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
| Author(s) | Gao, Yahui | |
| Author(s) | Liu, Shuli | |
| Author(s) | Baldwin, Ransom L. VI | |
| Author(s) | Connor, Erin E. | |
| Author(s) | Cole, John B. | |
| Author(s) | Ma, Li | |
| Author(s) | Fang, Lingzhao | |
| Author(s) | Li, Cong-jun | |
| Author(s) | Liu, George E. | |
| Date Accessioned | 2022-04-27T20:07:44Z | |
| Date Available | 2022-04-27T20:07:44Z | |
| Publication Date | 2022-02-10 | |
| Description | This article was originally published in Genomics. The version of record is available at: https://doi.org/10.1016/j.ygeno.2022.110296 | en_US |
| 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. | en_US |
| Sponsor | This work was supported in part by AFRI grant numbers 2013–67015-20951, 2016–67015-24886, 2019–67015-29321, and 2020–67015-02848 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. G.E. Liu was supported by appropriated project 8042–31000–001-00-D, “Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection” of the Agricultural Research Service of the United States Department of Agriculture. E.E. Connor, R.L Baldwin, and C-J Li were supported by appropriated project 8042–31310–078-00-D, “Improving Feed Efficiency and Environmental Sustainability of Dairy Cattle through Genomics and Novel Technologies.” J.B. Cole was supported by appropriated project 8042–31000–002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals.” | en_US |
| Citation | Gao, Yahui, Shuli Liu, Ransom L. Baldwin VI, Erin E. Connor, John B. Cole, Li Ma, Lingzhao Fang, Cong-jun Li, and George E. Liu. “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 114, no. 2 (2022): 110296. https://doi.org/10.1016/j.ygeno.2022.110296. | en_US |
| ISSN | 1089-8646 | |
| URL | https://udspace.udel.edu/handle/19716/30827 | |
| Language | en_US | en_US |
| Publisher | Genomics | en_US |
| Keywords | Cattle genome | en_US |
| Keywords | Functional annotation | en_US |
| Keywords | Rumen development | en_US |
| Keywords | Chromatin state | en_US |
| Keywords | Cell interaction | en_US |
| Keywords | Butyrate | en_US |
| Title | 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 | en_US |
| Type | Article | en_US |
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