猪脂肪沉积过程中染色质空间构象变化及其介导的转录调控

It is evident that DNA sequence polymorphism alone does not provide adequate explanations for the molecular basis of adipose deposition. Recently, the three-dimensional (3D) organization of chromosomes, which profoundly affects transcription, has gained a greater appreciation as an alternative perspective on the genetic basis of complex traits in mammals. Recent years have seen rapid proliferation of technologies to investigate genome organization and function. Nevertheless, current understanding of the roles of nuclear architecture during adipose deposition remains fairly rudimentary. In this proposal, we pay attention to the key issue of chromatin architecture reorganization in the nucleus of adipocyte in pig, and aim to explore the highly dynamic chromatin architecture reorganization-mediated transcription during adipose deposition. We aim to generate a high-resolution map of the 3D chromatin interactome during adipose deposition. We specially focus on the analyses of chromatin contact maps at various resolutions, which have revealed principles of hierarchical genome architecture, spanning from chromosome territories, compartments and topologically associating domains to contact domains, loops and other important contacts mediated by cis-regulatory elements. With functional evaluation of the specific long-range sequence interactions which vary significantly during adipose deposition, we envision that our discoveries will provide new information for the regulation of adipose-associated gene expression in the 3D genome. Equally important, studies of chromatin architecture reorganization in porcine adipocyte may also help uncover the molecular basis that underlies economic traits in pig, and will be an important step forward for maximizing the economic benefits in producing high quality pork products for the benefit of human society.

微效多基因与调控元件间的动态互作是决定脂肪表型这一典型数量性状的分子基础。针对猪脂肪沉积这一重要经济性状，申请人在前期“脂肪组学”的研究基础上，聚焦“染色质空间构象变化介导的转录调控”这一前沿热点科学命题，在合理提出一系列有趣、值得深入探讨的生物学问题和假设基础上，拟开展全面深入的探索性研究。旨在解析猪活体内脂肪沉积这一动态过程中脂肪细胞染色质组装的层级空间构象变化，鉴定并明确基因组关键拓扑结构单元（染色质疆域、区室、拓扑关联域和染色质环）介导的转录本与调控元件（增强子和绝缘子）间的远距离互作模式。进而在细胞水平和模式动物中针对关键远距离调控位点开展功能验证，深入阐明其机理，明确具体生物学效应。本课题有望从基因组三维空间结构的新视角揭示脂肪性状复杂的远距离调控机制，其结果将为深刻理解猪经济性状的遗传决定基础提供新思路和视野，并在相关领域产生重要影响。

染色质构象改变介导的转录调控影响脂肪沉积这一典型数量性状的表型,然而脂肪细胞核内染色质空间构象参与具体脂质代谢过程的分子机制尚不明确。猪作为重要的农业经济动物，其基因组大小、基因同源度、消化系统结构和新陈代谢特征与人高度相似。本项目以巴马猪为实验动物，通过高脂高能饮食以及限制采食的方式构建“增重和减重动物模型”，采集12头正常饲喂猪4种脂肪组织（ULB，背部皮下脂肪；GOM，大网膜脂肪；MAD，肠系膜脂肪；RAD，板油）进行转录组和Hi-C数据分析。与ULB相比，内脏脂肪组织中的高RPS的基因主要参与炎症和免疫反应, 与内脏脂肪组织相比，ULB中具有更高RPS的基因主要与脂质代谢有关。对于脂肪组织中的一些炎症基因而言，似乎存在“肥胖记忆”，尽管体重减轻，这些基因仍保持其炎症状态。成脂分化过程中观测到大量的染色质区室A/B的可塑性重排，位于这些染色质激活（即B到A转变）区域的表达量上调的基因富集在了与脂质代谢和肌肉发育等特异性功能相关的GO和KEGG通路上。成脂分化的标记基因，大部分都表现出了激活的染色质状态，约90%的上调成脂化标记基因的染色质状态更活跃，特别是脂肪转化因子CEBPA和PPARG及其靶基因PLIN1和FABP4。本项目揭示了染色质构象在猪脂肪沉积中的重要作用。