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Genome-wide identification of functional enhancers and their potential roles in pig breeding
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 t...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252078/ https://www.ncbi.nlm.nih.gov/pubmed/35781353 http://dx.doi.org/10.1186/s40104-022-00726-y |
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author | Wu, Yinqiao Zhang, Yuedong Liu, Hang Gao, Yun Liu, Yuyan Chen, Ling Liu, Lu Irwin, David M. Hou, Chunhui Zhou, Zhongyin Zhang, Yaping |
author_facet | Wu, Yinqiao Zhang, Yuedong Liu, Hang Gao, Yun Liu, Yuyan Chen, Ling Liu, Lu Irwin, David M. Hou, Chunhui Zhou, Zhongyin Zhang, Yaping |
author_sort | Wu, Yinqiao |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40104-022-00726-y. |
format | Online Article Text |
id | pubmed-9252078 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-92520782022-07-05 Genome-wide identification of functional enhancers and their potential roles in pig breeding Wu, Yinqiao Zhang, Yuedong Liu, Hang Gao, Yun Liu, Yuyan Chen, Ling Liu, Lu Irwin, David M. Hou, Chunhui Zhou, Zhongyin Zhang, Yaping J Anim Sci Biotechnol Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40104-022-00726-y. BioMed Central 2022-07-04 /pmc/articles/PMC9252078/ /pubmed/35781353 http://dx.doi.org/10.1186/s40104-022-00726-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Wu, Yinqiao Zhang, Yuedong Liu, Hang Gao, Yun Liu, Yuyan Chen, Ling Liu, Lu Irwin, David M. Hou, Chunhui Zhou, Zhongyin Zhang, Yaping Genome-wide identification of functional enhancers and their potential roles in pig breeding |
title | Genome-wide identification of functional enhancers and their potential roles in pig breeding |
title_full | Genome-wide identification of functional enhancers and their potential roles in pig breeding |
title_fullStr | Genome-wide identification of functional enhancers and their potential roles in pig breeding |
title_full_unstemmed | Genome-wide identification of functional enhancers and their potential roles in pig breeding |
title_short | Genome-wide identification of functional enhancers and their potential roles in pig breeding |
title_sort | genome-wide identification of functional enhancers and their potential roles in pig breeding |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252078/ https://www.ncbi.nlm.nih.gov/pubmed/35781353 http://dx.doi.org/10.1186/s40104-022-00726-y |
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