A prominent and conserved role for YY1 in Xist transcriptional activation, Nat. Commun., 5, 4878, 10.1038/ncomms5878
Sun, 2013, Jpx RNA activates Xist by evicting CTCF, Cell, 153, 1537, 10.1016/j.cell.2013.05.028
Kung, 2015, Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF, Mol. Cell, 57, 361, 10.1016/j.molcel.2014.12.006
Jeon, 2011, YY1 tethers Xist RNA to the inactive X nucleation center, Cell, 146, 119, 10.1016/j.cell.2011.06.026
Sheardown, 1997, Stabilization of Xist RNA mediates initiation of X chromosome inactivation, Cell, 91, 99, 10.1016/S0092-8674(01)80012-X
Panning, 1997, X chromosome inactivation is mediated by Xist RNA stabilization, Cell, 90, 907, 10.1016/S0092-8674(00)80355-4
Sun, 2006, A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization, Mol. Cell, 21, 617, 10.1016/j.molcel.2006.01.028
Ng, 2011, A system for imaging the regulatory noncoding Xist RNA in living mouse embryonic stem cells, Mol. Biol. Cell, 22, 2634, 10.1091/mbc.E11-02-0146
Gayen, 2016, Sex-specific silencing of X-linked genes by Xist RNA, Proc. Natl. Acad. Sci., 113, 201515971, 10.1073/pnas.1515971113
Sigova, 2015, Transcription factor trapping by RNA in gene regulatory elements, Science, 10.1126/science.aad3346
Razin, 2014, A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus, Chromosoma, 123, 217, 10.1007/s00412-014-0459-8
Simon, 2011, The nucleoskeleton as a genome-associated dynamic network of networks, Nat. Rev. Mol. Cell Biol., 12, 695, 10.1038/nrm3207
Minajigi, 2015, A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation, Science, 349, 6245, 10.1126/science.aab2276
Chu, 2015, Systematic Discovery of Xist RNA Binding Proteins, Cell, 404, 10.1016/j.cell.2015.03.025
West, 2014, The Long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites, Mol. Cell, 55, 791, 10.1016/j.molcel.2014.07.012
Moindrot, 2015, A pooled shRNA screen identifies Rbm15, Spen, and Wtap as factors required for Xist RNA-mediated silencing, Cell Rep., 12, 562, 10.1016/j.celrep.2015.06.053
Monfort, 2015, Identification of Spen as a crucial factor for Xist function through forward genetic screening in haploid embryonic stem cells, Cell Rep., 1
Agrelo, 2009, SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells, Dev. Cell, 16, 507, 10.1016/j.devcel.2009.03.006
Nechanitzky, 2012, Satb1 and Satb2 are dispensable for X chromosome inactivation in mice, Dev. Cell, 23, 866, 10.1016/j.devcel.2012.09.018
Helbig, 2003, Scaffold attachment factor A (SAF-A) is concentrated in inactive X chromosome territories through its RGG domain, Chromosoma, 112, 173, 10.1007/s00412-003-0258-0
Pullirsch, 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, 10.1242/dev.035956
Hasegawa, 2010, The matrix protein hnRNP U is required for chromosomal localization of Xist RNA, Dev. Cell, 19, 469, 10.1016/j.devcel.2010.08.006
Huelga, 2012, Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins, Cell Rep., 1, 167, 10.1016/j.celrep.2012.02.001
Xiao, 2012, Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation, Mol. Cell, 45, 656, 10.1016/j.molcel.2012.01.009
Kipp, 2000, SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA, Mol. Cell. Biol., 20, 7480, 10.1128/MCB.20.20.7480-7489.2000
Bi, 2013, H19 inhibits RNA polymerase II-mediated transcription by disrupting the hnRNP U-actin complex, Biochim. Biophys. Acta, 1830, 4899, 10.1016/j.bbagen.2013.06.026
Kukalev, 2005, Actin and hnRNP U cooperate for productive transcription by RNA polymerase II, Nat. Struct. Mol. Biol., 12, 238, 10.1038/nsmb904
Kim, 1999, hnRNP U inhibits carboxy-terminal domain phosphorylation by TFIIH and represses RNA polymerase II elongation, Mol. Cell. Biol., 19, 6833, 10.1128/MCB.19.10.6833
Hacisuleyman, 2014, Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre, Nat. Struct. Mol. Biol., 10.1038/nsmb.2764
Hall, 2014, Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes, Cell, 156, 907, 10.1016/j.cell.2014.01.042
Britten, 1968, Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms, Science, 161, 529, 10.1126/science.161.3841.529
Hall, 2002, An ectopic human XIST gene can induce chromosome inactivation in postdifferentiation human HT-1080 cells, Proc. Natl. Acad. Sci. U. S. A., 99, 8677, 10.1073/pnas.132468999
Nickerson, 1989, Chromatin architecture and nuclear RNA, Proc. Natl. Acad. Sci. U. S. A., 86, 177, 10.1073/pnas.86.1.177
Caudron-Herger, 2015, Coding RNAs with a non-coding function: maintenance of open chromatin structure, Nucleus, 2, 410, 10.4161/nucl.2.5.17736
Mondal, 2010, Characterization of the RNA content of chromatin, Genome Res., 20, 899, 10.1101/gr.103473.109
Schubert, 2012, Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin, Mol. Cell, 48, 434, 10.1016/j.molcel.2012.08.021
Cerase, 2015, Xist localization and function: new insights from multiple levels, Genome Biol., 16, 166, 10.1186/s13059-015-0733-y
Naughton, 2010, Analysis of active and inactive X chromosome architecture reveals the independent organization of 30 nm and large-scale chromatin structures, Mol. Cell, 40, 397, 10.1016/j.molcel.2010.10.013
Teller, 2011, A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at ≥20 Mb genomic length scales, Nucleus, 2, 465, 10.4161/nucl.2.5.17862
Smeets, 2014, Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci, Epigenet. Chromatin, 7, 8, 10.1186/1756-8935-7-8
BARTON, 1964, The positions of the sex chromosomes in the human cell in mitosis, Ann. Hum. Genet., 28, 123, 10.1111/j.1469-1809.1964.tb00467.x
Bourgeois, 1985, New data on the in situ position of the inactive X chromosome in the interphase nucleus of human fibroblasts, Hum. Genet., 69, 122, 10.1007/BF00293281
Bártová, 2008, Epigenome and chromatin structure in human embryonic stem cells undergoing differentiation, Dev. Dyn., 237, 3690, 10.1002/dvdy.21773
Zhang, 2007, Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing, Cell, 129, 693, 10.1016/j.cell.2007.03.036
Yang, 2015, The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation, Genome Biol., 16, 1, 10.1186/s13059-015-0618-0
Mohammad, 2008, Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region, Mol. Cell. Biol., 28, 3713, 10.1128/MCB.02263-07
Yusufzai, 2004, CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species, Mol. Cell, 13, 291, 10.1016/S1097-2765(04)00029-2
Zhao, 2008, Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome, Science, 322, 750, 10.1126/science.1163045
Hinsby, 2006, A wiring of the human nucleolus, Mol. Cell, 22, 285, 10.1016/j.molcel.2006.03.012
Narlikar, 2013, Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes, Cell, 154, 490, 10.1016/j.cell.2013.07.011
Culver-Cochran, 2012, The WSTF-ISWI chromatin remodeling complex transiently associates with the human inactive X chromosome during late S-phase prior to BRCA1 and γ-H2AX, PLoS One, 7, e50023, 10.1371/journal.pone.0050023
Guelen, 2008, Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions, Nature, 453, 948, 10.1038/nature06947
Padeken, 2014, Nucleolus and nuclear periphery: velcro for heterochromatin, Curr. Opin. Cell Biol., 28, 54, 10.1016/j.ceb.2014.03.001
Matheson, 2015, Grabbing the genome by the NADs, Chromosoma, 1
Takizawa, 2008, The meaning of gene positioning, Cell, 135, 9, 10.1016/j.cell.2008.09.026
Peric-Hupkes, 2010, Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation, Mol. Cell, 38, 603, 10.1016/j.molcel.2010.03.016
Németh, 2010, Initial genomics of the human nucleolus, PLoS Genet., 6, e1000889, 10.1371/journal.pgen.1000889
van Koningsbruggen, 2010, High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli, Mol. Biol. Cell., 21, 3735, 10.1091/mbc.E10-06-0508
Kind, 2013, Single-cell dynamics of genome-nuclear lamina interactions, Cell, 153, 178, 10.1016/j.cell.2013.02.028
Kind, 2015, Genome-wide maps of nuclear lamina interactions in single human cells, Cell, 163, 134, 10.1016/j.cell.2015.08.040
Kind, 2014, Stochastic genome-nuclear lamina interactions, Nucleus, 10.4161/nucl.28825
Reddy, 2008, Transcriptional repression mediated by repositioning of genes to the nuclear lamina, Nature, 452, 243, 10.1038/nature06727
Harr, 2015, Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins, J. Cell Biol., 208, 33, 10.1083/jcb.201405110
Zullo, 2012, DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina, Cell, 149, 1474, 10.1016/j.cell.2012.04.035
Meuleman, 2013, Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence, Genome Res., 23, 270, 10.1101/gr.141028.112
Solovei, 2009, Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution, Cell, 137, 356, 10.1016/j.cell.2009.01.052
Bailey, 2000, Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis, Proc. Natl. Acad. Sci. U. S. A., 97, 6634, 10.1073/pnas.97.12.6634
McNeil, 2006, Word frequency analysis reveals enrichment of dinucleotide repeats on the human X chromosome and [GATA]n in the X escape region, Genome Res., 16, 477, 10.1101/gr.4627606
Gartler, 1983, Mammalian X-chromosome inactivation, Annu. Rev. Genet., 17, 155, 10.1146/annurev.ge.17.120183.001103
Cattanach, 1966, The location of Cattanach’s translocation in the X-chromosome linkage map of the mouse, Genet. Res., 8, 253, 10.1017/S0016672300010107
Lyon, 1998, X-chromosome inactivation: a repeat hypothesis, Cytogenet. Cell Genet., 80, 133, 10.1159/000014969
Korenberg, 1988, Human genome organization: Alu, LINES, and the molecular structure of metaphase chromosome bands, Cell, 53, 391, 10.1016/0092-8674(88)90159-6
Boyle, 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. U. S. A., 87, 7757, 10.1073/pnas.87.19.7757
Lyon, 2006, Do LINEs have a role in X-chromosome inactivation?, J. Biomed. Biotechnol., 2006, 59746, 10.1155/JBB/2006/59746
Checchi, 2011, Heteromorphic sex chromosomes: navigating meiosis without a homologous partner, Mol. Reprod. Dev., 78, 623, 10.1002/mrd.21369
Boissinot, 2001, Selection against deleterious LINE-1-containing loci in the human lineage, Mol. Biol. Evol., 18, 926, 10.1093/oxfordjournals.molbev.a003893
Wichman, 1992, Transposable elements and the evolution of genome organization in mammals, Genetica, 86, 287, 10.1007/BF00133727
Kambere, 2009, Exceptional LINE density at V1R loci: the lyon repeat hypothesis revisited on autosomes, J. Mol. Evol., 68, 145, 10.1007/s00239-008-9195-0
Kambere, 2007, Co-regulation of a large and rapidly evolving repertoire of odorant receptor genes, BMC Neurosci., 3, S2, 10.1186/1471-2202-8-S3-S2
Giglio, 2001, Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements, Am. J. Hum. Genet., 68, 874, 10.1086/319506
Hansen, 2003, X inactivation-specific methylation of LINE-1 elements by DNMT3B: implications for the Lyon repeat hypothesis, Hum. Mol. Genet., 12, 2559, 10.1093/hmg/ddg268
Wang, 2006, Evidence of influence of genomic DNA sequence on human X chromosome inactivation, PLoS Comput. Biol., 2, e113, 10.1371/journal.pcbi.0020113
Carrel, 2006, Genomic environment predicts expression patterns on the human inactive X chromosome, PLoS Genet., 2, e151, 10.1371/journal.pgen.0020151
Popova, 2006, Attenuated spread of X-inactivation in an X;autosome translocation, Proc. Natl. Acad. Sci. U. S. A., 103, 7706, 10.1073/pnas.0602021103
Abrusán, 2008, Analysis of transposon interruptions suggests selection for L1 elements on the X chromosome, PLoS Genet., 4, e1000172, 10.1371/journal.pgen.1000172
Bala Tannan, 2014, DNA methylation profiling in X;autosome translocations supports a role for L1 repeats in the spread of X chromosome inactivation, Hum. Mol. Genet., 23, 1224, 10.1093/hmg/ddt553
Lahn, 1999, Four evolutionary strata on the human X chromosome, Science, 286, 964, 10.1126/science.286.5441.964
Sandstedt, 2004, Evolutionary strata on the mouse X chromosome correspond to strata on the human X chromosome, Genome Res., 14, 267, 10.1101/gr.1796204
Grahn, 2005, Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents, Cytogenet. Genome Res., 110, 407, 10.1159/000084973
Cantrell, 2008, Loss of LINE-1 activity in the megabats, Genetics, 178, 393, 10.1534/genetics.107.080275
Cantrell, 2009, X chromosome inactivation and Xist evolution in a rodent lacking LINE-1 activity, PLoS One, 4, e6252, 10.1371/journal.pone.0006252
Scott, 2006, X accumulation of LINE-1 retrotransposons in Tokudaia osimensis, a spiny rat with the karyotype XO, Cytogenet. Genome Res., 112, 261, 10.1159/000089880
Murakami, 2009, Identification of the chromatin regions coated by non-coding Xist RNA, Cytogenet. Genome Res., 125, 19, 10.1159/000207514
Engreitz, 2013, The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome, Science, 341, 1237973, 10.1126/science.1237973
Simon, 2013, High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation, Nature, 504, 465, 10.1038/nature12719
Simon, 2015, Insight into lncRNA biology using hybridization capture analyses, Biochim. Biophys. Acta
Dixon, 2012, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, 485, 376, 10.1038/nature11082
Calabrese, 2012, Site-specific silencing of regulatory elements as a mechanism of x inactivation, Cell, 151, 951, 10.1016/j.cell.2012.10.037
Duthie, 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, 10.1093/hmg/8.2.195
Smith, 2004, Ubiquitinated proteins including uH2A on the human and mouse inactive X chromosome: enrichment in gene rich bands, Chromosoma, 113, 324, 10.1007/s00412-004-0325-1
Dileep, 2015, Large-scale chromatin structure-function relationships during the cell cycle and development: insights from replication timing, Cold Spring Harb. Symp. Quant. Biol., 10.1101/sqb.2015.80.027284
Ryba, 2010, Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types, Genome Res., 20, 761, 10.1101/gr.099655.109
Pope, 2014, Topologically associating domains are stable units of replication-timing regulation, Nature, 515, 402, 10.1038/nature13986
Dimitrova, 1999, The spatial position and replication timing of chromosomal domains are both established in early G1 phase, Mol. Cell, 4, 983, 10.1016/S1097-2765(00)80227-0
Wu, 2005, Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states, Mol. Biol. Cell, 16, 2872, 10.1091/mbc.E04-11-0997
Splinter, 2011, The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA, Genes Dev., 25, 1371, 10.1101/gad.633311
Rao, 2014, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, 159, 1665, 10.1016/j.cell.2014.11.021
Deng, 2015, Bipartite structure of the inactive mouse X chromosome, Genome Biol., 16, 152, 10.1186/s13059-015-0728-8
Linnemann, 2009, Maintenance of a functional higher order chromatin structure: the role of the nuclear matrix in normal and disease states, Gene Ther. Mol. Biol., 13, 231
Hiratani, 2004, Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores, Proc. Natl. Acad. Sci. U. S. A., 101, 16861, 10.1073/pnas.0406687101
Hiratani, 2008, Global reorganization of replication domains during embryonic stem cell differentiation, PLoS Biol., 6, e245, 10.1371/journal.pbio.0060245
Hiratani, 2010, Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis, Genome Res., 20, 155, 10.1101/gr.099796.109
Takebayashi, 2012, Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding, Proc. Natl. Acad. Sci. U. S. A., 109, 12574, 10.1073/pnas.1207185109
Phillips-Cremins, 2013, Architectural protein subclasses shape 3D organization of genomes during lineage commitment, Cell, 153, 1281, 10.1016/j.cell.2013.04.053
de Wit, 2013, The pluripotent genome in three dimensions is shaped around pluripotency factors, Nature, 501, 227, 10.1038/nature12420
Denholtz, 2013, Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization, Cell Stem Cell, 13, 602, 10.1016/j.stem.2013.08.013
Hiratani, 2010, Autosomal lyonization of replication domains during early Mammalian development, Adv. Exp. Med. Biol., 695, 41, 10.1007/978-1-4419-7037-4_4
Vallender, 2004, How mammalian sex chromosomes acquired their peculiar gene content, Bioessays, 26, 159, 10.1002/bies.10393
Vicoso, 2006, Evolution on the X chromosome: unusual patterns and processes, Nat. Rev. Genet., 7, 645, 10.1038/nrg1914
Kelsey, 2015, Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST, Genome Biol., 16, 208, 10.1186/s13059-015-0774-2
Tang, 2010, Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation, Epigenet. Chromatin, 3, 10, 10.1186/1756-8935-3-10
Wakefield, 1997, Histone underacetylation is an ancient component of mammalian X chromosome inactivation, Proc. Natl. Acad. Sci. U. S. A., 94, 9665, 10.1073/pnas.94.18.9665
Namekawa, 2010, Two-step imprinted X inactivation: repeat versus genic silencing in the mouse, Mol. Cell. Biol., 30, 3187, 10.1128/MCB.00227-10
Cattanach, 1965, Genetic control over the inactivation of autosomal genes attached to the X-chromosome, Z. Vererbungslehre, 96, 313
Renard-Guillet, 2014, Temporal and spatial regulation of eukaryotic DNA replication: from regulated initiation to genome-scale timing program, Semin. Cell Dev. Biol., 30, 110, 10.1016/j.semcdb.2014.04.014
Wu, 2006, Uncoupling global and fine-tuning replication timing determinants for mouse pericentric heterochromatin, J. Cell Biol., 174, 185, 10.1083/jcb.200601113
Jørgensen, 2007, The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells, Genome Biol., 8, R169, 10.1186/gb-2007-8-8-r169
Casas-Delucchi, 2012, Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin, Nucleic Acids Res., 40, 159, 10.1093/nar/gkr723
Takebayashi, 2012, Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding, Nucleus, 3, 500, 10.4161/nucl.22318
Wilson, 2013, Relationship between DNA replication and the nuclear matrix, Genes Cells, 18, 17, 10.1111/gtc.12010
Cornacchia, 2012, Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells, EMBO J., 31, 3678, 10.1038/emboj.2012.214
Foti, 2016, Nuclear architecture organized by Rif1 underpins the Replication-Timing Program, Mol. Cell, 61, 260, 10.1016/j.molcel.2015.12.001
Chan, 2011, Diverse factors are involved in maintaining X chromosome inactivation, Proc. Natl. Acad. Sci. U. S. A., 108, 16699, 10.1073/pnas.1107616108
Guenther, 2001, The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3, Mol. Cell. Biol., 21, 6091, 10.1128/MCB.21.18.6091-6101.2001
Seto, 2014, Erasers of histone acetylation: the histone deacetylase enzymes, Cold Spring Harb. Perspect. Biol., 6, a018713, 10.1101/cshperspect.a018713
O’Neill, 1999, A developmental switch in H4 acetylation upstream of Xist plays a role in X chromosome inactivation, EMBO J., 18, 2897, 10.1093/emboj/18.10.2897
Diaz-Perez, 2006, A deletion at the mouse Xist gene exposes trans-effects that alter the heterochromatin of the inactive X chromosome and the replication time and DNA stability of both X chromosomes, Genetics, 174, 1115, 10.1534/genetics.105.051375
Thayer, 2012, Mammalian chromosomes contain cis-acting elements that control replication timing, mitotic condensation, and stability of entire chromosomes, Bioessays, 34, 760, 10.1002/bies.201200035
You, 2013, Nuclear receptor co-repressors are required for the histone-deacetylase activity of HDAC3 in vivo, Nat. Struct. Mol. Biol., 20, 182, 10.1038/nsmb.2476
Sun, 2013, Deacetylase-independent function of HDAC3 in transcription and metabolism requires nuclear receptor corepressor, Mol. Cell, 52, 769, 10.1016/j.molcel.2013.10.022
Wang, 2009, Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes, Cell, 138, 1019, 10.1016/j.cell.2009.06.049
Barish, 2012, The Bcl6-SMRT/NCoR cistrome represses inflammation to attenuate atherosclerosis, Cell Metab., 15, 554, 10.1016/j.cmet.2012.02.012
Casas-Delucchi, 2011, Histone acetylation controls the inactive X chromosome replication dynamics, Nat. Commun., 2, 222, 10.1038/ncomms1218
Koren, 2014, Random replication of the inactive X chromosome, Genome Res., 24, 64, 10.1101/gr.161828.113
Nishioka, 2002, PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin, Mol. Cell, 9, 1201, 10.1016/S1097-2765(02)00548-8
Beck, 2012, PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription, Genes Dev., 26, 325, 10.1101/gad.177444.111
Jorgensen, 2013, Histone H4 Lysine 20 methylation: key player in epigenetic regulation of genomic integrity, Nucleic Acids Res., 41, 2797, 10.1093/nar/gkt012
Rens, 2010, Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation, Proc. Natl. Acad. Sci. U. S. A., 107, 17657, 10.1073/pnas.0910322107
Grant, 2012, Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation, Nature, 487, 254, 10.1038/nature11171
McElroy, 2014, Are we there yet? Initial targeting of the male-specific lethal and polycomb group chromatin complexes in Drosophila, Open Biol., 4, 140006, 10.1098/rsob.140006
Sing, 2009, A vertebrate Polycomb response element governs segmentation of the posterior hindbrain, Cell, 138, 885, 10.1016/j.cell.2009.08.020
Woo, 2010, A region of the human HOXD cluster that confers polycomb-group responsiveness, Cell, 140, 99, 10.1016/j.cell.2009.12.022
Blackledge, 2014, Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation, Cell, 157, 1445, 10.1016/j.cell.2014.05.004
Ku, 2008, Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains, PLoS Genet., 4, e1000242, 10.1371/journal.pgen.1000242
Mendenhall, 2010, GC-rich sequence elements recruit PRC2 in mammalian ES cells, PLoS Genet., 6, e1001244, 10.1371/journal.pgen.1001244
Spitale, 2011, RNA templating the epigenome: long noncoding RNAs as molecular scaffolds, Epigenetics, 6, 539, 10.4161/epi.6.5.15221
Lee, 2013, X-inactivation, imprinting, and long noncoding RNAs in health and disease, Cell, 152, 1308, 10.1016/j.cell.2013.02.016
Brockdorff, 2013, Noncoding RNA and polycomb recruitment, RNA, 19, 429, 10.1261/rna.037598.112
Di Croce, 2013, Transcriptional regulation by Polycomb group proteins, Nat. Struct. Mol. Biol., 20, 1147, 10.1038/nsmb.2669
Guyochin, 2014, Live cell imaging of the nascent inactive X chromosome during the early differentiation process of naive ES cells towards epiblast stem cells, PLoS One, 9, e116109, 10.1371/journal.pone.0116109
Kalantry, 2006, The Polycomb group protein Eed protects the inactive X-chromosome from differentiation-induced reactivation, Nat. Cell Biol., 8, 195, 10.1038/ncb1351
Pinter, 2012, Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations, Genome Res., 22, 1864, 10.1101/gr.133751.111
Maenner, 2010, 2-D structure of the A region of Xist RNA and its implication for PRC2 association, PLoS Biol., 8, e1000276, 10.1371/journal.pbio.1000276
Sarma, 2014, ATRX directs binding of PRC2 to Xist RNA and polycomb targets, Cell, 159, 869, 10.1016/j.cell.2014.10.019
Baumann, 2009, ATRX marks the inactive X chromosome (Xi) in somatic cells and during imprinted X chromosome inactivation in trophoblast stem cells, Chromosoma, 118, 209, 10.1007/s00412-008-0189-x
Guil, 2012, Intronic RNAs mediate EZH2 regulation of epigenetic targets, Nat. Struct. Mol. Biol., 19, 664, 10.1038/nsmb.2315
Kaneko, 2013, PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells, Nat. Struct. Mol. Biol., 20, 1258, 10.1038/nsmb.2700
Davidovich, 2013, Promiscuous RNA binding by polycomb repressive complex 2, Nat. Struct. Mol. Biol., 20, 1250, 10.1038/nsmb.2679
Cifuentes-Rojas, 2014, Regulatory interactions between RNA and polycomb repressive complex 2, Mol. Cell, 55, 171, 10.1016/j.molcel.2014.05.009
Davidovich, 2015, Short article toward a consensus on the binding specificity and promiscuity of PRC2 for RNA, Mol. Cell, 57, 552, 10.1016/j.molcel.2014.12.017
Cerase, 2014, Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy, Proc. Natl. Acad. Sci. U. S. A., 111, 2235, 10.1073/pnas.1312951111
Sunwoo, 2015, The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells, Proc. Natl. Acad. Sci., 201503690
Kaneko, 2014, Nascent RNA interaction keeps PRC2 activity poised and in check, Genes Dev., 28, 1983, 10.1101/gad.247940.114
Margueron, 2009, Role of the polycomb protein EED in the propagation of repressive histone marks, Nature, 461, 762, 10.1038/nature08398
Yuan, 2012, Dense chromatin activates polycomb repressive complex 2 to regulate H3 lysine 27 methylation, Science, 337, 971, 10.1126/science.1225237
Simon, 2013, Occupying chromatin: polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put, Mol. Cell, 49, 808, 10.1016/j.molcel.2013.02.013
da Rocha, 2014, Jarid2 is implicated in the initial Xist-induced targeting of PRC2 to the inactive X chromosome, Mol. Cell, 53, 301, 10.1016/j.molcel.2014.01.002
Casanova, 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, 10.1242/dev.053652
Sanulli, 2015, Jarid2 methylation via the PRC2complex regulates H3K27me3 deposition during cell differentiation, Mol. Cell, 769, 10.1016/j.molcel.2014.12.020
Son, 2013, Nucleosome-binding activities within JARID2 and EZH1 regulate the function of PRC2 on chromatin, Genes Dev., 27, 2663, 10.1101/gad.225888.113
Kaneko, 2014, Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin, Mol. Cell, 53, 290, 10.1016/j.molcel.2013.11.012
Eskeland, 2010, Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination, Mol. Cell, 38, 452, 10.1016/j.molcel.2010.02.032
Endoh, 2012, Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity, PLoS Genet., 8, e1002774, 10.1371/journal.pgen.1002774
Stock, 2007, Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells, Nat. Cell Biol., 9, 1428, 10.1038/ncb1663
Schoeftner, 2006, Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing, EMBO J., 25, 3110, 10.1038/sj.emboj.7601187
Terranova, 2008, Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos, Dev. Cell, 15, 668, 10.1016/j.devcel.2008.08.015
Bernstein, 2006, Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin, Mol. Cell. Biol., 26, 2560, 10.1128/MCB.26.7.2560-2569.2006
Tavares, 2012, RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3, Cell, 148, 664, 10.1016/j.cell.2011.12.029
Gao, 2012, PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes, Mol. Cell, 45, 344, 10.1016/j.molcel.2012.01.002
Morey, 2013, RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells, Cell Rep., 3, 60, 10.1016/j.celrep.2012.11.026
Bomsztyk, 2004, hnRNP K: One protein multiple processes, Bioessays, 26, 629, 10.1002/bies.20048
Leeb, 2007, Ring1B is crucial for the regulation of developmental control genes and PRC1 proteins but not X inactivation in embryonic cells, J. Cell Biol., 178, 219, 10.1083/jcb.200612127
Zee, 2010, Global turnover of histone post-translational modifications and variants in human cells, Epigenet. Chromatin, 3, 22, 10.1186/1756-8935-3-22
Ogawa, 2005, Histone variant macroH2A1.2 is mono-ubiquitinated at its histone domain, Biochem. Biophys. Res. Commun., 336, 204, 10.1016/j.bbrc.2005.08.046
Chu, 2006, Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry, Mol. Cell. Proteom., 194, 10.1074/mcp.M500285-MCP200
Hernández-Muñoz, 2005, Stable X chromosome inactivation involves the PRC1 Polycomb complex and requires histone MACROH2A1 and the CULLIN3/SPOP ubiquitin E3 ligase, Proc. Natl. Acad. Sci. U. S. A., 102, 7635, 10.1073/pnas.0408918102
Creppe, 2012, MacroH2A1 regulates the balance between self-renewal and differentiation commitment in embryonic and adult stem cells, Mol. Cell. Biol., 32, 1442, 10.1128/MCB.06323-11
Pasque, 2012, Histone variant macroH2A marks embryonic differentiation in vivo and acts as an epigenetic barrier to induced pluripotency, J. Cell Sci., 125, 6094, 10.1242/jcs.113019
Pasque, 2011, Histone variant macroH2A confers resistance to nuclear reprogramming, EMBO J., 30, 2373, 10.1038/emboj.2011.144
Pasque, 2015, Epigenetic stability of repressed states involving the histone variant macroH2A revealed by nuclear transfer to Xenopus oocytes, Nucleus, 2, 533, 10.4161/nucl.2.6.17799
Gaspar-Maia, 2013, MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency, Nat. Commun., 4, 1565, 10.1038/ncomms2582
Barrero, 2013, Macrohistone variants preserve cell identity by preventing the gain of H3K4me2 during reprogramming to pluripotency, Cell Rep., 3, 1005, 10.1016/j.celrep.2013.02.029
Swigut, 2007, H3K27 demethylases, at long last, Cell, 131, 29, 10.1016/j.cell.2007.09.026
Scheuermann, 2015, Histone H2A monoubiquitination and polycomb repression: the missing pieces of the puzzle, Fly (Austin), 6, 162, 10.4161/fly.20986
Gaume, 2015, Regulation of reprogramming and cellular plasticity through histone exchange and histone variant incorporation, Cold Spring Harb. Symp. Quant. Biol., 10.1101/sqb.2015.80.027458
Yildirim, 2014, A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters, PLoS Genet., 10, e1004515, 10.1371/journal.pgen.1004515
Boulard, 2010, Histone variant macroH2A1 deletion in mice causes female-specific steatosis, Epigenet. Chromatin, 3, 8, 10.1186/1756-8935-3-8
Tanasijevic, 2011, X chromosome inactivation and differentiation occur readily in ES cells doubly-deficient for macroH2A1 and macroH2A2, PLoS One, 6, e21512, 10.1371/journal.pone.0021512
Pehrson, 2014, Mice without macroH2A histone variants, Mol. Cell. Biol., 34, 4523, 10.1128/MCB.00794-14
Kalashnikova, 2013, The role of the nucleosome acidic patch in modulating higher order chromatin structure, J. R. Soc. Interface., 10, 20121022, 10.1098/rsif.2012.1022
du Preez, 2013, Secondary structures of the core histone N-terminal tails: their role in regulating chromatin structure, Subcell. Biochem., 61, 37, 10.1007/978-94-007-4525-4_2
Mulligan, 2008, CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation, Mol. Cell, 32, 718, 10.1016/j.molcel.2008.10.025
Zhang, 2011, Corepressor protein CDYL functions as a molecular bridge between polycomb repressor complex 2 and repressive chromatin mark trimethylated histone lysine 27, J. Biol. Chem., 286, 42414, 10.1074/jbc.M111.271064
Escamilla-Del-Arenal, 2013, Cdyl, a new partner of the inactive X chromosome and potential reader of H3K27me3 and H3K9me2, Mol. Cell. Biol., 33, 5005, 10.1128/MCB.00866-13
Wu, 2010, Histone methyltransferase G9a contributes to H3K27 methylation in vivo, Cell Res., 21, 365, 10.1038/cr.2010.157
Mozzetta, 2014, The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing, Mol. Cell, 53, 277, 10.1016/j.molcel.2013.12.005
Maier, 2015, Functional proteomic analysis of repressive histone methyltransferase complexes reveals ZNF518B as a G9A regulator, Mol. Cell. Proteom., 14, 1435, 10.1074/mcp.M114.044586
Minkovsky, 2014, The Mbd1-Atf7ip-Setdb1 pathway contributes to the maintenance of X chromosome inactivation, Epigenet. Chromatin, 7, 12, 10.1186/1756-8935-7-12
Blewitt, 2008, SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation, Nat. Genet., 40, 663, 10.1038/ng.142
Gendrel, 2012, Smchd1-dependent and -independent pathways determine developmental dynamics of CpG Island methylation on the inactive X chromosome, Dev. Cell, 23, 265, 10.1016/j.devcel.2012.06.011
Gendrel, 2013, Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes, Mol. Cell. Biol., 33, 3150, 10.1128/MCB.00145-13
Nozawa, 2013, Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway, Nat. Struct. Mol. Biol., 20, 566, 10.1038/nsmb.2532
Brideau, 2015, Independent mechanisms target SMCHD1 to trimethylated histone H3 lysine 9-modified chromatin and the inactive X chromosome, Mol. Cell. Biol., 35, 4053, 10.1128/MCB.00432-15