雌性生殖干细胞全基因组范围选择性多聚腺苷酸化位点分析

Genome-wide profiling of alternative polyadenylation in mouse female germline stem cells

目的描绘小鼠雌性生殖干细胞(FGSCs)和胚胎干细胞(ESCs)全基因组范围内选择性多聚腺苷酸化(APA)位点,通过细胞间的比较,分析生殖干细胞特异性的APA位点对其生物学特性的影响。方法利用本实验室之前建立的基于高通量测序的转录本3’末端poly(A)位点捕获方法3T-seq确定并比较两个细胞系中所有APA位点,通过DAVID对具有APA位点差异的基因进行Gene Ontology分析。结果在两种细胞系中共确定16 973个基因的50 243个APA位点,发现FGSCs中相较于ESCs 3’UTR发生长度变化的基因1148个,其中795个(66%)3’UTR变短,353个(34%)基因3’UTR变长,与生殖发育密切相关的基因3’UTR存在显著的缩短现象。结论 FGSCs存在与ESCs不同的APA谱,APA介导的3’UTR变化参与生殖发育相关的生物学过程,揭示了生殖干细胞的基因转录后调控机制。

Objective To perform a genome- wide alternative polyadenylation（APA） profiling in both mouse female germline stem cells（FGSCs） and embryonic stem cells（ESCs） and explore the role of germline-specific APA in the biological behaviors of FGSCs. Methods We used a high-throughput sequencing-based method 3T-Seq to profile the genome-wide 3＇ termini of the transcripts and delineate all the APA sites in mouse FGSCs and ESCs. The genes with altered APA sites in FGSCs compared with ESCs were analyzed with DAVID Gene Ontology tool for their biological roles. Results We identified a total of 50243 APA sites in 16973 genes. In FGSCs, 1148 genes were shown to have alterations in 3＇UTR length, among which 795（66%） genes had shortened and 353（34%） had lengthened 3＇UTR. Some of the genes with shortened 3＇UTR were involved in germ cell development. Conclusions Our genome-wide APA profiling analysis reveals a cell type-specific APA alternation in FGSCs, and APA- mediated 3＇UTR alteration contributes to germline- related biological process. This study provides a framework for understanding the post-transcriptional regulation mechanisms in FGSCs.