水稻三维基因组结构及其与表观遗传修饰的关系研究

三维基因组结构研究及其揭示的基因表达调控机理丰富了功能基因组的研究成果，促进了人和小鼠基因组结构及其与基因组表观修饰关系的认识。但是，在水稻中还未见相关研究。本项目拟利用本课题组建立的植物高效三维基因组研究方法Long-read ChIA-PET，构建水稻不同苗期幼叶和幼穗两个组织的RNA聚合酶II、活跃表达基因组蛋白修饰标记H3K4me3和转座子组蛋白修饰标记H3K9me2的高分辨率基因组三维互作图谱，解析水稻基因组三维结构的组织形式及其在不同发育时期的动态变化。系统地研究不同的表观修饰控制水稻基因组顺式元件或基因的三维互作机理。最后，通过一个水稻组蛋白修饰酶的突变体，研究该突变体中组蛋白甲基化修饰水平的变化影响三维基因组结构和基因表达变化的机制，建立三维基因组、基因组表观修饰、基因表达调控和突变表型四者之间的联系，进而阐明突变表型产生的三维基因组基础.

The achievement of three-dimensional genome organization principle and their functions in transcriptional regulation has extended our knowledge on functional genomics, and widen our understanding of the relationship between 3D genome structure and epigenomic modifications in human and mouse. However, little information about this field is available in rice. Here, we propose to map high-resolution 3D genome structure in two different tissues in rice, by utilizing an efficient 3D genome mapping technology (Long-read ChIA-PET). We will generate three types of Long-read ChIA-PET data, including RNA polymerase II, H3K4me3 that marks active genes and H3K9me2 for transposon related elements marks. By combining these chromatin interactions data together, we will reveal comprehensive high-resolution rice 3D genome structure and their dynamics in two tissues as well as hierarchical transcriptional regulation. At the end, we will use a jmj703 mutant as a model to illustrate the 3D genome basis of altering epigenetic modifications, gene expression dynamics and mutant phenotype. The expecting results will provide alternative strategy for studying molecular mechanism of complex agricultural traits in rice and other crops.