Histone methylation and acetylation participate in the modulation of gene expression. Here, chromatin immunoprecipitation sequencing (ChIP-Seq) was used to determine genome-wide patterns of three histone modifications, H3K4me3, H3K36me3, and H3K9ac (associated with actively expressed genes) and their associations with gene expression in Paulownia fortunei following phytoplasma infection and recovery from Paulownia witches’ broom (PaWB) disease after methyl methane sulfonate treatment. The three histone marks were preferentially deposited in genic regions, especially downstream of transcription start sites, and were highly concurrent with gene expression. Genes with all three histone marks exhibited the highest expression levels. Based on the comparison scheme, we detected 365, 2244, and 752 PaWB-associated genes with H3K4me3, H3K36me3, and H3K9ac marks, separately. KEGG pathway analysis showed that these genes were involved in plant-pathogen interaction, plant hormone signal transduction, and starch and sucrose metabolism. A small proportion of differentially modified genes showed changes in expression in response to phytoplasma infection, including genes involved in calcium ion signal transduction, abscisic acid signal transduction, and ethylene biosynthesis. This comprehensive analysis of genome-wide histone modifications and gene expression in Paulownia following phytoplasma infection provides new insights into the epigenetic responses to phytoplasma infection and will be useful for further studies on epigenetic regulation mechanisms in plants under biotic stress.

组蛋白甲基化和乙酰化参与基因表达的调节。在这里，染色质免疫沉淀测序 (ChIP-Seq) 用于确定三种组蛋白修饰 H3K4me3、H3K36me3 和 H3K9ac（与活跃表达的基因相关）的全基因组模式及其与泡桐中基因表达的关联在植原体感染和从泡桐病 (PaWB) 病中恢复后，经过甲基磺酸盐处理。三个组蛋白标记优先沉积在基因区域，尤其是转录起始位点的下游，与基因表达高度同步。具有所有三个组蛋白标记的基因表现出最高的表达水平。基于比较方案，我们分别检测到 365、2244 和 752 个带有 H3K4me3、H3K36me3 和 H3K9ac 标记的 PaWB 相关基因。KEGG通路分析表明，这些基因参与植物-病原体相互作用、植物激素信号转导以及淀粉和蔗糖代谢。一小部分差异修饰基因在响应植原体感染时表现出表达变化，包括参与钙离子信号转导、脱落酸信号转导和乙烯生物合成的基因。这种对植原体感染后泡桐的全基因组组蛋白修饰和基因表达的综合分析为对植原体感染的表观遗传反应提供了新的见解，并将有助于进一步研究生物胁迫下植物的表观遗传调控机制。