小鼠精原干细胞中APA位点研究及3'UTR使用频率数据库构建

Alternative ployadenylation (APA) of a gene has emerged as critical roles in post-transcriptional gene regulations. Spermatogonial stem cells (SSCs) are adult stem cells, which can generate to mature spermatozoa though mitosis, meiosis and spermatogenesis. Several microarrys and high-throughput sequencing methods have been developed to characterize APA globally.Here we first isolated and purified SSCs, and use a recently developed SAPAS method, a approach based on second-generation sequencing, to profile tandem ployA events in SSC, ES and MEF cell lines. We identify of about 1200 genes highly expressed in SSCs, and those genes are highly agreed with the functions characteristic of the SSCs. Still, our study uncovered 300 genes both highly expressed in SSCs and ES cells. Over 600 genes were shows significant changes of ployA site use (or APA) in SSCs. Furthermore, we observed broad trends for 3'UTR lengthening and shortening in ES cells. And motif analysis of the 3'end of those genes indicated enrichment of trans-elements．Our result suggesting that global modulation of lengthening of 3'end may contribute to posttranscriptional regulation of gene expression in SSCs. The founding of molecular makers and regulatory mechanism of self-renewal and differentiation of SSCs, provides guidance for future studies of other stem cells. Still, we development a tool that can import data from 3'UTR deep sequencing, and run as pipeline according to the default parameters or those customized by the user. By obtained 3'UTRs sequencing data form public database, we constructed a 3'UTR usage database, provid advanced search tool allows the user to perform searches of 3'UTR usage pattern between diffenent samples.

mRNA的3'末端非编码区(3'UTR)区在mRNA表达网络中起着重要的调控作用，通过选择性剪切Ploy(A)位点（APA），形成不同的3'UTR异构体（tandem 3'UTRs）,3'UTR与反式作用因子（包括蛋白和miRNA等）相互作用完成3'UTR的调控作用。精原干细胞(SSC)是一类能自我更新并拥有多向分化潜能的细胞，是精子发生的基础。本项目采用被称为SAPAS的mRNA 3'末端高通量测序方法，在基因组范围内定位小鼠精原干细胞、胚胎干细胞和成纤维细胞的APA，发现了1200多个SSC中特异表达的基因和400多个PloyA使用模式差异的基因。运用3'UTR图谱，寻找新的SSCs标记分和参与干细胞调控的反式作用因子，及探讨APA相关的自我更新与分化的调控机理，以期为该领域提供新的研究思路。同时结合已经发表的3'末端深度测序数据，构建3'UTR测序数据分析平台和其使用频率数据库。

mRNA的3'末端非编码区(3'UTR)区在mRNA表达网络中起着重要的调控作用，通过选择性剪切Ploy(A)位点（APA），形成不同的3’UTR异构体（tandem 3’UTRs）,3’UTR与反式作用因子（包括蛋白和miRNA等）相互作用完成3’UTR的调控作用。精原干细胞(SSC)是一类能自我更新并拥有多向分化潜能的细胞，是精子发生的基础。本项目采用被称为SAPAS的mRNA 3’末端高通量测序方法，在基因组范围内定位小鼠精原干细胞、胚胎干细胞和成纤维细胞的APA，发现了1200多个SSC中特异表达的基因和400多个PloyA使用模式差异的基因。运用3’UTR图谱，寻找新的SSCs标记分和参与干细胞调控的反式作用因子，对这些关键调控因子，为该领域提供了新的研究思路，团队的生物学家已经展开了探讨SSC调控机制的分子生物学机理研究。最新的研究进展包括已经构建了基于RNA-Seq数据检测APA位点的算法和软件，并应用于RNA-Seq数据处理，构建APA表达数据库。