水稻非整倍性基因组表达与表观遗传调控特征研究

Aneuploidy involves changes in chromosomal copy number compared with normal euploid genotypes. Aneuploidy causes severe developmental defects and is a condition frequently found in tumor cells. Aneuploidy genome is in the state of unbalance,which affects the global genome transcriptional and epigenetic regulation. Studies of gene expression in aneuploids in a variety of species have claimed many different types of responses. Studies of individual genes suggest that there are both structural gene dosage effects and compensation in aneuploids, and that subtle trans-acting effects across the genome are quite prevalent. Moreover，researches of epigenomic in aneuploidy in less species have widespread alterations, such as DNA methylation and histone modification..Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations instructure, expression, and epigenetic modification of aneuploidy genome is still sparse. Plants generally tolerate aneuploidy better than animals. Through colchicine treatment and breeding strategies, we have obtained a set of trisomy in rice. This possibility, combined with the genomics and epigenetics tools available for rice, provides a powerful means to assess systematically the epigenomic and transcriptomic signatures of aneuploidy. In preliminary studies, we analyzed two kinds of aneuploidy genome expression characteristics. The results showed that the expression of genes involved in cell metabolism and reproduction has common characteristics in different aneuploidy genome. .In this project, We are going to profile gene expression, genome-wide specific DNA methylation and histone modificationin a set of trisomic byusing the following approaches: Q-PCR, RT-PCR, ChIP-PCR, MSPCR, RNA-seq, MeDIP-seq and ChIP-seq. The results will reveal characteristics of gene expression and epigenetic regulation in rice aneuploidy genome. We will focus on the key to exploit the characteristics of genes involved in cell metabolism and reproduction. Furthemore, combined with gene functional analysis and its effect on the phenotype, cell division behavior, the results will provide the construction of regulation network associated with gene expression and epigenetic modifications.

非整倍性变异是染色体数目变异主要类型之一。研究表明由于非整倍体基因组处于不平衡状态，因此整个基因组转录和表观遗传调控都会受到影响。本实验室在多年的水稻细胞遗传研究过程中，积累了一系列水稻非整倍性材料，为深入研究非整倍性基因组表达与表观遗传调控特征提供了丰富遗传资源。在前期研究中，我们分析了两种非整倍性基因组的表达特征，并且发现细胞代谢与繁殖相关基因的表达在不同非整倍体中具有共性特征。本研究拟以水稻成套初级三体材料为重点研究对象，以叶片和愈伤组织为研究材料，通过Q-PCR、RT-PCR、ChIP-PCR、MSPCR、RNA-seq、MeDIP-seq、ChIP-seq等研究技术明确水稻基因表达特征和表观遗传调控特征。并结合基因功能分析及其对表型、分裂行为的影响，挖掘非整倍性基因组在细胞代谢和繁殖相关基因表达、表观遗传调控特征，构建相关基因表达与表观修饰调控网络。

非整倍性变异是染色体数目变异主要类型之一。研究表明由于非整倍体基因组处于不平衡状态，因此整个基因组转录和表观遗传调控都会受到影响。通过本项目的实施，发现剂量效应与剂量补偿效应共存于不同非整倍体材料中，绝大多数基因表现为补偿效应，剂量效应的基因所占比例较小。通过GO富集分析和pathway富集分析发现在两个不同来源的非整倍体中存在与环境压力应激反应，细胞代谢、繁殖相关基因的共同上调或下调的共性特征，而与所添加染色体不存在相关性。对染色体片段重复材料进行转录组分析发现片段重复会影响基因组的表达。重复片段区域34.60%的基因表现出正剂量效应，经有性繁殖后，子代中表现剂量效应的基因数目发生下调。表明染色体片段重复区域的基因表现出明显的剂量效应，却对全基因组表达影响较小。说明水稻应对片段重复存在自我调控的能力，特别是通过有性繁殖减少其对自身生长发育的影响。另外通过LC-MS/MS、ChIP-PCR、ChIP-seq等技术对新型组蛋白修饰在水稻蛋白组分布特征及调控基因表达特征进行研究，发现新型组蛋白巴豆酰化和丁酰化修饰程度与基因表达成正相关，并且可以与乙酰化修饰共同促进基因的表达。为解析非整倍体的组蛋白修饰的表观遗传调控特征奠定基础。相关结果发表SCI论文5篇，中文权威1篇；培养博、硕士生6名。项目主持人2016年入选江苏省333工程第三层次培养对象。