Genome-wide identification of functional enhancers and their potential roles in pig breeding

Wu, Yinqiao1,2,3; Zhang, Yuedong1,2,3,4,5; Liu, Hang1,2,3; Gao, Yun1,2; Liu, Yuyan4,5; Chen, Ling4,5; Liu, Lu1,2,6; Irwin, David M.7; Hou, Chunhui1,2,8; Zhou, Zhongyin1,2; Zhang, Yaping1,2,9

2022-07-04

10.1186/s40104-022-00726-y

JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY   Impact Factor & Quartile

1674-9782

2049-1891

Background The pig is an economically important livestock species and is a widely applied large animal model in medical research. Enhancers are critical regulatory elements that have fundamental functions in evolution, development and disease. Genome-wide quantification of functional enhancers in the pig is needed. Results We performed self-transcribing active regulatory region sequencing (STARR-seq) in the porcine kidney epithelial PK15 and testicular ST cell lines, and reliably identified 2576 functional enhancers. Most of these enhancers were located in repetitive sequences and were enriched within silent and lowly expressed genes. Enhancers poorly overlapped with chromatin accessibility regions and were highly enriched in chromatin with the repressive histone modification H3K9me3, which is different from predicted pig enhancers detected using ChIP-seq for H3K27ac or/and H3K4me1 modified histones. This suggests that most pig enhancers identified with STARR-seq are endogenously repressed at the chromatin level and may function during cell type-specific development or at specific developmental stages. Additionally, the PPP3CA gene is associated with the loin muscle area trait and the QKI gene is associated with alkaline phosphatase activity that may be regulated by distal functional enhancers. Conclusions In summary, we generated the first functional enhancer map in PK15 and ST cells for the pig genome and highlight its potential roles in pig breeding.

Breeding Functional enhancers Pig STARR-seq

SCI

English

Others

National Natural Science Foundation of China[32100502] ; Ministry of Agriculture of China[2016ZX08009003006] ; Science & Technology Department of Yunnan Province[202102AE090039]

Agriculture

Agriculture, Dairy & Animal Science

WOS:000820229400001

BMC

2-s2.0-85133365319

Web of Science

1.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Yunnan, Peoples R China
2.Chinese Acad Sci, Kunming Inst Zool, Yunnan Lab Mol Biol Domest Anim, Kunming 650223, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650204, Yunnan, Peoples R China
4.Yunnan Univ, State Key Lab Conservat & Utilizat Bioresource Yu, Kunming 650091, Yunnan, Peoples R China
5.Yunnan Univ, Sch Life Sci, Kunming 650091, Yunnan, Peoples R China
6.Anhui Univ, Inst Phys Sci & Informat Technol, Hefei 230601, Anhui, Peoples R China
7.Univ Toronto, Dept Lab Med & Pathobiol, Toronto, ON, Canada
8.Southern Univ Sci & Technol, Sch Life Sci, Dept Biol, Shenzhen 518055, Peoples R China
9.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China

Wu, Yinqiao,Zhang, Yuedong,Liu, Hang,et al. Genome-wide identification of functional enhancers and their potential roles in pig breeding[J]. JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY,2022,13(1).

Wu, Yinqiao.,Zhang, Yuedong.,Liu, Hang.,Gao, Yun.,Liu, Yuyan.,...&Zhang, Yaping.(2022).Genome-wide identification of functional enhancers and their potential roles in pig breeding.JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY,13(1).

Wu, Yinqiao,et al."Genome-wide identification of functional enhancers and their potential roles in pig breeding".JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY 13.1(2022).