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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...insertions and lineage-specific duplicated genes. Our findings suggest independent evolution of subterminal caps converging on a common genetic and epigenetic structure that promoted ectopic exchange as well as the emergence of novel genes at transition regions between euchromatin and heterochromatin...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...armigera, Polycomb group (PcG) proteins regulate PTTH production and prevent diapause entry through the control of H3K27me3 (Lu et al. 2013). By ovary-specific knockdown of histone mark writers and erasers, DiVito Evans et al. (2023) showed that H3K4me3 and H3K36me1 depletion promotes reproductive diapause...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
...of the wheat are marked by constitutive heterochromatin (IWGSC 2018; Li et al. 2019; Concia et al. 2020). Additionally, H3K27me2 associates with crossover suppression in wheat, despite distal enrichment (Liu et al. 2021). However, fine-scale relationships between chromatin, meiotic recombination, axis...
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Research: Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos
- Guowei Bu,
- Wei Zhu,
- Xin Liu,
- Jingjing Zhang,
- Longtao Yu,
- Kai Zhou,
- Shangke Wang,
- Zhekun Li,
- Zhengang Fan,
- Tingting Wang,
- Taotao Hu,
- Ruifeng Hu,
- Zhiting Liu,
- Tao Wang,
- Linhui Wu,
- Xia Zhang,
- Shuhong Zhao,
- and Yi-Liang Miao
Genome Res. August 2022 32: 1487-1501; Published in Advance July 22, 2022, doi:10.1101/gr.276207.121
...into sharp peaks again during ZGA. By simultaneous depletion of H3K4me3 demethylase KDM5B and KDM5C, we determined that broad H3K4me3 domain maintenance impaired ZGA gene expression, suggesting its function to prevent premature ZGA entry. In contrast, broad H3K27me3 domains underwent global removal upon...
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Research: Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division
- Yajing Hao,
- Dongpeng Wang,
- Shuheng Wu,
- Xiao Li,
- Changwei Shao,
- Peng Zhang,
- Jia-Yu Chen,
- Do-Hwan Lim,
- Xiang-Dong Fu,
- Runsheng Chen,
- and Shunmin He
Genome Res. November 2020 30: 1570-1582; Published in Advance October 15, 2020, doi:10.1101/gr.256131.119
...-rich and gene-poor regions, corresponding to euchromatin and heterochromatin, respectively. Heterochromatin can be further divided into two classes: facultative, which is dynamic and marked by H3K27me3, and constitutive, which is largely stable and marked by H3K9me2/3 (Grewal and Jia 2007). Constitutive...
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Research: The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
- Xianglin Zhang,
- Xuehui Liu,
- Zhenhai Du,
- Lei Wei,
- Huan Fang,
- Qiongye Dong,
- Jing Niu,
- Yanda Li,
- Juntao Gao,
- Michael Q. Zhang,
- Wei Xie,
- and Xiaowo Wang
Genome Res. July 2021 31: 1121-1135; Published in Advance June 17, 2021, doi:10.1101/gr.275235.121
...by DNA damage harboring the “loss of heterochromatin” phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, show different alterations. Facultative heterochromatin tends...
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Research: Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin
- Sophie Chantalat,
- Arnaud Depaux,
- Patrick Héry,
- Sophie Barral,
- Jean-Yves Thuret,
- Stefan Dimitrov,
- and Matthieu Gérard
Genome Res. September 2011 21: 1426-1437; Published in Advance July 29, 2011, doi:10.1101/gr.118091.110
...heterochromatin formation is often associated with histone H3 trimethylated at lysine 27 (H3K27me3), a mark that is absent in constitutive heterochromatin (Peters et al. 2003). H3K27me3, which is catalyzed in mammals by Polycomb 5Corresponding authors. E-mail chantalat@cng.fr. E-mail matthieu...
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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
...,b; Adhvaryu et al. 2014). Neurospora dim-5mutants lack detectable H3K9me3 and cytosine DNAmethylation (Tamaru and Selker 2001; Tamaru et al. 2003; Lewis et al. 2008), HP1 is mislocalized but retained within the nucleus (Freitag et al. 2004), and H3K27me2/3 is redistributed to former H3K9me3 regions (Basenko...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...of the depleted samples over the whole range considered (from ∼3.5- to ∼13-fold), with the highest gains at the lowest amounts of sequencing data (6 to 25 million fragments) (Fig. 4A). Because a genotyped position does not necessarily allow the variant to be identified (this also depends on allele coverage), we...
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Research: Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin
- Anastassiia Vertii,
- Jianhong Ou,
- Jun Yu,
- Aimin Yan,
- Hervé Pagès,
- Haibo Liu,
- Lihua Julie Zhu,
- and Paul D. Kaufman
Genome Res. August 2019 29: 1235-1249; Published in Advance June 14, 2019, doi:10.1101/gr.247072.118
...inaccessible to transcription factors, and H3K27me3, a hallmark of facultative heterochromatin that is frequently regulated in a tissue-specific manner and is accessible to transcription factors and associated with paused RNA polymerase (Becker et al. 2016). We observed that almost half of the NAD regions...

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