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Updated: Mar 25, 2026
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
[Genome-wide profiling of alternative polyadenylation in mouse female germline stem cells]
Ting-Ting Shen1, Xiao-Li Zhang, Pan Zhang
1Shanghai Center of Systems Biomedicine, Key Laboratory of Systems Biomedicine of Ministry of Education, Shanghai Jiaotong University, Shanghai 200240, China.
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.
