Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data.
Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3' end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3'UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.|The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
Hongyang
H
Wang
Department of Animal Sciences, Washington State University, Pullman, WA, United States.
Rui
R
Li
Department of Animal Sciences, Washington State University, Pullman, WA, United States.
Xiang
X
Zhou
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.|The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
Liyao
L
Xue
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.|The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
Xuewen
X
Xu
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.|The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
Bang
B
Liu
D000738:Androsterone / Q000378:metabolism; D000818:Animals; D005260:Female; D008099:Liver / Q000737:chemistry; D008297:Male; D026723:Polyadenylation; D059368:RNA Isoforms / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D034421:Sus scrofa / Q000235:genetics*; D013552:Swine; D013737:Testis / Q000737:chemistry
D059368:RNA Isoforms; D012333:RNA, Messenger; D000738:Androsterone