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Establishment and transcriptomic analyses of a cattle rumen epithelial primary cells (REPC) culture by bulk and single-cell RNA sequencing to elucidate interactions of butyrate and rumen development

Shudai Lin, Lingzhao Fang, Xiaolong Kang, Shuli Liu, Mei Liu, Erin E. Connor, Ransom L. Baldwin, George Liu, Cong-Jun Li
Heliyon 2020 v.6 no.6 pp. e04112
Holstein, biochemical mechanisms, bulls, butyrates, calves, cell differentiation, chromatin, cultured cells, developmental stages, epigenetics, epithelial cells, epithelium, gene expression regulation, gene regulatory networks, genomics, rumen, rumen development, sequence analysis, transcription factors, transcriptomics
As a critical and high-value tool to study the development of rumen, we established a stable rumen epithelial primary cell (REPC) culture from a two-week-old Holstein bull calf rumen epithelial tissue. The transcriptomic profiling of the REPC and the direct effects of butyrate on gene expression were assessed. Correlated gene networks elucidated the putative roles and mechanisms of butyrate action in rumen epithelial development. The top networks perturbed by butyrate were associated with epithelial tissue development. Additionally, two critical upstream regulators, E2F1 and TGFB1, were identified to play critical roles in the differentiation, development, and growth of epithelial cells. Significant expression changes of upstream regulators and transcription factors provided further evidence in support that butyrate plays a specific and central role in regulating genomic and epigenomic activities influencing rumen development. This work is the essential component to obtain a complete global landscape of regulatory elements in cattle and to explore the dynamics of chromatin states in rumen epithelial cells induced by butyrate at early developmental stages.