植物胚乳印迹基因的比较和进化基因组学研究以及计算生物学预测

Due to the unique expression pattern, the vital function with independent origins and evolution in animals and plants, imprinted genes have attracted the most attention from geneticists. However, the methods identifying plant imprinted genes are limited and no one of the existing theories can be used to explain all the phenomena indicated by the plant imprinted genes. .To better understand the mechanism underlying plant gene imprinting, we will further investigate plant imprinted genes by virtue of a combined methodologies as shown below: 1) identifying imprinted genes of outcrossing Brassica campestris L. and comparing them with their orthologous genes of selfing Arabidopsis thaliana in terms of the imprinting status ; 2) studying the imprinted genes at DNA sequence and expression levels using the comparative and evolutionary genomics as a framework with focus on the birth-and-death evolutionary pace of imprinted genes and their conservation cross species. We also aim to build a cross-species endosperm-specific gene functional network to dissect the function and the interaction mode of imprinted genes as a whole; 3)developing in silico methods to identify plant imprinted genes and determine the factors responsible for the imprinting behaviors of these genes..With the completion of this project, we will gain a better understanding of the functions, activities and mechanisms of imprinted genes. And we will be in a stronger position than even to reexamine the popular kinship theory, which is fundamentally important to our knowledge of the origins and evolution of gene imprinting. Meanwhile, the successful implementation of computation method in predicting imprinted genes may offer additional and more biological clue to imprinted genes, providing a powerful tool to study gene imprinting in plants with tiny endosperm with difficulties to dissect from the embedded seeds. Most importantly, endosperm is biologically and economically important storage tissue where the gene imprinting almost exclusively occurred, so it is of both great theoretically and practically significance to perform this research project.

基因印迹是遗传学研究热点。 然而目前鉴定植物印迹基因的方法仍相对单一，并且缺乏一套能解释植物印迹基因起源和进化的完整理论。. 本课题拟进行以下研究：1）利用RNA-seq技术对异交生殖的白菜型油菜胚乳印迹基因进行鉴定，然后与拟南芥印迹基因进行比较研究；2）用比较和进化基因组学方法研究印迹基因的序列进化和表达模式，阐明印迹基因的跨物种（不）保守性和适应性进化。构建出跨物种保守的胚乳基因功能互作网络，在此背景下研究印迹基因的功能和互作方式。3）运用计算生物学方法进行植物印迹基因的预测，明确印迹基因的决定机制。. 本项目有望加深对植物印迹基因的生物学功能，活动和作用方式的认识。由于植物基因印迹几乎只发生在胚乳，本身具有的重要经济价值，因此本项目具有重要的理论意义和重大的实际价值。

印记基因是一类受表观调控并呈现出等位基因特异性表达的基因,对动植物的正常生长、发育起着重要的调控作用，特别是对于植物种子大小、淀粉含量的积累等具有重要影响。然而，除了少数印记基因的功能被实验证实外，绝大多数的印记基因，尤其是在植物中的印记基因，其功能仍不清楚。另外，印记基因之间是否具有密切的功能关系也不得而知。更为重要的是，印记基因与非印记在序列特征、功能网络等方面的差异以及在进化过程中驱动印记基因的产生和丢失等原因仍没有详细地报道过。本项目通过生物信息学手段在序列水平，如序列长度、CpG岛、串联重复元件等方面进行了分析，发现印记基因具有较长的序列，基因body 区显著富集了串联重复序列和CpG岛，启动子区富集组织特异的TFBS；对植物印记基因的跨物种保守情况进行了分析，发现不同类型的印记基因的进化速率在不同物种中呈现出不同的情况；对印记基因的跨多个组织、发育时期的表达谱进行分析，揭示了印记基因和非印记基因的表达模式的差异；通过构建拟南芥基因功能网络，对拟南芥的印记基因的功能网络属性进行了分析，揭示了印记基因之间的功能互作关系。本研究的实施，为进一步深入理解植物印记基因功能和基因印记机制提供了新的数据和见解。