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LETTER: H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
- Florian M. Pauler,
- Mathew A. Sloane,
- Ru Huang,
- Kakkad Regha,
- Martha V. Koerner,
- Ido Tamir,
- Andreas Sommer,
- Andras Aszodi,
- Thomas Jenuwein,
- and Denise P. Barlow
Genome Res. February 2009 19: 221-233; Published in Advance December 1, 2008, doi:10.1101/gr.080861.108
...gene clusters. In contrast, -wide profiles of the Drosophila show that H3K27me3 covers large genomic domains containing silent genes that included genic and intergenic regions ( Schwartz et al. 2006 ; Beisel et al. 2007 ). Mammalian chromosomes are known to be longitudinally organized in a manner...
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Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- Andre J. Faure,
- Dominic Schmidt,
- Stephen Watt,
- Petra C. Schwalie,
- Michael D. Wilson,
- Huiling Xu,
- Robert G. Ramsay,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
...binding events connect enhancers to their target genes by looping out the intervening DNA, thereby reducing the effective distance and increasing the probability of interactions between linearly distant genomic regulatory regions. We therefore searched for genes where this configuration has the potential...
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Research: PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination
- Petros Kolovos,
- Koutarou Nishimura,
- Aditya Sankar,
- Simone Sidoli,
- Paul A. Cloos,
- Kristian Helin,
- and Jesper Christensen
Genome Res. August 2020 30: 1119-1130; Published in Advance August 3, 2020, doi:10.1101/gr.261016.120
...Figure 4. PR-DUB and PRC1/2 share a limited set of bivalent target genes. (A) Euler diagram showing the overlap between BAP1, SUZ12, and RING1B binding regions in wild-type proliferating mESCs. (B) Hidden Markov analysis for the 1457 BAP1-bound regions positions not associated with SUZ12 or RING1B in m...
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Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
- Christelle Cayrou,
- Benoit Ballester,
- Isabelle Peiffer,
- Romain Fenouil,
- Philippe Coulombe,
- Jean-Christophe Andrau,
- Jacques van Helden,
- and Marcel Méchali
Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
...IP-seq signals for 5hmC, H3K27me3, SUZ12, and H3K4me3 around ±7 kb from the center of Class 2 and Class 3a IS. Cayrou et al. 1878 Genome Research www..org Figure 5. Sequencemotifs at origins. (A,B) Distribution of OGRE sites around IS inmouse (A) and human (B) ES cells. PWM-based scanning of 1-kb regions on both...
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Research: Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin
- Kirsty Jamieson,
- Elizabeth T. Wiles,
- Kevin J. McNaught,
- Simone Sidoli,
- Neena Leggett,
- Yanchun Shao,
- Benjamin A. Garcia,
- and Eric U. Selker
Genome Res. January 2016 26: 97-107; Published in Advance November 4, 2015, doi:10.1101/gr.194555.115
...) demonstrated that the amino terminus of histone H3 is recognized by the Nurf55-Suz12 submodule of PRC2 and that this binding is blocked by marks of active chromatin, namely, K4me3 and K36me2/3. Although the mechanism of such “crosstalk” is sometimes reasonably obvious, more often it is not, as illustrated...
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Research: De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
- Felix Schlesinger,
- Andrew D. Smith,
- Thomas R. Gingeras,
- Gregory J. Hannon,
- and Emily Hodges
Genome Res. October 2013 23: 1601-1614; Published in Advance June 28, 2013, doi:10.1101/gr.157271.113
...and differentiated cells. (A) Genomic distribution of hypomethylated regions (HMR) in H1 ESCs and B cells. Colors in each bar indicate whether an HMR is shared between the two cell types, specific to one, or shared but expanding, i.e., significantly larger in one cell type than in the other. (B) Overlap between i...
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Methods: A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations
- Vijay K. Tiwari,
- Leslie Cope,
- Kelly M. McGarvey,
- Joyce E. Ohm,
- and Stephen B. Baylin
Genome Res. July 2008 18: 1171-1179; Published in Advance May 23, 2008, doi:10.1101/gr.073452.107
...binds to silenced regions of the in a cell-type-specific manner . Genome Res. 16 : 890 – 900 . ↵ Tolhuis, B. , Palstra, R.J. , Splinter, E. , Grosveld, F. , de Laat, W. ( 2002 ) Looping and interaction between hypersensitive sites in the active beta-globin locus . Mol. Cell 10 : 1453 – 1465 . ↵ Wurtele...
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Resource: Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
- Bony De Kumar,
- Mark E. Parrish,
- Brian D. Slaughter,
- Jay R. Unruh,
- Madelaine Gogol,
- Christopher Seidel,
- Ariel Paulson,
- Hua Li,
- Karin Gaudenz,
- Allison Peak,
- William McDowell,
- Brian Fleharty,
- Youngwook Ahn,
- Chengqi Lin,
- Edwin Smith,
- Ali Shilatifard,
- and Robb Krumlauf
Genome Res. August 2015 25: 1229-1243; Published in Advance May 29, 2015, doi:10.1101/gr.184978.114
...course of differentiation. Antibodies were used against (1) H3K27me3, a repressive mark; (2) SUZ12, a member of the PRC2 complex and a mark of chromatin silencing; (3) H3K4me3, a mark for active chromatin state; and (4) Pol II, a mark of active transcription.In accord with published studies (Boyer et al...
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Research: Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
- Phil Arnold,
- Anne Schöler,
- Mikhail Pachkov,
- Piotr J. Balwierz,
- Helle Jørgensen,
- Michael B. Stadler,
- Erik van Nimwegen,
- and Dirk Schübeler
Genome Res. January 2013 23: 60-73; Published in Advance September 10, 2012, doi:10.1101/gr.142661.112
...important developmental regulators inmouse embryonic stem (ES) cells (Boyer et al. 2006) and are in part cell-type specific (Bracken et al. 2006; Mikkelsen et al. 2007; Mohn et al. 2008). Although DNA binding 6These authors contributed equally to this work. 7Corresponding authors E-mail dirk@fmi.ch E...
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Method: Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
- Shilin Zhang,
- Yichen Wang,
- Lin Jia,
- Xue Wen,
- Zhonghua Du,
- Cong Wang,
- Yajing Hao,
- Dehai Yu,
- Lei Zhou,
- Naifei Chen,
- Jingcheng Chen,
- Huiling Chen,
- Hui Zhang,
- Ilkay Celik,
- Günhan Gülsoy,
- Jianjun Luo,
- Baoming Qin,
- Xueling Cui,
- Zhonghui Liu,
- Songling Zhang,
- Miguel A. Esteban,
- Ferhat Ay,
- Wei Xu,
- Runsheng Chen,
- Wei Li,
- Andrew R. Hoffman,
- Ji-Fan Hu,
- and Jiuwei Cui
Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
...is organized as a highly dynamic structure in a cell-type–specific manner and is tightly coupled with gene transcription (Cavalli and Misteli 2013; Sawyer and Dundr 2017; Wang et al. 2017; Watson and Tsai 2017). Chromatin domains can be subdivided into transcriptionally active and inactive territories based...
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