Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages
-
Published:2023-07-04
Issue:13
Volume:24
Page:11076
-
ISSN:1422-0067
-
Container-title:International Journal of Molecular Sciences
-
language:en
-
Short-container-title:IJMS
Author:
Bai Jingyi1, Lin Yu1, Zhang Jiaman1, Chen Ziyu1, Wang Yujie1, Li Mingzhou1ORCID, Li Jing1
Affiliation:
1. Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Abstract
The study of chromatin accessibility across tissues and developmental stages is essential for elucidating the transcriptional regulation of various phenotypes and biological processes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development remain poorly investigated. Here, we used ATAC-seq and rRNA-depleted RNA-seq to profile open chromatin maps and transcriptional features of heart, kidney, liver, lung, skeletal muscle, and spleen in newborn pigs and porcine liver tissue in the suckling and adult stages, respectively. Specifically, by analyzing a union set of protein-coding genes (PCGs) and two types of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage. As expected, the PCGs with tissue-specific accessible promoters had active transcription and were relevant to tissue-specific functions. In addition, other non-coding tissue-specific peaks were involved in both physical activity and the morphogenesis of neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands our current understanding of epigenetic regulation in mammalian tissues and organ development, which can benefit both economic trait improvement and improve the biomedical usage of pigs.
Funder
National Key R&D Program of China National Natural Science Foundation of China
Subject
Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis
Reference74 articles.
1. Kawai, Y., Tohyama, S., Shimizu, H., Fukuda, K., and Kobayashi, E. (2019). Xenotransplantation—Comprehensive Study, IntechOpen. 2. Wu, G. (2022). Recent Advances in Animal Nutrition and Metabolism, Springer International Publishing. 3. Selected physiologic compatibilities and incompatibilities between human and porcine organ systems;Ibrahim;Xenotransplantation,2006 4. The pig: A model for human infectious diseases;Meurens;Trends Microbiol.,2012 5. Wernersson, R., Schierup, M.H., Jørgensen, F.G., Gorodkin, J., Panitz, F., Staerfeldt, H.H., Christensen, O.F., Mailund, T., Hornshøj, H., and Klein, A. (2005). Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics, 6.
Cited by
2 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|