2. Academic Validation
  3. Genome-wide identification of functional enhancers and their potential roles in pig breeding

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

  • J Anim Sci Biotechnol. 2022 Jul 4;13(1):75. doi: 10.1186/s40104-022-00726-y.
Yinqiao Wu  # 1 2,  Yuedong Zhang  # 1 2 3 4,  Hang Liu 1 2,  Yun Gao 1,  Yuyan Liu 3 4,  Ling Chen 3 4,  Lu Liu 1 5,  David M Irwin 6,  Chunhui Hou 1 7,  Zhongyin Zhou 8,  Yaping Zhang 9 10
Affiliations

Affiliations

  • 1 State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
  • 2 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China.
  • 3 State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China.
  • 4 School of Life Science, Yunnan University, Kunming, 650091, Yunnan, China.
  • 5 Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China.
  • 6 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
  • 7 Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
  • 8 State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. [email protected].
  • 9 State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. [email protected].
  • 10 Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. [email protected].
  • # Contributed equally.
PMID: 35781353 DOI: 10.1186/s40104-022-00726-y
Abstract

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.

Keywords

Breeding; Functional enhancers; Pig; STARR-seq.

Figures
Products