Epigenomics of rats' liver and its cross-species functional annotation reveals key regulatory genes underlying short term heat-stress response

Genomics. 2022 Sep;114(5):110449. doi: 10.1016/j.ygeno.2022.110449. Epub 2022 Aug 17.

Abstract

Molecular responses to heat stress are multifaceted and under a complex cellular post-transcriptional control. This study explores the epigenetic and transcriptional alterations induced by heat stress (42 °C for 120 min) in the liver of rats, by integrating ATAC-seq, RNA-Seq, and WGBS information. Out of 2586 differential ATAC-seq peaks induced by heat stress, 36 up-regulated and 22 down-regulated transcript factors (TFs) are predicted, such as Cebpα, Foxa2, Foxo4, Nfya and Sp3. Furthermore, 150,189 differentially methylated regions represent 2571 differentially expressed genes (DEGs). By integrating all data, 45 DEGs are concluded as potential heat stress response markers in rats. To comprehensively annotate and narrow down predicted markers, they are integrated with GWAS results of heat stress parameters in cows, and PheWAS data in humans. Besides better understanding of heat stress responses in mammals, INSR, MAPK8, RHPN2 and BTBD7 are proposed as candidate markers for heat stress in mammals.

Keywords: ATAC-seq; DNA methylation; Genetic marker; Multi-omics analysis; RNA-sequencing; Transcription factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics
  • Animals
  • Cattle
  • Epigenomics*
  • Female
  • Forkhead Transcription Factors / genetics
  • Gene Expression Profiling* / methods
  • Genes, Regulator
  • Heat-Shock Response / genetics
  • Humans
  • Liver
  • Mammals / genetics
  • Rats

Substances

  • Adaptor Proteins, Signal Transducing
  • BTBD7 protein, human
  • FOXO4 protein, rat
  • Forkhead Transcription Factors