Epigenetic basis for the establishment of ruminal tissue-specific functions in bovine fetuses and adults

Jing Wang; Wen Yuan; Fang Liu; Guangbo Liu; Xiaoxiong Geng; Chen Li; Chenchen Zhang; Nan Li; Xueling Li

doi:10.1016/j.jgg.2024.10.008

Volume 52 Issue 1

Jan. 2025

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Epigenetic basis for the establishment of ruminal tissue-specific functions in bovine fetuses and adults

doi: 10.1016/j.jgg.2024.10.008

a. State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Research Center for Laboratory Animal Science, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China;
b. College of Chemistry and Chemical Engineering, Engineering Research Center of Dairy Quality and Safety Control Technology, Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China

Funds:

This research was funded by the Science and Technology Major Project of the Inner Mongolia Autonomous Region of China to the State Key Laboratory of Reproductive Regulation (2023KYPT0010 and 2021ZD0048), STI 2030-Major Projects (2023ZD0407504) of China, the development plan for young scientific and technological talents in colleges and universities of Inner Mongolia Autonomous Region of China (NMGIRT2204), and the National Natural Science Foundation of China (32160172).

Received Date: 2024-08-01
Accepted Date: 2024-10-27
Rev Recd Date: 2024-10-24

Available Online: 2025-07-11

Publish Date: 2024-11-05

Abstract

Abstract

Epigenetic regulation in the rumen, a unique ruminant organ, remains largely unexplored compared with other tissues studied in model species. In this study, we perform an in-depth analysis of the epigenetic and transcriptional landscapes across fetal and adult bovine tissues as well as pluripotent stem cells. Among the extensive methylation differences across various stages and tissues, we identify tissue-specific differentially methylated regions (tsDMRs) unique to the rumen, which are crucial for regulating epithelial development and energy metabolism. These tsDMRs cluster within super-enhancer regions that overlap with transcription factor (TF) binding sites. Regression models indicate that DNA methylation, along with H3K27me3 and H3K27ac, can be used to predict enhancer activity. Key upstream TFs, including SOX2, FOSL1/2, and SMAD2/3, primarily maintain an inhibitory state through bivalent modifications during fetal development. Downstream functional genes are maintained mainly in a stable repressive state via DNA methylation until differentiation is complete. Our study underscores the critical role of tsDMRs in regulating distal components of rumen morphology and function, providing key insights into the epigenetic regulatory mechanisms that may influence bovine production traits.
- Rumen,
- Epigenetics,
- DNA methylation,
- tsDMRs,
- Enhancers

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References(85)

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