Differentially CTCF-binding sites in cattle rumen tissue during weaning

Authors: Boschiero, Clarissa; GAO, YAHUI - University Of Maryland; Baldwin, Ransom - Randy; MA, LI - University Of Maryland; Li, Congjun - Cj; Liu, Ge - George

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/11/2022
Publication Date: 8/13/2022
Citation: Boschiero, C., Gao, Y., Baldwin, R.L., Ma, L., Li, C., Liu, G. 2022. Differentially CTCF-binding sites in cattle rumen tissue during weaning. International Journal of Molecular Sciences. 23(16):9070. https://doi.org/10.3390/ijms23169070.
DOI: https://doi.org/10.3390/ijms23169070

Interpretive Summary: Weaning plays important roles in rumen development. We studied CTCF-binding regions and regulatory elements in rumen epithelial tissue during the weaning using ChIP-seq. These results fill our knowledge gaps and provide the foundation for incorporating new knowledge into the future animal breeding program. Farmers, breeders, scientists, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: The weaning transition in calves is characterized by major structural changes such as an increase in the rumen capacity and surface area due to diet changes from milk to solid feed. Studies evaluating rumen development in calves are vital to identify genetic mechanisms affected by weaning, and this may result in new approaches to improve the health of weaned calves. This study aimed to provide a genome-wide characterization of CTCF-binding sites and differentially CTCF-binding sites (DCBS) in rumen tissue during the weaning transition of four Holstein calves to uncover regulatory elements in rumen epithelial tissue using ChIP-seq. Our study generated 67,280 CTCF peaks for the before weaning (BW) condition and 39,891 for after weaning (AW). Then, 7,401 DCBS were identified for the AW vs. BW comparison representing 0.15% of the cattle genome, comprising ~54% of induced DCBS and ~46% of repressed DCBS. Most of the induced and repressed DCBS were in distal intergenic regions, showing a potential role as insulators. However, more repressed sites were located in promoter regions compared to the induced, while more induced sites were in exons. Gene ontology enrichment revealed many shared GO terms for the induced and the repressed DCBS, mainly related to cellular migration, proliferation, growth, differentiation, cellular adhesion, digestive tract morphogenesis, and response to TGFß. In addition, shared KEGG pathways were obtained for adherens junction and focal adhesion. Interestingly, other relevant KEGG pathways were observed for the induced DCBS like gastric acid secretion, salivary secretion, bacterial invasion of epithelial cells, apelin signaling, and mucin type O-glycan biosynthesis. IPA analysis further revealed pathways with potential roles in rumen development during weaning including TGFß, Integrin-linked kinase, and Integrin signaling. Several putative transcription factor binding sites were identified for CTCF, BORIS, E2A, MITF, ASCL2, ATF3, TGIF1/2, SMAD2/3, ETV1, and others. When DCBS were further integrated with RNA-seq data, 36 putative target genes were identified for the repressed DCBS, including KRT84, COL9A2, MATN3, TSPAN1, and AJM1. This study successfully identified DCBS in cattle rumen tissue after weaning on a genome-wide scale and revealed several candidate target genes that may have a role in rumen development such as TGFß, integrins, keratins, and SMADs. The information generated in this study is a valuable resource for the cattle research community and provides insights into bovine genome regulation and chromatin landscape.