GSE143288 A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome

Contributors : Yunxia Zhao ; Ye Hou ; Yueyuan Xu ; Shuhong ZhaoSeries Type : Other ; Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Sus scrofaAlthough major advances in genomics have initiated an exciting new era of research, the lack of information about cis-regulatory elements has limited the genetic improvement or manipulation of pig as meat source and biomedical model. Here, we systematically characterize the cis-regulatory elements and their functions in the pig genome in 12 diverse tissues from 4 pig breeds through RNA-Seq, ATAC-Seq, and ChIP-Seq analyses. In total, we generated 199 datasets and identified more than 220,000 pig cis-regulatory elements. We find that cis-regulatory elements are more conserved between humans and pigs than that between humans and mice. To further explore the three dimension structure of pig genome, we performed high-throughput chromosome conformation capture (Hi-C) experiment. The rearrangements of TADs between pig and human have apparently contributed to the evolution of head and face phenotypes. Beyond generating a major new benchmark resource for pig epigenetics research, our study provides basic epigenetic comparative data for using pig as a model for human biomedical research.

Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Other Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Sus scrofa Source Type: research