Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages.

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  • Additional Information
    • Source:
      Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
    • Publication Information:
      Original Publication: Basel, Switzerland : MDPI, [2000-
    • Subject Terms:
      Chromatin*/genetics ; Epigenesis, Genetic*; Animals ; Swine/genetics ; Gene Expression Regulation ; Chromatin Immunoprecipitation Sequencing ; Promoter Regions, Genetic ; Mammals/genetics
    • 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.
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    • Grant Information:
      U19A2036 National Natural Science Foundation of China; 32225046 National Natural Science Foundation of China; 32102507 National Natural Science Foundation of China; U22A20507 National Natural Science Foundation of China; 2022YFF1000100 National Key R&D Program of China; 2020YFA0509500 National Key R&D Program of China
    • Contributed Indexing:
      Keywords: epigenomic profile; liver; newborn pigs; postnatal development; transcriptional regulation
    • Accession Number:
      0 (Chromatin)
    • Publication Date:
      Date Created: 20230714 Date Completed: 20230717 Latest Revision: 20230718
    • Publication Date:
      20230718
    • Accession Number:
      PMC10341957
    • Accession Number:
      10.3390/ijms241311076
    • Accession Number:
      37446255