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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...distinct forms, which contribute to gene repression through different mechanisms. Facultative heterochromatin tends to silence genes in a developmental or cell type–specific manner (Kim and Kingston 2022). It is depleted in histone acetylation and is distinguished by enrichment of H3K27 trimethylation (H3K...
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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
...by observations of H3K27me3 redistribution in response to defects in constitutive heterochromatin. More than a decade ago, Peters et al. (2003) noticed that mouse cells defective in both of the SUV39H methyltransferases, which are responsible for the trimethylation of histone H3 lysine 9 (H3K9me3) characteristic...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...in plants (Montgomery et al. 2020), and H3K9me2 mark took over the constitutive silencing, leading to the observed dichotomy between facultative and constitutive heterochromatin (Déléris et al. 2021). Mutants of MET1, a major player in constitutive heterochromatin establishment, showed compensation by H3K27...
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Research: SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells
- Qi Fei,
- Xiaoqin Yang,
- Hua Jiang,
- Qian Wang,
- Yanyan Yu,
- Yiling Yu,
- Wei Yi,
- Shaolian Zhou,
- Taiping Chen,
- Chris Lu,
- Peter Atadja,
- Xiaole Shirley Liu,
- En Li,
- Yong Zhang,
- and Jianyong Shou
Genome Res. September 2015 25: 1325-1335; Published in Advance July 9, 2015, doi:10.1101/gr.177576.114
...reduced EZH2 binding as well as histone 3 lysine 27 (H3K27) trimethylation level at SETDB1 solo peaks and facilitated neural differentiation. Furthermore, we found that H3K27me3 inhibits SETDB1 methyltransferase activity. The currently identified reciprocal action between SETDB1 and PRC2 reveals a novel...
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Research: Neurospora chromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3
- Jonathan M. Galazka,
- Andrew D. Klocko,
- Miki Uesaka,
- Shinji Honda,
- Eric U. Selker,
- and Michael Freitag
Genome Res. August 2016 26: 1069-1080; Published in Advance June 3, 2016, doi:10.1101/gr.203182.115
...of heterochromatin, namely, the histone H3 lysine 9 methyltransferase DIM-5, Heterochromatin Protein 1 (HP1), which specifically binds to the product of DIM-5 (trimethylated H3 lysine 9 [H3K9me3]), and DIM-3 (importin alpha), which is involved in DIM-5 localization. The average genome configuration of the wild...
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Research: Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- Nicole C. Riddle,
- Aki Minoda,
- Peter V. Kharchenko,
- Artyom A. Alekseyenko,
- Yuri B. Schwartz,
- Michael Y. Tolstorukov,
- Andrey A. Gorchakov,
- Jacob D. Jaffe,
- Cameron Kennedy,
- Daniela Linder-Basso,
- Sally E. Peach,
- Gregory Shanower,
- Haiyan Zheng,
- Mitzi I. Kuroda,
- Vincenzo Pirrotta,
- Peter J. Park,
- Sarah C.R. Elgin,
- and Gary H. Karpen
Genome Res. February 2011 21: 147-163; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110
...Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin Nicole C. Riddle 1 , 9 , Aki Minoda 2 , 9 , Peter V. Kharchenko 3 , 9 , Artyom A. Alekseyenko 4 , Yuri B. Schwartz 5 , 6...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...; Mattei et al. 2022; Shang and He 2022). Histone methylation, central to defining chromatin states, distinguishes transcriptionally active euchromatin from repressive heterochromatin. Histone methylation occurs at specific lysine residues of histones H3, H4, and H2B, including H3K4, H3K9, H3K27, H3K36, H4...
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Research: Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B
- Torunn Rønningen,
- Akshay Shah,
- Anja R. Oldenburg,
- Kristin Vekterud,
- Erwan Delbarre,
- Jan Øivind Moskaug,
- and Philippe Collas
Genome Res. December 2015 25: 1825-1835; Published in Advance September 10, 2015, doi:10.1101/gr.193748.115
...and are overall gene-poor and transcriptionally inactive (Guelen et al. 2008; Meuleman et al. 2013; Lund et al. 2014). Accordingly, LADs are enriched in histone modifications marking silent chromatin, including H3 lysine 9 di- or trimethylation (H3K9me2/3) (Guelen et al. 2008; Kind et al. 2013; Sadaie et al. 2013...
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Method: Application of histone modification-specific interaction domains as an alternative to antibodies
- Goran Kungulovski,
- Ina Kycia,
- Raluca Tamas,
- Renata Z. Jurkowska,
- Srikanth Kudithipudi,
- Chisato Henry,
- Richard Reinhardt,
- Paul Labhart,
- and Albert Jeltsch
Genome Res. November 2014 24: 1842-1853; Published in Advance October 9, 2014, doi:10.1101/gr.170985.113
...PTMs. The MPHOSPH8 Chromo domain binds specifically to histone H3 trimethylated on lysine 9 through the same conserved recognition mechanism as the Chromo domains of the HP1 protein family (including human CBX1) (Li et al. 2011). On the peptide array, MPHOSPH8 Chromo bound most prominently to H3K9me3...
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Research: Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome
- Masako Suzuki,
- Mayumi Oda,
- María-Paz Ramos,
- Marién Pascual,
- Kevin Lau,
- Edyta Stasiek,
- Frederick Agyiri,
- Reid F. Thompson,
- Jacob L. Glass,
- Qiang Jing,
- Richard Sandstrom,
- Melissa J. Fazzari,
- R. Scott Hansen,
- John A. Stamatoyannopoulos,
- Andrew S. McLellan,
- and John M. Greally
Genome Res. November 2011 21: 1833-1840; Published in Advance September 28, 2011, doi:10.1101/gr.116509.110
...for this article.] The original definition of heterochromatin was wholly derived from cytological studies, identifying it as unusually compacted nuclear material as opposed to the less-condensed euchromatin. Heterochromatin in the eukaryotic is subclassified as facultative and constitutive. Whereas sites...

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