Guangrun Yu , Baowang Zhang , Qi Chen , Zequan Huang , Baohong Zhang , Kai Wang , Jinlei Han
{"title":"木薯冷胁迫反应中的 DNA 甲基化动态修饰","authors":"Guangrun Yu , Baowang Zhang , Qi Chen , Zequan Huang , Baohong Zhang , Kai Wang , Jinlei Han","doi":"10.1016/j.ygeno.2024.110871","DOIUrl":null,"url":null,"abstract":"<div><p>Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.</p></div>","PeriodicalId":3,"journal":{"name":"ACS Applied Electronic Materials","volume":null,"pages":null},"PeriodicalIF":4.3000,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000922/pdfft?md5=e262674eac04fa817b70bd6048696df7&pid=1-s2.0-S0888754324000922-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Dynamic DNA methylation modifications in the cold stress response of cassava\",\"authors\":\"Guangrun Yu , Baowang Zhang , Qi Chen , Zequan Huang , Baohong Zhang , Kai Wang , Jinlei Han\",\"doi\":\"10.1016/j.ygeno.2024.110871\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.</p></div>\",\"PeriodicalId\":3,\"journal\":{\"name\":\"ACS Applied Electronic Materials\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.3000,\"publicationDate\":\"2024-05-26\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S0888754324000922/pdfft?md5=e262674eac04fa817b70bd6048696df7&pid=1-s2.0-S0888754324000922-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACS Applied Electronic Materials\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0888754324000922\",\"RegionNum\":3,\"RegionCategory\":\"材料科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"ENGINEERING, ELECTRICAL & ELECTRONIC\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Applied Electronic Materials","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0888754324000922","RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"ENGINEERING, ELECTRICAL & ELECTRONIC","Score":null,"Total":0}
引用次数: 0
摘要
木薯是一种重要的热带作物,面临着冷胁迫的挑战,因此有必要探索其分子响应。在这里,我们研究了DNA甲基化在调节木薯对中度冷胁迫(10 °C)的反应中的作用。利用全基因组亚硫酸氢盐测序技术,我们研究了在对照条件、5 小时和 48 小时冷胁迫条件下叶片和叶柄的 DNA 甲基化模式。观察到了组织特异性反应,叶片表现出微妙的变化,而叶柄在冷胁迫下的甲基化水平明显下降。我们确定了冷胁迫诱导的差异甲基化区域(DMRs),这些区域显示了组织和处理的特异性。重要的是,这些甲基化区域富集在表达发生变化的基因中,这意味着它们具有功能相关性。与DMRs相关的冷反应转录因子ERF105是跨组织和跨处理的重要且保守的调节因子。此外,我们还研究了转座元件的DNA甲基化动态,强调了具有bHLH结合基序的MITE对冷胁迫的敏感性。这些发现深入揭示了木薯对冷胁迫反应的表观遗传调控,有助于了解这种热带植物对胁迫适应的分子机制。
Dynamic DNA methylation modifications in the cold stress response of cassava
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.