Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning

Yahui Gao; Shuli Liu; Ransom L Baldwin Vi; Erin E Connor; John B Cole; Li Ma; Lingzhao Fang; Cong-Jun Li; George E Liu

doi:10.1016/j.ygeno.2022.110296

Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning

Genomics. 2022 Mar;114(2):110296. doi: 10.1016/j.ygeno.2022.110296. Epub 2022 Feb 8.

Authors

Yahui Gao¹, Shuli Liu², Ransom L Baldwin Vi³, Erin E Connor⁴, John B Cole⁵, Li Ma⁶, Lingzhao Fang⁷, Cong-Jun Li⁸, George E Liu⁹

Affiliations

¹ Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
² Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
³ Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA. Electronic address: Ransom.Baldwin@usda.gov.
⁴ Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA. Electronic address: eeconnor@udel.edu.
⁵ Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
⁶ Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA. Electronic address: lima@umd.edu.
⁷ MRC Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom. Electronic address: Lingzhao.fang@igmm.ed.ac.uk.
⁸ Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA. Electronic address: Congjun.Li@usda.gov.
⁹ Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA. Electronic address: George.liu@usda.gov.

PMID: 35143887
DOI: 10.1016/j.ygeno.2022.110296

Abstract

We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development.

Keywords: Butyrate; Cattle genome; Cell interaction; Chromatin state; Functional annotation; Rumen development.

Publication types

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

MeSH terms

Animals
Cattle / genetics
Chromatin* / genetics
Chromatin* / metabolism
DNA Methylation
Rumen* / metabolism
Transcription Initiation Site
Weaning

Substances

Chromatin