Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure

Xiaolong Kang; Chenglong Li; Shuli Liu; Ransom L Baldwin 6th; George E Liu; Cong-Jun Li

doi:10.3390/biom13071137

Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure

Biomolecules. 2023 Jul 16;13(7):1137. doi: 10.3390/biom13071137.

Authors

Xiaolong Kang^{1

2}, Chenglong Li², Shuli Liu¹, Ransom L Baldwin 6th¹, George E Liu¹, Cong-Jun Li¹

Affiliations

¹ Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA.
² Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.

Abstract

Butyrate contributes epigenetically to the changes in cellular function and tissue development of the rumen in ruminant animals, which might be achieved by its genetic or epigenetic regulation of gene expression. To explore the role of butyrate on bovine rumen epithelial function and development, this study characterized genome-wide H3K27ac modification changes and super-enhancer profiles in rumen epithelial primary cells (REPC) induced with butyrate by ChIP-seq, and analyzed its effects on gene expression and functional pathways by integrating RNA-seq data. The results showed that genome-wide acetylation modification was observed in the REPC with 94,675 and 48,688 peaks in the butyrate treatment and control group, respectively. A total of 9750 and 5020 genes with increased modification (H3K27ac-gain) and decreased modification (H3K27ac-loss) were detected in the treatment group. The super-enhancer associated genes in the butyrate-induction group were involved in the AMPK signaling pathway, MAPK signaling pathway, and ECM-receptor interaction. Finally, the up-regulated genes (PLCG1, CLEC3B, IGSF23, OTOP3, ADTRP) with H3K27ac gain modification by butyrate were involved in cholesterol metabolism, lysosome, cell adhesion molecules, and the PI3K-Akt signaling pathway. Butyrate treatment has the role of genome-wide H3K27ac acetylation on bovine REPC, and affects the changes in gene expression. The effect of butyrate on gene expression correlates with the acetylation of the H3K27ac level. Identifying genome-wide acetylation modifications and expressed genes of butyrate in bovine REPC cells will expand the understanding of the biological role of butyrate and its acetylation.

Keywords: H3K27ac; acetylation; butyrate; cattle; rumen; super-enhancer.

Publication types

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

MeSH terms

Acetylation
Animals
Butyrates / metabolism
Butyrates / pharmacology
Cattle
Epigenesis, Genetic*
Histones* / metabolism
Phosphatidylinositol 3-Kinases / metabolism
Rumen / metabolism

Substances

Histones
Butyrates
Phosphatidylinositol 3-Kinases

Grants and funding

This work was supported in part by AFRI grant numbers 2013-67015-20951, 2016-67015-24886, 2019-67015-29321, 2020-67015-02848, and 2021-67015-33409 from the USDA National Institute of Food and Agriculture (NIFA) Animal Genome and Reproduction Programs and BARD grant number US-4997-17 from the US–Israel Binational Agricultural Research and Development (BARD) Fund. GEL was supported by appropriated project 8042-31000-112-00-D, “Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection”, of the Agricultural Research Service of the United States Department of Agriculture. RLB and CJL were supported by appropriated project 8042-31310-114-00-D, “Improving Dairy Cow Feed Efficiency and Environmental Sustainability Using Genomics and Novel Technologies to Identify Physiological Contributions and Adaptations.”