|GAO, YAHUI - University Of Maryland|
|LIU, SHULI - China Agricultural University|
|Baldwin, Ransom - Randy|
|CONNOR, ERIN - University Of Delaware|
|MA, LI - University Of Maryland|
|FANG, LINGZHAO - University Of Edinburgh|
|Li, Congjun - Cj|
|Liu, Ge - George|
Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2022
Publication Date: 2/8/2022
Publication URL: https://handle.nal.usda.gov/10113/7671987
Citation: Gao, Y., Liu, S., Baldwin, R.L., Connor, E.E., Cole, J.B., Ma, L., Fang, L., Li, C., Liu, G. 2022. 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. 114:110296. https://doi.org/10.1016/j.ygeno.2022.110296.
Interpretive Summary: Fucntional annotation of animal genomes will benefit our understanding of genetic bases for complex traits. We provided the first maps of regulatory elements in cattle rumen. These results fill our knowledge gaps and provide the foundation for incorporating new transcriptome insights into the future animal breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.
Technical Abstract: In this study, we profiled in vivo landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. We first established the global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle, through genome-wide profiling of four histone modifications, CTCF-binding sites, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. We revealed that each chromatin state presented specific enrichment for sequence ontology, transcription, methylation, trait-associated variants, gene expression-associated variants, selection signatures, and evolutionarily conserved elements, indicating distinct biological functions. During weaning, we found that the weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states, occurred in tandem with significant variations in gene expression and DNA methylation, which was significantly associated with stature, production and reproduction economic traits. Through comparing with the bovine in vitro cultured epithelial cells and human gastrointestinal tissues, we showed the commonness and uniqueness of these bovine rumen in vivo results, especially the roles of cell interactions and mitochondrial activities in tissue development. Our results confirm the crucial role of functional genome annotation for understanding genome regulation and complex trait variation in livestock, suggesting cell interactions are vital in rumen tissue architecture, function and development.