Profiling the immune epigenome across global cattle breeds
Background Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences betw...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/130526 |
| _version_ | 1855521067687215104 |
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| author | Powell, J. Talenti, A. Fisch, A. Hemmink, Johanneke D. Paxton, E. Toye, Philip G. Santos, I. Ferreira, B.R. Connelley, T.K. Morrison, Liam J. Prendergast, J.G.D. |
| author_browse | Connelley, T.K. Ferreira, B.R. Fisch, A. Hemmink, Johanneke D. Morrison, Liam J. Paxton, E. Powell, J. Prendergast, J.G.D. Santos, I. Talenti, A. Toye, Philip G. |
| author_facet | Powell, J. Talenti, A. Fisch, A. Hemmink, Johanneke D. Paxton, E. Toye, Philip G. Santos, I. Ferreira, B.R. Connelley, T.K. Morrison, Liam J. Prendergast, J.G.D. |
| author_sort | Powell, J. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences between breeds, variation at the epigenetic and chromatin levels remains poorly characterized. Here, we generate, sequence and analyse over 150 libraries at base-pair resolution to explore the dynamics of DNA methylation and chromatin accessibility of the bovine immune system across three distinct cattle lineages.
Results
We find extensive epigenetic divergence between the taurine and indicine cattle breeds across immune cell types, which is linked to the levels of local DNA sequence divergence between the two cattle sub-species. The unique cell type profiles enable the deconvolution of complex cellular mixtures using digital cytometry approaches. Finally, we show distinct sub-categories of CpG islands based on their chromatin and methylation profiles that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states.
Conclusions
Our study provides a comprehensive resource of DNA methylation, chromatin accessibility and RNA expression profiles of three diverse cattle populations. The findings have important implications, from understanding how genetic editing across breeds, and consequently regulatory backgrounds, may have distinct impacts to designing effective cattle epigenome-wide association studies in non-European breeds. |
| format | Journal Article |
| id | CGSpace130526 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1305262024-01-12T10:00:54Z Profiling the immune epigenome across global cattle breeds Powell, J. Talenti, A. Fisch, A. Hemmink, Johanneke D. Paxton, E. Toye, Philip G. Santos, I. Ferreira, B.R. Connelley, T.K. Morrison, Liam J. Prendergast, J.G.D. cattle immunology genetics Background Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences between breeds, variation at the epigenetic and chromatin levels remains poorly characterized. Here, we generate, sequence and analyse over 150 libraries at base-pair resolution to explore the dynamics of DNA methylation and chromatin accessibility of the bovine immune system across three distinct cattle lineages. Results We find extensive epigenetic divergence between the taurine and indicine cattle breeds across immune cell types, which is linked to the levels of local DNA sequence divergence between the two cattle sub-species. The unique cell type profiles enable the deconvolution of complex cellular mixtures using digital cytometry approaches. Finally, we show distinct sub-categories of CpG islands based on their chromatin and methylation profiles that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states. Conclusions Our study provides a comprehensive resource of DNA methylation, chromatin accessibility and RNA expression profiles of three diverse cattle populations. The findings have important implications, from understanding how genetic editing across breeds, and consequently regulatory backgrounds, may have distinct impacts to designing effective cattle epigenome-wide association studies in non-European breeds. 2023-05-22 2023-05-30T12:28:10Z 2023-05-30T12:28:10Z Journal Article https://hdl.handle.net/10568/130526 en Open Access Springer Powell, J., Talenti, A., Fisch, A., Hemmink, J.D., Paxton, E., Toye, P., Santos, I., Ferreira, B.R., Connelley, T.K., Morrison, L.J. and Prendergast, J.G.D. 2023. Profiling the immune epigenome across global cattle breeds. Genome Biology 24: 127. |
| spellingShingle | cattle immunology genetics Powell, J. Talenti, A. Fisch, A. Hemmink, Johanneke D. Paxton, E. Toye, Philip G. Santos, I. Ferreira, B.R. Connelley, T.K. Morrison, Liam J. Prendergast, J.G.D. Profiling the immune epigenome across global cattle breeds |
| title | Profiling the immune epigenome across global cattle breeds |
| title_full | Profiling the immune epigenome across global cattle breeds |
| title_fullStr | Profiling the immune epigenome across global cattle breeds |
| title_full_unstemmed | Profiling the immune epigenome across global cattle breeds |
| title_short | Profiling the immune epigenome across global cattle breeds |
| title_sort | profiling the immune epigenome across global cattle breeds |
| topic | cattle immunology genetics |
| url | https://hdl.handle.net/10568/130526 |
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