Dang Thach A, Morimoto Atsumi, Kobayashi Natsuki, Pham Kieu, Ikeda Ken-Ichi, Nakayashiki Hitoshi
Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
Commun Biol. 2025 Jul 22;8(1):1086. doi: 10.1038/s42003-025-08473-2.
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.
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。
