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Related Experiment Video

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Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning.

Clarissa Boschiero1, Yahui Gao1,2, Ransom L Baldwin1

  • 1Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA.

International Journal of Molecular Sciences
|August 26, 2022
PubMed
Summary

Weaning calves undergo significant rumen development, with CTCF-binding sites playing a key role in regulating gene expression. This study identified differentially CTCF-binding sites (DCBS) in rumen tissue, revealing potential target genes crucial for bovine rumen development.

Keywords:
CTCFChIP-seqcattleepithelial tissueregulatory elementsrumen developmentweaning

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Area of Science:

  • Genomics and Epigenetics
  • Animal Science and Ruminant Physiology
  • Molecular Biology and Gene Regulation

Background:

  • Calf weaning involves major rumen structural changes driven by diet.
  • Understanding genetic mechanisms of rumen development is crucial for calf health.
  • CTCF-binding sites (CBS) are key regulators of genome architecture and gene expression.

Purpose of the Study:

  • To perform a genome-wide characterization of CTCF-binding sites (CBS) and differentially CTCF-binding sites (DCBS) in bovine rumen tissue during the weaning transition.
  • To uncover regulatory elements and candidate genes involved in rumen epithelial development.
  • To provide insights into the chromatin landscape and bovine genome regulation.

Main Methods:

  • Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify CTCF peaks in rumen tissue before (BW) and after (AW) weaning.
  • Differential binding site analysis was performed to identify DCBS between AW and BW.
  • Gene Ontology (GO) and KEGG pathway enrichment analyses were conducted on DCBS.
  • Integration with RNA-sequencing data identified putative target genes.

Main Results:

  • A total of 67,280 CTCF peaks (BW) and 39,891 (AW) were identified.
  • 7401 DCBS were identified, with most located in distal intergenic regions, suggesting roles as insulators.
  • Enrichment analyses revealed DCBS are involved in cellular growth, differentiation, and digestive tract morphogenesis.
  • Integration with RNA-seq data identified 36 putative target genes for repressed DCBS, including KRT84, COL9A2, and AJM1.

Conclusions:

  • This study provides the first genome-wide characterization of DCBS in cattle rumen tissue during weaning.
  • Identified DCBS and candidate genes (e.g., TGFβ, integrins, keratins, SMADs) offer new insights into rumen development regulation.
  • The findings contribute to understanding bovine genome regulation and chromatin dynamics during a critical developmental transition.