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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #396842
Research Project: Improving Feed Efficiency and Environmental Sustainability of Dairy Cattle through Genomics and Novel Technologies

Location: Animal Genomics and Improvement Laboratory

Title: Butyrate induces modifications of the CTCF-binding landscape in cattle cells

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

Submitted to: Biomolecules EISSN 2218-273X
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/23/2022
Publication Date: 8/25/2022
Citation: Boschiero, C., Gao, Y., Baldwin, R.L., Ma, L., Li, C., Liu, G. 2022. Butyrate induces modifications of the CTCF-binding landscape in cattle cells. Biomolecules. 12(9):1177. https://doi.org/10.3390/biom12091177.
DOI: https://doi.org/10.3390/biom12091177

Interpretive Summary: Butyrate is produced in the rumen from microbial fermentation and is related to several functions, including cell differentiation and proliferation. Butyrate supplementation in calves can accelerate rumen development. Although CTCF-binding sites have been identified recently in cattle, a deeper characterization, including differentially CTCF-binding sites, is vital for a better understanding butyrate’s role in the chromatin landscape. We studied CTCF-binding regions and regulatory elements using ChIP-seq in a cattle MDBK cell line. These results fill our knowledge gaps and provide the foundation for incorporating new knowledge into the future animal breeding program. These results provide a better understanding of the function of butyrate in cattle cells and chromatin landscape regulation.

Technical Abstract: Butyrate is produced in the rumen from microbial fermentation and is related to several functions, including cell differentiation and proliferation. Butyrate supplementation in calves can accelerate rumen development. DNA-protein interactions, such as the CCCTC-binding factor (CTCF), play essential roles in chromatin organization and gene expression regulation. Although CTCF-binding sites have been identified recently in cattle, a deeper characterization, including differentially CTCF-binding sites (DCBS), is vital for a better understanding of butyrate’s role in the chromatin landscape. This study aimed to identify CTCF-binding regions and DCBS under a butyrate-induced condition using ChIP-seq in bovine cells. 61,915 CTCF peaks were identified in the butyrate and 51,347 in control. From these regions, 2,265 DCBS was obtained for the BT vs. CT comparison, comprising ~90% of induced sites. Most of the butyrate DCBS were in distal intergenic regions, showing a potential role as insulators. Gene ontology enrichment showed crucial GO terms for the induced DCBS, mainly related to cellular proliferation, cell adhesion, and growth regulation. Interestingly, the ECM-receptor interaction pathway was observed for the induced DCBS. Motif enrichment analysis further identified transcription factors in the induced and repressed DCBS, including CTCF, BORIS, TGIF2, and ZIC3. When DCBS was integrated with RNA-seq data, putative genes were identified for the repressed DCBS, including GATA4. Our study revealed promising candidate genes in bovine cells by a butyrate-induced condition that might be related to the regulation of rumen development, such as integrins, keratins, and collagens. These results provide a better understanding of the function of butyrate in cattle rumen development and chromatin landscape regulation.