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. 2022 Aug 13;23(16):9070.
doi: 10.3390/ijms23169070.

Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning

Clarissa Boschiero  1 , Yahui Gao  1   2 , Ransom L Baldwin 6th  1 , Li Ma  2 , Cong-Jun Li  1 , George E Liu  1
Affiliations

Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning

Clarissa Boschiero et al. Int J Mol Sci. .

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. Studies evaluating rumen development in calves are vital to identify genetic mechanisms affected by weaning. 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) and 39,891 for after weaning (AW). Then, 7401 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. 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 TGFβ. 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 TGFβ, Integrin-linked kinase, and Integrin signaling. 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 TGFβ, integrins, keratins, and SMADs. The information generated in this preliminary study provides new insights into bovine genome regulation and chromatin landscape.

Keywords: CTCF; ChIP-seq; cattle; epithelial tissue; regulatory elements; rumen development; weaning.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
(A) Annotation of induced and repressed differentially CTCF-binding sites (DCBS) after weaning. (B) Distribution of the induced and repressed DCBS after weaning relative to TSS.
Figure 2
Figure 2
GO enrichment results for the induced (A) and repressed (B) differentially CTCF-binding sites after weaning. The top 30 hits of GO terms are shown in this figure. Biological processes are ranked according to the fold enrichment values. Bubble colors represent the p-value of the False Discovery Rate (FDR). The most significant processes are highlighted in red, and the less significant processes are highlighted in blue according to log10 (FDR) values. Bubble sizes indicate the number of genes. Blue arrows indicate GO terms present in both induced and repressed sites.
Figure 3
Figure 3
GO enrichment analysis for the induced (A) and repressed (B) differentially CTCF-binding sites after weaning. The top 30 hits of GO terms are shown in this figure. Cellular components are ranked according to the fold enrichment values. Bubble colors represent the p-value of the false discovery rate (FDR). The most significant processes are highlighted in red, and the less significant processes are highlighted in blue according to log10 (FDR) values. Bubble sizes indicate the number of genes. Blue arrows indicate GO terms present in both induced and repressed sites.
Figure 4
Figure 4
KEGG gastric acid secretion pathway obtained from the induced differentially CTCF-binding sites (DCBS). Genes from the induced DCBS are highlighted in red.
Figure 5
Figure 5
KEGG TGF-β signaling pathway obtained from the repressed differentially CTCF-binding sites (DCBS). Genes from the repressed DCBS are highlighted in red.
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