Study / S48WB6QO82024-04-09
Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
Chao Wang, Choulin Chen, Bowen Lei, Shenghua Qin, Yuanyuan Zhang et al.
About this study
Background: Enhancer RNAs (eRNAs) play a crucial role in transcriptional regulation. While significant progress has been made in understanding epigenetic regulation mediated by eRNAs, research on the construction of eRNA-mediated gene regulatory networks (eGRN) and the identification of critical network components that influence complex traits is lacking. Results: Here, employing the pig as a model, we conducted a comprehensive study using H3K27ac histone ChIP-seq and RNA-seq data to construct eRNA expression profiles from multiple tissues of two distinct pig breeds, namely Enshi Black (ES) and Duroc. In addition to revealing the regulatory landscape of eRNAs at the tissue level, we developed an innovative network construction and refinement method by integrating RNA-seq, ChIP-seq, genome-wide association study (GWAS) signals and enhancer-modulating effects of single nucleotide polymorphisms (SNPs) measured by self-transcribing active regulatory region sequencing (STARR-seq) experiments. Using this approach, we unraveled eGRN that significantly influence the growth and development of muscle and fat tissues, and identified several novel genes that affect adipocyte differentiation in a cell line model. Conclusions: Our work not only provides novel insights into the genetic basis of economic pig traits, but also offers a generalizable approach to elucidate the eRNA-mediated transcriptional regulation underlying a wide spectrum of complex traits for diverse organisms.
Full author list & citation
Chao Wang, Choulin Chen, Bowen Lei, Shenghua Qin, Yuanyuan Zhang, Kui Li, Song Zhang, Yuwen Liu. Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs. 2024-04-09. https://doi.org/10.1186/s12711-024-00897-4
Experiments 1
E4E3WI0NY
A capture STARR-seq library of 22 pig enhancer regions containing 107 population-differentiated SNP candidates was cloned into the hSTARR-seq_ORI episomal self-transcribing reporter and transfected into mouse 3T3-L1 fibroblasts. Pooled pig DNA from eight eastern and eight western pigs supplied the alleles; input plasmid DNA and 24-hour reporter RNA were sequenced, and allele-specific enhancer activity was quantified as the output/input change in alternate-allele fraction.