Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells
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...
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MDPI AG
2022-08-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/12/9/1177 |
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| author | Clarissa Boschiero Yahui Gao Ransom L. Baldwin Li Ma Cong-jun Li George E. Liu |
| author_facet | Clarissa Boschiero Yahui Gao Ransom L. Baldwin Li Ma Cong-jun Li George E. Liu |
| author_sort | Clarissa Boschiero |
| collection | DOAJ |
| description | 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 the control. From these regions, 2265 DCBS were obtained for the butyrate vs. control 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 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, including CTCF, BORIS, TGIF2, and ZIC3. When DCBS was integrated with RNA-seq data, putative genes were identified for the repressed DCBS, including <i>GATA4</i>. 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. |
| first_indexed | 2024-03-10T00:37:18Z |
| format | Article |
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| language | English |
| last_indexed | 2024-03-10T00:37:18Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-68f3983626eb4503891645cdc6a410b82023-11-23T15:14:10ZengMDPI AGBiomolecules2218-273X2022-08-01129117710.3390/biom12091177Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle CellsClarissa Boschiero0Yahui Gao1Ransom L. Baldwin2Li Ma3Cong-jun Li4George E. Liu5Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USAAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USAAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USADepartment of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USAAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USAAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USAButyrate 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 the control. From these regions, 2265 DCBS were obtained for the butyrate vs. control 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 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, including CTCF, BORIS, TGIF2, and ZIC3. When DCBS was integrated with RNA-seq data, putative genes were identified for the repressed DCBS, including <i>GATA4</i>. 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.https://www.mdpi.com/2218-273X/12/9/1177CTCFcattlebutyratedifferentially CTCF-binding sitesMDBK cells |
| spellingShingle | Clarissa Boschiero Yahui Gao Ransom L. Baldwin Li Ma Cong-jun Li George E. Liu Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells Biomolecules CTCF cattle butyrate differentially CTCF-binding sites MDBK cells |
| title | Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells |
| title_full | Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells |
| title_fullStr | Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells |
| title_full_unstemmed | Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells |
| title_short | Butyrate Induces Modifications of the CTCF-Binding Landscape in Cattle Cells |
| title_sort | butyrate induces modifications of the ctcf binding landscape in cattle cells |
| topic | CTCF cattle butyrate differentially CTCF-binding sites MDBK cells |
| url | https://www.mdpi.com/2218-273X/12/9/1177 |
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