基于全长转录谱的人类、恒河猴比较基因组学研究

As a non-human primate model animal closely-related to human, rhesus macaque represents a unique model in studies of the molecular basis underpinning human-specific traits. Despite these unique advantages, several unresolved issues have limited the current use of the model due to the limited resource, such as inadequate functional genomics annotations. Especially, the majority of macaque transcripts in current annotation were predicted on the basis of the transcript structures of human homologs, considerably limiting their applications in comparative genomics study. In previous studies, we performed comprehensive functional genomics studies in rhesus macaque, refined the local fine-scale structures of the macaque transcripts, conducted preliminary studies of the full-length structures of the macaque transcripts, developed an online accessible database, the “RhesusBase”, to provide an information-rich framework for monkey genomics studies, and performed a series of comparative genomics studies in the context of rhesus macaque. Here, by integrating the second generation and the third generation sequencing technologies, we propose to profile a full-length transcript atlas in multiple comparable tissue samples of human and rhesus macaque. Further, we prepare to carry out human-macaque comparative genomics study to pinpoint the cross-species differences of alternative RNA processing events, as well as the structure and composition of full-length transcripts. We prepare to further investigate the mechanisms of the cross-species differences in terms of cis- and trans-regulations, and clarify their functions in terms of the regulated nuclear transportation, RNA stability and protein products. This project may provide novel insights into the molecular basis underlying human-specific traits, from the perspective of the full-length transcript evolution in primates.

恒河猴作为人类近源模式动物，为研究人类特有性状的分子基础提供了独特视角。然而，受资源限制，恒河猴研究存在功能基因组学数据匮乏等瓶颈，尤其是现有注释中猴转录本结构多源于人类注释的同源预测，制约了人、猴比较基因组学研究。申请人前期通过深入开展恒河猴基因组学研究，实现了对猴转录本的局部结构修正并初步探究了猴全长转录本结构，建立了猴基因组知识库RhesusBase，并开展了一系列以猴为模式动物的比较基因组学研究。本课题拟在此基础上，结合二代测序和三代单分子测序技术，获取人、猴多个重要组织的全长转录谱。通过比较基因组学研究，揭示人、猴可变转录调控事件差异、转录本全长结构差异以及转录本组成差异，并从顺式和反式调控角度分析这些差异形成的原因。进一步，探究人、猴差异转录本在转录本出核、稳定性、蛋白编码等方面的差异，并结合实验验证，从转录本演化角度为认识人类特有性状的分子基础提供依据。

作为人类近源模式生物，恒河猴为研究人类特有性状的遗传基础提供了新视角。然而，现有基因注释中，恒河猴转录本结构多源自人类注释的同源预测，严重制约了该领域研究。本项目结合二代测序和三代单分子测序技术，对恒河猴大脑、心脏、小脑和睾丸4个组织进行基于第三代测序技术的全长转录组研究，得到了800万条平均长度超过14 Kb的测序读段，并结合传统的短读长数据，实现了对51605个恒河猴全长基因结构的精确定义。以此为基础，项目系统探究了多聚腺苷酸化、RNA编辑等重要调控的特征和规律，并从顺式和反式调控角度分析这些差异形成的原因，及其在人类转录本演化中的作用。尤为值得一提的是，课题组发现在转录本演化过程中，在人类中出现了74个起源自lncRNA的新蛋白编码基因，对这些新基因的起源模式开展了系统研究，解释了这类基因“起源即有功能”的特征，并结合人源类脑器官模型和转基因小鼠模型，对一例以上述模式起源的新基因开展了功能研究，揭示了该基因在促进人脑增大等人类适应性演化中的关键作用。在项目支持下，课题负责人担任通讯作者在Nature Ecology & Evolution, Genome Biology, Briefings in Bioinformatics, Nature Communications发表四项工作，为揭示人类特有性状的遗传基础提供了独特角度和重要例证。