Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs

Abstract

The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74-75) and adult (postnatal days 132-150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue-and developmental stage-specific peaks (which regulate gene pathways matching tissue-and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results (http://segtp.jxau.edu.cn/pencode/?genome=susScr11).

A comparative investigation on H3K27ac enhancer activities in the brain and liver tissues between wild boars and domesticated pigs

“…To the best of our knowledge, this is the first study reporting H3K27ac signals in the brain and liver of Chinese wild boars, the samples of which are relatively hard to access. Among the high-activity peaks identified in the brain and liver of CWBs, only 19.40% and 42.21% overlapped with the peaks previously identified from brain and liver tissue (Zhao et al, 2021), and only 25.79% and 26.85% overlapped with those in another study, respectively (Zhu et al, 2022), therefore, highlighting the dataset as a novel resource that contributes to the argument of pig H3K27ac activity repositories.…”

Profiling of N6-methyladenosine methylation in porcine longissimus dorsi muscle and unravelling the hub gene ADIPOQ promotes adipogenesis in an m6A-YTHDF1–dependent manner

“…For IP data, m 6 A peak calling was conducted by MACS2 with “--nomodel -g 2.5e9 --broad --keep-dup all” on whole transcript level. Differentially peaks were identified with in-house R script according to previous study [ 31 , 32 ]. Briefly, bedtools was used to combine all peaks from High and Low group into a reference peak.…”

Origin, evolution, and tissue-specific functions of the porcine repetitive element 1

“…The raw WGBS and RNA-seq reads are deposited in the China National Center for Bioinformation database (PRJCA003221, https://bigd.big.ac.cn/ ). The ongoing Functional Annotation of Animal Genomes (FAANG) Project shared the unpublished regional Bam files from ChIP-seq [ 26 ], miRNA-seq and Iso-seq. Mapping depth was extracted using SAMtools [ 27 ] and visualized with the Integrative Genomics Viewer (IGV) tool [ 28 ].…”