The impact of different feeds on DNA methylation, glycolysis/gluconeogenesis signaling pathway, and gene expression of sheep muscle

Feng Song; Zaccheaus Pazamilala Akonyani; Ying Li; Deqiqige Su; Lantuya Wu; Yue Pang; Sile Hu; Dubala Wu; Chun Li; Ding Yang; Jianghong Wu

doi:10.7717/peerj.13455

The impact of different feeds on DNA methylation, glycolysis/gluconeogenesis signaling pathway, and gene expression of sheep muscle

PeerJ. 2022 May 26:10:e13455. doi: 10.7717/peerj.13455. eCollection 2022.

Authors

Feng Song^#¹, Zaccheaus Pazamilala Akonyani^#¹, Ying Li¹, Deqiqige Su¹, Lantuya Wu¹, Yue Pang¹, Sile Hu², Dubala Wu¹, Chun Li¹, Ding Yang³, Jianghong Wu^{1

3}

Affiliations

¹ College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, Inner Mongolia, China.
² College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, Inner Mongolia, China.
³ Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, Inner Mongolia, China.

^# Contributed equally.

Abstract

DNA methylation is an important epigenetic regulatory form that regulates gene expression and tissue development. This study compared the effects of high fiber, low protein (HFLP) and low fiber, high protein (LFHP) diets on the DNA methylation profile of twin lambs' muscles, their effect on glycolysis/gluconeogenesis and related pathways by transcriptome and deep whole-genome bisulfite sequencing (WGBS). Results identified 1,945 differentially methylated regions (DMRs) and 1,471 differentially methylated genes (DMGs). Also, 487 differentially expressed transcripts belonging to 368 differentially expressed genes (DEGs) were discovered between the twin lambs under different diets. Eleven overlapped genes were detected between the DEGs and the DMGs. FKBP5 and FOXO1 were detected to be significantly different. The FOXO1 regulated cAMP and the glycolysis/gluconeogenesis pathways. The glycolysis/gluconeogenesis, and the FOXO pathways were significantly enriched. The expressions of HOMER1 and FOXO1 in the HFLP group were significantly higher than those in the LFHP group. There is a significant correlation between the upregulated gene expression and hypomethylation of HOMER1 and FOXO1 gene in HFLP group. The results showed that FOXO1 induces PDK4 expression in muscle while regulating FKBP5 activity, which stimulates glucose production by activating specific gluconeogenesis target genes. The FOXO1 was able to regulate the glucose metabolism, the cAMP and the occurrence of glycolysis/gluconeogenesis pathways. This study showed that feed type can affect the methylation levels of the glycolysis related gluconeogenesis genes and interaction pathways, providing new ideas for a better understanding of the regulation of muscle energy metabolism and feed development.

Keywords: DNA methylation; Glucose metabolism; Glycolysis/Gluconeogenesis; Whole-genome bisulfite sequencing; cAMP pathway.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
DNA Methylation* / genetics
Gluconeogenesis* / genetics
Glycolysis / genetics
Muscles
Sheep / genetics
Signal Transduction / genetics
Transcriptome

Grants and funding

This work was supported by the National Natural Science Foundation of China (31560623), the Inner Mongolia Autonomous Region’s Key Technology Tackling Plan (2021GG0008, 2020GG0069), the Doctoral Scientific Research Foundation of Inner Mongolia Minzu University (BS527, BS526) to Dr. Jianghong Wu and Sile Hu. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.