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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
...). Acetylation marks like H3K9ac and H3K27ac and H3K4 methylation are enriched at promoters of actively transcribed SM genes, promoting RNA polymerase II recruitment and transcription initiation (Liu et al. 2015). H3K27 methylation, deposited by PRC2, represses SM clusters in facultative heterochromatin under...
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Research: Decoding the function of bivalent chromatin in development and cancer
- Dhirendra Kumar,
- Senthilkumar Cinghu,
- Andrew J. Oldfield,
- Pengyi Yang,
- and Raja Jothi
Genome Res. December 2021 31: 2170-2184; Published in Advance October 19, 2021, doi:10.1101/gr.275736.121
...profiles for H3K4me3 (green) and H3K27me3 (red) in various cell types. Also shown are read density profiles for gene expression (blue; RNA-seq). (HSCs) hematopoietic stem cells; (PBMCs) peripheral blood mononuclear cells; (HMECs) human mammary epithelial cells; (NHEKs) normal human embryonic kidneys...
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Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
- Haifen Chen,
- Bo Hu,
- Cynthia Horth,
- Eric Bareke,
- Phillip Rosenbaum,
- Sin Young Kwon,
- Jacinthe Sirois,
- Daniel N. Weinberg,
- Faith M. Robison,
- Benjamin A. Garcia,
- Chao Lu,
- William A. Pastor,
- and Jacek Majewski
Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
...importance of each of those enzymes appears to be cell type–specific (Bennett et al. 2017; Farhangdoost et al. 2021; Li et al. 2021a). In mESCs, it has been shown that depletion of the NSD1 histone methyltransferase by siRNA reduces the levels of H3K36me2 and alters the patterns of lysine 27 methylation...
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Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
- Sachin Pundhir,
- Jinyu Su,
- Marta Tapia,
- Anne Meldgaard Hansen,
- James Seymour Haile,
- Klaus Hansen,
- and Bo Torben Porse
Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
...opposite (Fig. 2A). These findings clearly highlight both the canonical and paradoxical impact of SWI/SNF and NuRD remodelers on gene expression.View larger version: In this window In a new window Figure 2. Mutually exclusive binding of RNA Pol II and PRC2 explains the paradox in the antagonistic...
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Resource: High-resolution mapping of open chromatin in the rice genome
- Wenli Zhang,
- Yufeng Wu,
- James C. Schnable,
- Zixian Zeng,
- Michael Freeling,
- Gregory E. Crawford,
- and Jiming Jiang
Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
...are frequently associated with DH sites To exploit the relationship between the gene expression levels and DH sites, we conducted massively parallel pyrosequencing of mRNAs (RNA-seq) using the same seedling and callus tissues that were used for DNase-seq. Two biological replicates of each tissue were applied...
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Research: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm
- Shan-Fu Wu,
- Haiying Zhang,
- and Bradley R. Cairns
Genome Res. April 2011 21: 578-589; Published in Advance March 7, 2011, doi:10.1101/gr.113167.110
...of the gene by the attraction of PRC2/H3K27 by the nascent RNAs produced (Zhao et al. 2008; Lee 2009; Tsai et al. 2010) and deacetylation through resident H3K36me3 and its recruitment of HDACs (Carrozza et al. 2005; Joshi and Struhl 2005; Keogh et al. 2005). The purpose of zebrafish sperm chromatin Loci...
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Method: Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression
- Di Huang,
- Hanna M. Petrykowska,
- Brendan F. Miller,
- Laura Elnitski,
- and Ivan Ovcharenko
Genome Res. April 2019 29: 657-667; Published in Advance March 18, 2019, doi:10.1101/gr.247007.118
...inhibits gene transcription by impeding or poising the occupancy of RNA polymerase II (van Kruijsbergen et al. 2015). Transcriptional dynamics during development and disease initiation have been attributed to H3K27me3 (Simon and Kingston 2009; Sexton et al. 2012; Jiang et al. 2013; Pinello et al. 2014...
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Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
- Nina Koenecke,
- Jeff Johnston,
- Qiye He,
- Samuel Meier,
- and Julia Zeitlinger
Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
.... The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Res 26: 896–907. Bier E, De Robertis EM. 2015. EMBRYO DEVELOPMENT. BMP gradients: a paradigm for morphogen-mediated developmental patterning. Science 348: aaa5838. Bonn S, Zinzen RP,Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme...
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Methods: Inferring causal relationships among different histone modifications and gene expression
- Hong Yu,
- Shanshan Zhu,
- Bing Zhou,
- Huiling Xue,
- and Jing-Dong J. Han
Genome Res. August 2008 18: 1314-1324; Published in Advance June 18, 2008, doi:10.1101/gr.073080.107
...performed chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) in human T cells, using antibodies against 20 human histone lysine and arginine methylations, as well as histone variant H2A.Z, RNA polymerase II (Pol II), and the insulator binding protein CTCF, to map...

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