Division of Plant Biology, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh 226001, India.
Genomics. 2022 Jul;114(4):110433. doi: 10.1016/j.ygeno.2022.110433. Epub 2022 Jul 18.
Cultivated in tropical and subtropical regions, Oryza sativa L. ssp. indica is largely affected by cold-stress, especially at the seedling stage. The present model of the stress-responsive regulatory network in plants entails the role of genetic and epigenetic factors in stress-responsive gene expression. Despite extensive transcriptomic studies, the regulation of various epigenetic factors in plants cold-stress response is less explored. The present study addresses the effect of genome-wide changes of H3K27 modifications on gene expression in IR64 rice, during cold-stress. Our results suggest a positive correlation between the changes in H3K27 modifications and stress-responsive gene activation in indica rice. Cold-induced enrichment of H3K27 acetylation promotes nucleosomal rearrangement, thereby facilitating the accessibility of the transcriptional machinery at the stress-responsive loci for transcription activation. Although H3K27ac exhibits uniform distribution throughout the loci of enriched genes; occupancy of H3K27me3 is biased to intergenic regions. Integration of the ChIP-seq data with transcriptome indicated that upregulation of stress-responsive TFs, photosynthesis-TCA-related, water-deficit genes, redox and JA signalling components, was associated with differential changes of H3K27ac and H3K27me3 levels. Furthermore, cold-induced upregulation of histone acetyltransferases and downregulation of DNA methyltransferases was noted through the antagonistic switch of H3K27ac and H3K27me3. Moreover, motif analysis of H3K27ac and H3K27me3 enriched regions are associated with putative stress responsive transcription factors binding sites, GAGA element and histone H3K27demethylase. Collectively our analysis suggests that differential expression of various chromatin and DNA modifiers coupled with increased H3K27ac and depleted H3K27me3 increases DNA accessibility, thereby promoting transcription of the cold-responsive genes in indica rice.
在热带和亚热带地区种植的 Oryza sativa L. ssp. indica 主要受到冷胁迫的影响，尤其是在幼苗期。目前的植物应激反应调控网络模型涉及遗传和表观遗传因素在应激反应基因表达中的作用。尽管进行了广泛的转录组研究，但植物冷应激反应中各种表观遗传因素的调控仍未得到充分探索。本研究探讨了全基因组范围内 H3K27 修饰变化对 IR64 水稻冷胁迫响应中基因表达的影响。我们的结果表明，H3K27 修饰变化与 indica 水稻中应激响应基因的激活呈正相关。冷诱导的 H3K27 乙酰化富集促进核小体重排，从而使转录机器在应激响应基因座上的可及性增加，促进转录激活。尽管 H3K27ac 在富含基因的基因座上呈均匀分布，但 H3K27me3 的占据偏向于基因间区。ChIP-seq 数据与转录组的整合表明，应激响应 TF、光合作用-TCA 相关、水分亏缺基因、氧化还原和 JA 信号成分的上调与 H3K27ac 和 H3K27me3 水平的差异变化有关。此外，通过 H3K27ac 和 H3K27me3 的拮抗开关，观察到冷诱导的组蛋白乙酰转移酶上调和 DNA 甲基转移酶下调。此外，富集的 H3K27ac 和 H3K27me3 区域的基序分析与假定的应激响应转录因子结合位点、GAGA 元件和组蛋白 H3K27 去甲基酶有关。总之，我们的分析表明，各种染色质和 DNA 修饰物的差异表达与 H3K27ac 的增加和 H3K27me3 的减少相结合，增加了 DNA 的可及性，从而促进了 indica 水稻中冷响应基因的转录。
