Dynamics of gene silencing during X inactivation using allele-specific RNA-seq
暂无分享,去创建一个
Erik Splinter | Alice Jouneau | Cornelis A. Albers | Joost Gribnau | Wouter de Laat | René A. M. Dirks | Hendrik G. Stunnenberg | Hendrik Marks | Tomas Babak | T. Babak | C. A. Albers | H. Stunnenberg | Austin G Smith | W. de Laat | E. Splinter | J. Gribnau | H. Marks | T. Kalkan | Shuang-Yin Wang | Tahsin Stefan Barakat | A. Jouneau | Hindrik H. D. Kerstens | Austin Smith | Guido van Mierlo | O. Joshi | Tüzer Kalkan | Shuang-Yin Wang | Onkar Joshi | Guido van Mierlo | H. Kerstens
[1] R. Jaenisch,et al. A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. , 2000, Molecular cell.
[2] P. Avner,et al. Role play in X-inactivation [published erratum appears in Hum Mol Genet 1994 Nov;3(11):2092] , 1994 .
[3] V. Chapman,et al. Escape from X inactivation of Smcx is preceded by silencing during mouse development , 1998, Nature Genetics.
[4] Susan J Clark,et al. Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis. , 2007, Human molecular genetics.
[5] R. Sandberg,et al. Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells , 2014, Science.
[6] M. Lyon. Gene Action in the X-chromosome of the Mouse (Mus musculus L.) , 1961, Nature.
[7] Heng Li,et al. Toward better understanding of artifacts in variant calling from high-coverage samples , 2014, Bioinform..
[8] Hanlin Gao,et al. Transcriptome-Wide Survey of Mouse CNS-Derived Cells Reveals Monoallelic Expression within Novel Gene Families , 2012, PloS one.
[9] G. Daley,et al. Dynamic instability of genomic methylation patterns in pluripotent stem cells , 2010, Epigenetics & Chromatin.
[10] C. Disteche,et al. Dosage compensation in mammals: fine-tuning the expression of the X chromosome. , 2006, Genes & development.
[11] M. Gut,et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. , 2013, Cell stem cell.
[12] E. Lander,et al. The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome , 2013, Science.
[13] Carolyn J. Brown,et al. 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, Cell.
[14] R. Jaenisch,et al. Antisense Transcription through theXist Locus Mediates Tsix Function in Embryonic Stem Cells , 2001, Molecular and Cellular Biology.
[15] Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.
[16] L. Jouneau,et al. Stable methylation at promoters distinguishes epiblast stem cells from embryonic stem cells and the in vivo epiblasts. , 2014, Stem cells and development.
[17] William Stafford Noble,et al. Escape from X Inactivation Varies in Mouse Tissues , 2015, PLoS genetics.
[18] J. Gribnau,et al. X chromosome inactivation in the cycle of life , 2012, Development.
[19] Hengbin Wang,et al. Role of Histone H3 Lysine 27 Methylation in X Inactivation , 2003, Science.
[20] J. Gribnau,et al. Combined DNA-RNA fluorescent in situ hybridization (FISH) to study X chromosome inactivation in differentiated female mouse embryonic stem cells. , 2014, Journal of visualized experiments : JoVE.
[21] E. Heard,et al. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. , 2006, Genes & development.
[22] Joost Gribnau,et al. The trans-activator RNF12 and cis-acting elements effectuate X chromosome inactivation independent of X-pairing. , 2014, Molecular cell.
[23] Edith Heard,et al. High-resolution analysis of epigenetic changes associated with X inactivation. , 2009, Genome research.
[24] M. Blasco,et al. Telomere shortening relaxes X chromosome inactivation and forces global transcriptome alterations , 2009, Proceedings of the National Academy of Sciences.
[25] J. Gribnau,et al. RNF12 Activates Xist and Is Essential for X Chromosome Inactivation , 2011, PLoS genetics.
[26] Toshiro K. Ohsumi,et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations , 2012, Genome research.
[27] Serban Nacu,et al. Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..
[28] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[29] Jeannie T. Lee,et al. The Long Noncoding RNA, Jpx, Is a Molecular Switch for X Chromosome Inactivation , 2010, Cell.
[30] Araxi O. Urrutia,et al. Genes that Escape X-Inactivation in Humans Have High Intraspecific Variability in Expression, Are Associated with Mental Impairment but Are Not Slow Evolving , 2015, Molecular biology and evolution.
[31] Thomas M. Keane,et al. Sequence-based characterization of structural variation in the mouse genome , 2011, Nature.
[32] R. Jaenisch,et al. X Chromosome Inactivation Is Mediated by Xist RNA Stabilization , 1997, Cell.
[33] E. Barillot,et al. Developmental dynamics and disease potential of random monoallelic gene expression. , 2014, Developmental cell.
[34] J. Nichols,et al. Klf4 reverts developmentally programmed restriction of ground state pluripotency , 2009, Development.
[35] Jeannie T. Lee,et al. New and Xisting regulatory mechanisms of X chromosome inactivation. , 2012, Current opinion in genetics & development.
[36] B. Doble,et al. The ground state of embryonic stem cell self-renewal , 2008, Nature.
[37] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[38] L. Jouneau,et al. Nuclear Transfer‐Derived Epiblast Stem Cells Are Transcriptionally and Epigenetically Distinguishable from Their Fertilized‐Derived Counterparts , 2010, Stem cells.
[39] C. Disteche,et al. Comparative sequence and x-inactivation analyses of a domain of escape in human xp11.2 and the conserved segment in mouse. , 2004, Genome research.
[40] N. Brockdorff,et al. Global hypomethylation of the genome in XX embryonic stem cells , 2005, Nature Genetics.
[41] Laurent Duret,et al. Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. , 2011, Human molecular genetics.
[42] Emmanuel Barillot,et al. HiTC - Exploration of High Throughput ’C’ experiments , 2013 .
[43] H. Willard,et al. X-inactivation profile reveals extensive variability in X-linked gene expression in females , 2005, Nature.
[44] N. Brockdorff,et al. Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. , 2003, Developmental cell.
[45] N. Blüthgen,et al. The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network. , 2014, Cell stem cell.
[46] R. McKay,et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells , 2007, Nature.
[47] Michael R. Green,et al. Maternal Rnf12/RLIM is required for imprinted X chromosome inactivation in mice , 2010, Nature.
[48] Jeannie T. Lee,et al. Targeted Mutagenesis of Tsix Leads to Nonrandom X Inactivation , 1999, Cell.
[49] P. Avner,et al. Role play in X-inactivation. , 1994, Human molecular genetics.
[50] R. Jaenisch,et al. Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation , 1999, Nature Genetics.
[51] F. Grosveld,et al. RNF12 Is an X-Encoded Dose-Dependent Activator of X Chromosome Inactivation , 2009, Cell.
[52] Martin Leeb,et al. Xist and the order of silencing , 2007, EMBO reports.
[53] M. Trotter,et al. Derivation of pluripotent epiblast stem cells from mammalian embryos , 2007, Nature.
[54] C. Disteche,et al. Trisomy eight in ES cells is a common potential problem in gene targeting and interferes with germ line transmission , 1997, Developmental dynamics : an official publication of the American Association of Anatomists.
[55] M. Daly,et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.
[56] J. Tukey,et al. Variations of Box Plots , 1978 .
[57] FGF signalling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency , 2013, Clinical Epigenetics.
[58] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[59] Jeroen Demmers,et al. RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation , 2012, Nature.
[60] Wei Sun,et al. Site-Specific Silencing of Regulatory Elements as a Mechanism of X Inactivation , 2012, Cell.
[61] W. V. van IJcken,et al. The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. , 2011, Genes & development.
[62] A. Wutz. Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation , 2011, Nature Reviews Genetics.
[63] J. Mcneil,et al. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure , 1996, The Journal of cell biology.
[64] J. Shendure,et al. Global survey of escape from X inactivation by RNA-sequencing in mouse. , 2010, Genome research.
[65] William Stafford Noble,et al. Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation. , 2013, Developmental cell.
[66] Kirsten R. McEwen,et al. Naïve pluripotency is associated with global DNA hypomethylation , 2013, Nature Structural &Molecular Biology.
[67] Jeannie T. Lee,et al. Jpx RNA Activates Xist by Evicting CTCF , 2013, Cell.
[68] Thomas M. Keane,et al. Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.
[69] P. Avner,et al. Tsix-mediated repression of Xist accumulation is not sufficient for normal random X inactivation. , 2001, Human molecular genetics.
[70] Jeannie T. Lee,et al. Dosage Compensation in the Mouse Balances Up-Regulation and Silencing of X-Linked Genes , 2007, PLoS biology.
[71] L. Carrel,et al. Clustered transcripts that escape X inactivation at mouse XqD , 2011, Mammalian Genome.
[72] W. Reik,et al. FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency , 2013, Clinical Epigenetics.
[73] Jennifer Nichols,et al. The Transcriptional and Epigenomic Foundations of Ground State Pluripotency , 2012, Cell.
[74] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[75] J. Mcneil,et al. The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[76] R. Jaenisch,et al. X chromosome choice occurs independently of asynchronous replication timing , 2005, The Journal of cell biology.
[77] Eleazar Eskin,et al. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains , 2007, Nature.
[78] J. Mattick,et al. Genome-wide analysis of long noncoding RNA stability , 2012, Genome research.
[79] Nicola Festuccia,et al. Molecular coupling of Tsix regulation and pluripotency , 2010, Nature.
[80] M. A. Goldman,et al. Mammalian X chromosome inactivation. , 1992, Molecular genetic medicine.
[81] Austin G Smith,et al. Inhibition of glycogen synthase kinase-3 alleviates Tcf3 repression of the pluripotency network and increases embryonic stem cell resistance to differentiation , 2012, Nature Cell Biology.
[82] Dominic P. Norris,et al. 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, Cell.