Abstract: 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.