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

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. O...

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Published in:Genomics (San Diego, Calif.) Calif.), 2022-09, Vol.114 (5), p.110449-110449, Article 110449
Main Authors: Dou, Jinhuan, Luo, Hanpeng, Sammad, Abdul, Lou, Wenqi, Wang, Di, Schenkel, Flavio, Yu, Ying, Fang, Lingzhao, Wang, Yachun
Format: Article
Language:English
Subjects:
ATAC-seq
DNA methylation
Genetic marker
Multi-omics analysis
RNA-sequencing
Transcription factor
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Summary: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. •Heat stress responses are under a complex epigenetic control dominated by cellular and metabolic changes in rat liver.•ATAC-seq reveals 36 up-regulated and 22 down-regulated transcription factors, like Cebpα, Foxa2, Foxo4, Nfya and Sp3.•Integrative omics reveals 45 DEGs (e.g. Adipoq, Kank1, Abcb1a, and Osb) as potential heat stress response markers in rats.•Ultimately, our study concluded INSR, MAPK8, RHPN2 and BTBD7 as candidate markers for heat stress.
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2022.110449