Cargando…
Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages
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 developm...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341957/ https://www.ncbi.nlm.nih.gov/pubmed/37446255 http://dx.doi.org/10.3390/ijms241311076 |
_version_ | 1785072385683095552 |
---|---|
author | Bai, Jingyi Lin, Yu Zhang, Jiaman Chen, Ziyu Wang, Yujie Li, Mingzhou Li, Jing |
author_facet | Bai, Jingyi Lin, Yu Zhang, Jiaman Chen, Ziyu Wang, Yujie Li, Mingzhou Li, Jing |
author_sort | Bai, Jingyi |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10341957 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-103419572023-07-14 Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages Bai, Jingyi Lin, Yu Zhang, Jiaman Chen, Ziyu Wang, Yujie Li, Mingzhou Li, Jing Int J Mol Sci Article 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. MDPI 2023-07-04 /pmc/articles/PMC10341957/ /pubmed/37446255 http://dx.doi.org/10.3390/ijms241311076 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Bai, Jingyi Lin, Yu Zhang, Jiaman Chen, Ziyu Wang, Yujie Li, Mingzhou Li, Jing Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages |
title | Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages |
title_full | Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages |
title_fullStr | Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages |
title_full_unstemmed | Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages |
title_short | Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages |
title_sort | profiling of chromatin accessibility in pigs across multiple tissues and developmental stages |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341957/ https://www.ncbi.nlm.nih.gov/pubmed/37446255 http://dx.doi.org/10.3390/ijms241311076 |
work_keys_str_mv | AT baijingyi profilingofchromatinaccessibilityinpigsacrossmultipletissuesanddevelopmentalstages AT linyu profilingofchromatinaccessibilityinpigsacrossmultipletissuesanddevelopmentalstages AT zhangjiaman profilingofchromatinaccessibilityinpigsacrossmultipletissuesanddevelopmentalstages AT chenziyu profilingofchromatinaccessibilityinpigsacrossmultipletissuesanddevelopmentalstages AT wangyujie profilingofchromatinaccessibilityinpigsacrossmultipletissuesanddevelopmentalstages AT limingzhou profilingofchromatinaccessibilityinpigsacrossmultipletissuesanddevelopmentalstages AT lijing profilingofchromatinaccessibilityinpigsacrossmultipletissuesanddevelopmentalstages |