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组蛋白修饰相互作用分析揭示了稻瘟病菌兼性异染色质中的两个不同结构域。

Analysis of histone modification interplay reveals two distinct domains in facultative heterochromatin in Pyricularia oryzae.

作者信息

Dang Thach A, Morimoto Atsumi, Kobayashi Natsuki, Pham Kieu, Ikeda Ken-Ichi, Nakayashiki Hitoshi

机构信息

Graduate School of Agricultural Science, Kobe University, Kobe, Japan.

Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.

出版信息

Commun Biol. 2025 Jul 22;8(1):1086. doi: 10.1038/s42003-025-08473-2.

Abstract

Histone post-translational modifications (PTMs) interact in complex ways to regulate chromatin structure and gene expression. To investigate this interplay, we analyze ChIP-seq and RNA-seq data from knock-out mutants lacking enzymes responsible for H3K4me2/3, H3K9me3, or H3K27me3 in the phytopathogenic fungus Pyricularia oryzae. Loss of specific PTMs alters other PTMs and gene expression in a compartment-specific manner, with distinct effects across H3K4me2-rich euchromatin (EC), H3K27me3-rich facultative heterochromatin (fHC), H3K9me3-rich constitutive heterochromatin (cHC), and centromeres. We identify two distinct fHC subcompartments: K4-fHC, adjacent to EC, and K9-fHC, adjacent to cHC. Both contain poorly conserved genes, but K9-fHC harbors more transposable elements, while K4-fHC is more enriched for genes upregulated during infection, including effector-like genes. H3K27me3 levels in K4-fHC respond to changes in other PTMs, especially H3K9me3, and to environmental conditions. These findings suggest that K4-fHC functions as a reservoir of genes highly responsive to chromatin context and environmental cues.

摘要

组蛋白翻译后修饰(PTMs)以复杂的方式相互作用,以调节染色质结构和基因表达。为了研究这种相互作用,我们分析了来自植物致病真菌稻瘟病菌中缺乏负责H3K4me2/3、H3K9me3或H3K27me3的酶的基因敲除突变体的ChIP-seq和RNA-seq数据。特定PTM的缺失以区室特异性方式改变其他PTM和基因表达,在富含H3K4me2的常染色质(EC)、富含H3K27me3的兼性异染色质(fHC)、富含H3K9me3的组成型异染色质(cHC)和着丝粒之间具有不同的影响。我们鉴定出两个不同的fHC亚区室:与EC相邻的K4-fHC和与cHC相邻的K9-fHC。两者都含有保守性较差的基因,但K9-fHC含有更多的转座元件,而K4-fHC在感染期间上调的基因中更为富集,包括效应样基因。K4-fHC中的H3K27me3水平对其他PTM的变化,尤其是H3K9me3的变化以及环境条件作出反应。这些发现表明,K4-fHC作为对染色质环境和环境线索高度响应的基因库发挥作用。

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