M. F. Lyon, Gene action in the X-chromosome of the mouse (Mus musculus L.), Nature, vol.190, pp.372-373, 1961.

A. V. Gendrel and E. Heard, Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation, Annu. Rev. Cell. Dev. Biol, vol.30, pp.561-580, 2014.

C. J. 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, Cell, vol.71, pp.527-542, 1992.

N. Brockdorff, The product of the mouse Xist gene is a 15 kb inactive Xspecific transcript containing no conserved ORF and located in the nucleus, Cell, vol.71, pp.515-526, 1992.

G. D. Penny, G. F. Kay, S. A. Sheardown, S. Rastan, and N. Brockdorff, Requirement for Xist in X chromosome inactivation, Nature, vol.379, pp.131-137, 1996.

J. T. Lee and R. Jaenisch, Long-range cis effects of ectopic X-inactivation centres on a mouse autosome, Nature, vol.386, pp.275-279, 1997.

M. I. Aladjem and H. Fu, A new light on DNA replication from the inactive X chromosome, Bioessays, vol.36, pp.591-597, 2014.

E. P. Nora, Spatial partitioning of the regulatory landscape of the Xinactivation centre, Nature, vol.485, pp.381-385, 2012.

J. R. Dixon, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.485, pp.376-380, 2012.

Y. Guo, CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function, Cell, vol.162, pp.900-910, 2015.

E. P. Nora, Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization, Cell, vol.169, p.22, 2017.

S. S. Rao, Cohesin loss eliminates all loop domains, Cell, vol.171, p.24, 2017.

W. Schwarzer, Two independent modes of chromatin organization revealed by cohesin removal, Nature, vol.551, pp.51-56, 2017.

L. Giorgetti, Structural organization of the inactive X chromosome in the mouse, Nature, vol.535, pp.575-579, 2016.

S. S. Rao, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, vol.159, pp.1665-1680, 2014.

X. Deng, Bipartite structure of the inactive mouse X chromosome, Genome Biol, vol.16, p.152, 2015.

A. Minajigi, A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation, Science, vol.349, p.2276, 2015.

E. M. Darrow, Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture, Proc. Natl Acad. Sci. USA, vol.113, pp.4504-4512, 2016.

B. Moindrot, A pooled shRNA screen identifies Rbm15, Spen, and Wtap as factors required for Xist RNA-mediated silencing, Cell Rep, vol.12, pp.562-572, 2015.

C. Chu, Systematic discovery of Xist RNA binding proteins, Cell, vol.161, pp.404-416, 2015.

A. Monfort, Identification of Spen as a crucial factor for Xist function through forward genetic screening in haploid embryonic stem cells, Cell Rep, vol.12, pp.554-561, 2015.

C. A. Mchugh, The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3, Nature, vol.521, pp.232-236, 2015.

J. Silva, Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes, Dev. Cell, vol.4, pp.481-495, 2003.

K. Plath, Role of histone H3 lysine 27 methylation in X inactivation, Science, vol.300, pp.131-135, 2003.

M. De-napoles, Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation, Dev. Cell, vol.7, pp.663-676, 2004.

M. Almeida, PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome inactivation, Science, vol.356, pp.1081-1084, 2017.

G. Pintacuda, hnRNPK recruits PCGF3/5-PRC1 to the Xist RNA BRepeat to establish polycomb-mediated chromosomal silencing, Mol. Cell, vol.68, p.10, 2017.

C. K. Chen, Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing, Science, vol.354, pp.468-472, 2016.

D. P. Patil, m 6 A RNA methylation promotes XIST-mediated transcriptional repression, Nature, vol.537, pp.369-373, 2016.
DOI : 10.1038/nature19342

URL : http://europepmc.org/articles/pmc5509218?pdf=render

J. E. Mermoud, C. Costanzi, J. R. Pehrson, and N. Brockdorff, Histone macroH2A1.2 relocates to the inactive X chromosome after initiation and propagation of X-inactivation, J. Cell. Biol, vol.147, pp.1399-1408, 1999.

A. V. Gendrel, SmcHD1-dependent and-independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome, Dev. Cell, vol.23, pp.265-279, 2012.

M. E. Blewitt, SmcHD1, containing a structural-maintenance-ofchromosomes hinge domain, has a critical role in X inactivation, Nat. Genet, vol.40, pp.663-669, 2008.
DOI : 10.1038/ng.142

N. J. Brideau, Independent mechanisms target SMCHD1 to trimethylated histone H3 lysine 9-modified chromatin and the inactive X chromosome, Mol. Cell. Biol, vol.35, pp.4053-4068, 2015.
DOI : 10.1128/mcb.00432-15

URL : https://mcb.asm.org/content/35/23/4053.full.pdf

A. V. Gendrel, Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes, Mol. Cell. Biol, vol.33, pp.3150-3165, 2013.

A. W. Mould, SmcHD1 regulates a subset of autosomal genes subject to monoallelic expression in addition to being critical for X inactivation, Epigenetics Chromatin, vol.6, p.19, 2013.

R. S. Nozawa, Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway, Nat. Struct. Mol. Biol, vol.20, pp.566-573, 2013.
DOI : 10.1038/nsmb.2532

K. Chen, Genome-wide binding and mechanistic analyses of SmcHD1mediated epigenetic regulation, Proc. Natl Acad. Sci. USA, vol.112, pp.3535-3544, 2015.

I. Maza, Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors, Nat. Biotechnol, vol.33, pp.769-774, 2015.

A. Hellman and A. Chess, Gene body-specific methylation on the active X chromosome, Science, vol.315, pp.1141-1143, 2007.

M. Weber, Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells, Nat. Genet, vol.37, pp.853-862, 2005.

H. Marks, High-resolution analysis of epigenetic changes associated with X inactivation, Genome Res, vol.19, pp.1361-1373, 2009.

E. Lieberman-aiden, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, vol.326, pp.289-293, 2009.

L. Guelen, Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions, Nature, vol.453, pp.948-951, 2008.

A. Koren and S. A. Mccarroll, Random replication of the inactive X chromosome, Genome Res, vol.24, pp.64-69, 2014.

B. D. Pope, Topologically associating domains are stable units of replication-timing regulation, Nature, vol.515, pp.402-405, 2014.

J. B. Berletch, Escape from X inactivation varies in mouse tissues, PLoS. Genet, vol.11, p.1005079, 2015.

J. M. Calabrese, Site-specific silencing of regulatory elements as a mechanism of X inactivation, Cell, vol.151, pp.951-963, 2012.

A. C. Bell and G. Felsenfeld, Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene, Nature, vol.405, pp.482-485, 2000.

W. Mak, Mitotically stable association of polycomb group proteins eed and enx1 with the inactive x chromosome in trophoblast stem cells, Curr. Biol, vol.12, pp.1016-1020, 2002.

S. M. Duthie, Xist RNA exhibits a banded localization on the inactive X chromosome and is excluded from autosomal material in cis, Hum. Mol. Genet, vol.8, pp.195-204, 1999.

A. Dhayalan, The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation, J. Biol. Chem, vol.285, pp.26114-26120, 2010.

T. Baubec, Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation, Nature, vol.520, pp.243-247, 2015.

S. Hiraga, Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex, Genes Dev, vol.28, pp.372-383, 2014.

J. H. Gibcus, A pathway for mitotic chromosome formation, Science, vol.359, p.6135, 2018.

M. H. Kagey, Mediator and cohesin connect gene expression and chromatin architecture, Nature, vol.467, pp.430-435, 2010.

E. Splinter, The inactive X chromosome adopts a unique threedimensional conformation that is dependent on Xist RNA, Genes Dev, vol.25, pp.1371-1383, 2011.

C. Y. Wang, T. Jegu, H. P. Chu, H. J. Oh, and J. Lee, SMCHD1 merges chromosome compartments and assists formation of super-structures on the inactive X, Cell, vol.174, pp.406-421, 2018.

Y. Sakakibara, Role of SmcHD1 in establishment of epigenetic states required for the maintenance of the X-inactivated state in mice, Development, vol.145, p.166462, 2018.

N. Jansz, Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters, Nat. Struct. Mol. Biol, vol.25, pp.766-777, 2018.

S. Chuma and N. Nakatsuji, Autonomous transition into meiosis of mouse fetal germ cells in vitro and its inhibition by gp130-mediated signaling, Dev. Biol, vol.229, pp.468-479, 2001.

L. Cong, Multiplex genome engineering using CRISPR/Cas systems, Science, vol.339, pp.819-823, 2013.

J. D. Dignam, R. M. Lebovitz, and R. G. Roeder, Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei, Nucleic Acids Res, vol.11, pp.1475-1489, 1983.

T. Nojima, Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing, Cell, vol.161, pp.526-540, 2015.

A. Koren, Differential relationship of DNA replication timing to different forms of human mutation and variation, Am. J. Hum. Genet, vol.91, pp.1033-1040, 2012.

J. M. Belton, Hi-C: a comprehensive technique to capture the conformation of genomes, Methods, vol.58, pp.268-276, 2012.

F. Krueger, S. R. Andrews, and . Snpsplit, Allele-specific splitting of alignments between genomes with known SNP genotypes, vol.5, p.1479, 2016.

A. Dobin, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013.

S. Anders, P. T. Pyl, and W. Huber, HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-169, 2015.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

S. Wingett, HiCUP: pipeline for mapping and processing Hi-C data, vol.4, p.1310, 2015.

N. C. Durand, Juicer provides a one-click system for analyzing loopresolution Hi-C experiments, Cell Syst, vol.3, pp.95-98, 2016.

K. Kruse, C. B. Hug, B. Hernandez-rodriguez, and J. M. Vaquerizas, TADtool: visual parameter identification for TAD-calling algorithms, Bioinformatics, vol.32, pp.3190-3192, 2016.

N. Servant, HiTC: exploration of high-throughput 'C' experiments, Bioinformatics, vol.28, pp.2843-2844, 2012.

F. Krueger and S. R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, vol.27, pp.1571-1572, 2011.