在盐胁迫响应过程中水稻基因表达及染色质结构状态表观变化的研究

Abiotic stress responses and adaptations are one of prerequisites for plant survival. Adaptation of plants to abiotic stresses can be improved through regulating changes of physiological and biochemical responses, expression of stress responsive genes and epigenetic modifications et al. Thus, investigation about the relationships between epigenetic changes and abiotic stress responses in plants will not only help to elucidate epigenetic mechanisms for plant stress responses, but also provide theoretical supports for epigenetics-based crop breeding in the future. The research proposed herein first aims to analyze epigenetic mechanisms of salinity stress responses in rice, which includes changes occurred at the levels of open chromatins, differential genes expression, histone modifications and mRNA alternative splicing et al. through applying DNase-seq, mRNA-seq and ChIP-seq et al. omics methodologies, respectively. This research will then investigate genetic and epigenetic mechanisms about expression of salinity responsive genes, which are regulated by salinity inducible promoters. And this research will investigate the mechanisms that salinity stress specific DHSs play a role in salinity stress responses in rice. The success of this project will help us understand epigenetic mechanisms about salinity stress responses in rice. It will deepen our understanding of the molecular mechanisms about expression of salinity stress responsive genes regulated by salinity inducible promoters. It will also be beneficial to the selection and application of salinity inducible promoters in rice molecular breeding.

对非生物逆境胁迫应答及适应是植物赖以生存的前提条件之一。植物体通过调节自身的生理生化、逆境相关基因的表达以及表观修饰等变化，提高自身对逆境胁迫的适应性。因此，研究表观变化与植物逆境胁迫应答的关系，不仅有利于阐明植物逆境胁迫响应的表观机理，而且为将来基于表观遗传的作物育种提供理论支持。本项目首先运用DNase-seq、mRNA-seq及ChIP-seq等组学方法，分别从基因组开放性染色质位点、基因差异性表达、组蛋白修饰以及mRNA选择性剪切等水平，解析水稻对盐胁迫响应的表观遗传学分子机制。其次，探讨盐胁迫诱导型启动子调控盐胁迫相关基因表达的遗传及表观遗传学分子机理。最后，探讨盐诱导型DHSs在水稻盐胁迫响应中的作用机制。预期研究成果将有助于了解水稻对盐胁迫响应的表观遗传学机理，深化人们对盐诱导型启动子的分子作用机制的认识、选择与利用。

植物体通过调节自身的生理生化、基因表达以及表观修饰等变化，提高自身对盐胁迫的适应性。因此，研究表观变化与植物对盐胁迫应答的关系，不仅有利于阐明植物对盐胁迫响应的表观机理，而且为将来基于表观遗传的作物耐盐分子育种提供理论支持。本项目运用了mRNA-seq、ChIP-seq及DNase-seq等组学方法，在全基因组水平分别研究了叶片和根2种组织在盐处理后基因差异表达、组蛋白修饰、染色质状态和开放性染色质结构等表观变化；解析了组蛋白修饰和mRNA选择性剪切的相关性；分析了盐处理前后相关DH位点所对应DNA的motif序列特征；最后，选取了3个受盐诱导高表达基因的启动子区DH作为盐诱导型启动子或增强子候选进行瞬时转化验证。研究结果表明，叶片和根中，激活型修饰与下调基因表达呈正相关，而抑制型修饰与下调基因表达呈负相关，但在上调基因中，H4K12ac和H3K9ac 2种修饰与叶片中与上调基因表达正相关，H3K36me3修饰与根中与上调基因表达正相关，而其它修饰丰度在两种组织上调基因中均明显下降。在染色质状态水平，CS1-3和9-10与叶片和根中上调基因表达正相关；CS2-3和9-10与叶片中下调基因表达正相关；CS3-4和9与根中下调基因表达正相关。水稻中组蛋白修饰和可变剪切相关性分析结果显示，H3K36me3与外显子跳跃相关；乙酰化修饰与内含子滞留有关。开放性染色质位点分析结果表明，与对照相比，盐处理引起全基因组水平DH丰度下降。水稻叶片中上下调基因有关的DH均有明显的motif富集，例如，上调表达基因相关的DH序列主要有A(GG/CA)TGG、TGGGCC、CGG 和CCACC等4种motif；进一步分析发现，这些motif均有明显的footprint，说明相应DH位点可能存在调控蛋白结合位点。总之，通过本项目的实施，我们发现盐处理引起水稻基因组基因差异表达、组蛋白修饰、染色质状态、开放性染色质位点以及可变剪切等表观变化，特别是我们首次在植物里发现乙酰化修饰与内含子滞留有关。因此，我们研究结果将有助于了解水稻对盐胁迫响应的表观遗传学机理，深化人们对盐诱导型功能元件的分子作用机制的认识、选择与利用。