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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
...variously reported to cause redistribution of H3K27me3. In Neurospora , we found that elimination of any member of the DCDC H3K9 methylation complex caused massive changes in the distribution of H3K27me; regions of facultative heterochromatin lost H3K27me3, while regions that are normally marked by H3K9me3...
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Research: Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
- Anish Dattani,
- Damian Kao,
- Yuliana Mihaylova,
- Prasad Abnave,
- Samantha Hughes,
- Alvina Lai,
- Sounak Sahu,
- and A. Aziz Aboobaker
Genome Res. October 2018 28: 1543-1554; Published in Advance August 24, 2018, doi:10.1101/gr.239848.118
...catalyzed by the PRC2 complex, and H3K4me1, a mark mediated by the MLL3/4 family of histone methyltransferases that correlates both with active enhancers and inactive promoter regions (Calo and Wysocka 2013; Cheng et al. 2014).Genes that are categorized as being X1 enriched have low levels of H3K27me3...
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Research: Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains
- Kevin Van Bortle,
- Edward Ramos,
- Naomi Takenaka,
- Jingping Yang,
- Jessica E. Wahi,
- and Victor G. Corces
Genome Res. November 2012 22: 2176-2187; Published in Advance June 21, 2012, doi:10.1101/gr.136788.111
...commonly flank the borders of H3K27me3 domains The correlation of dCTCF with SU(HW) and BEAF-32 is striking, but why dCTCF clusters with other insulator proteins requires further exploration. Recent interrogation of chromosome architecture in D. melanogaster revealed recurrent combinations of insulators...
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Research: Correlated alterations in genome organization, histone methylation, and DNA–lamin A/C interactions in Hutchinson-Gilford progeria syndrome
- Rachel Patton McCord,
- Ashley Nazario-Toole,
- Haoyue Zhang,
- Peter S. Chines,
- Ye Zhan,
- Michael R. Erdos,
- Francis S. Collins,
- Job Dekker,
- and Kan Cao
Genome Res. February 2013 23: 260-269; Published in Advance November 14, 2012, doi:10.1101/gr.138032.112
...over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 19: 221– 233. Pinskaya M, Morillon A. 2009. Histone H3 lysine 4 di-methylation: A novel mark for transcriptional fidelity? Epigenetics 4: 302–306. Robertson G, Hirst M...
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Method: Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
- Arie B. Brinkman,
- Hongcang Gu,
- Stefanie J.J. Bartels,
- Yingying Zhang,
- Filomena Matarese,
- Femke Simmer,
- Hendrik Marks,
- Christoph Bock,
- Andreas Gnirke,
- Alexander Meissner,
- and Hendrik G. Stunnenberg
Genome Res. June 2012 22: 1128-1138; Published in Advance March 30, 2012, doi:10.1101/gr.133728.111
...me3 -wide profile showed H3K27me3 enrichments over broad regions, comprising genes and intergenic regions (Fig. 2A; Supplemental Figs. S2C, S3C). This pattern resembled the H3K27me3 ‘‘BLOCs’’ profile in mouse and human fibroblast cells (Pauler et al. 2009; Hawkins et al. 2010) and differs fromH3K27me...
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Letter: High-resolution analysis of epigenetic changes associated with X inactivation
- Hendrik Marks,
- Jennifer C. Chow,
- Sergei Denissov,
- Kees-Jan Françoijs,
- Neil Brockdorff,
- Edith Heard,
- and Hendrik G. Stunnenberg
Genome Res. August 2009 19: 1361-1373; Published in Advance July 6, 2009, doi:10.1101/gr.092643.109
...and can be used to analyze repeat regions (see below). Moreover, the complete is profiled allowing direct comparisons of the X chromosome with autosomes. We performed H3K27me3 ChIP-seq profiling for E14 and LF2 undifferentiated cells, as well as 10-d EBs from the same batches of chromatin as used for Ch...
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Research: Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis
- Shaofang Li,
- Lee E. Vandivier,
- Bin Tu,
- Lei Gao,
- So Youn Won,
- Shengben Li,
- Binglian Zheng,
- Brian D. Gregory,
- and Xuemei Chen
Genome Res. February 2015 25: 235-245; Published in Advance November 20, 2014, doi:10.1101/gr.182238.114
...together with DDM1 and histone H1 also maintains CHHmethylation, but mainly acts at pericentromeric regions (Zemach et al. 2013; Stroud et al. 2014). Together, DRM2 and CMT2 are responsible for nearly all CHHmethylation in the , and the DRM2-targeted and CMT2-targeted sites are nonoverlapping. Although si...
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Method: Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
- Maxwell W. Libbrecht,
- Ferhat Ay,
- Michael M. Hoffman,
- David M. Gilbert,
- Jeffrey A. Bilmes,
- and William Stafford Noble
Genome Res. April 2015 25: 544-557; Published in Advance February 12, 2015, doi:10.1101/gr.184341.114
...) quiescent domains, which lack any activity; (2) constitutive heterochromatin, which represses permanently silent regions and is marked with the histone modification H3K9me3; (3) facultative heterochromatin, which represses cell-type-specific regions and is marked with the histone modification H3K27me3; (4...

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