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Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning

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 gen...

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Autores principales: Boschiero, Clarissa, Gao, Yahui, Baldwin, Ransom L., Ma, Li, Li, Cong-jun, Liu, George E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9408924/
https://www.ncbi.nlm.nih.gov/pubmed/36012336
http://dx.doi.org/10.3390/ijms23169070
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author Boschiero, Clarissa
Gao, Yahui
Baldwin, Ransom L.
Ma, Li
Li, Cong-jun
Liu, George E.
author_facet Boschiero, Clarissa
Gao, Yahui
Baldwin, Ransom L.
Ma, Li
Li, Cong-jun
Liu, George E.
author_sort Boschiero, Clarissa
collection PubMed
description 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.
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spelling pubmed-94089242022-08-26 Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning Boschiero, Clarissa Gao, Yahui Baldwin, Ransom L. Ma, Li Li, Cong-jun Liu, George E. Int J Mol Sci Article 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. MDPI 2022-08-13 /pmc/articles/PMC9408924/ /pubmed/36012336 http://dx.doi.org/10.3390/ijms23169070 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Boschiero, Clarissa
Gao, Yahui
Baldwin, Ransom L.
Ma, Li
Li, Cong-jun
Liu, George E.
Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning
title Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning
title_full Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning
title_fullStr Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning
title_full_unstemmed Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning
title_short Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning
title_sort differentially ctcf-binding sites in cattle rumen tissue during weaning
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9408924/
https://www.ncbi.nlm.nih.gov/pubmed/36012336
http://dx.doi.org/10.3390/ijms23169070
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