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• W3040365013 abstract "Abstract Background Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. Results Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. Conclusions This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits." @default.
• W3040365013 created "2020-07-10" @default.
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• W3040365013 date "2020-07-06" @default.
• W3040365013 modified "2023-10-13" @default.
• W3040365013 title "Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns" @default.
• W3040365013 cites W1085378696 @default.
• W3040365013 cites W153023584 @default.
• W3040365013 cites W1817858605 @default.
• W3040365013 cites W1821797507 @default.
• W3040365013 cites W1873376748 @default.
• W3040365013 cites W1967574320 @default.
• W3040365013 cites W1973723696 @default.
• W3040365013 cites W1978474225 @default.
• W3040365013 cites W1982615434 @default.
• W3040365013 cites W1984562049 @default.
• W3040365013 cites W1986849101 @default.
• W3040365013 cites W1998271864 @default.
• W3040365013 cites W1998782141 @default.
• W3040365013 cites W2005643112 @default.
• W3040365013 cites W2014852291 @default.
• W3040365013 cites W2024848067 @default.
• W3040365013 cites W2025785494 @default.
• W3040365013 cites W2026077982 @default.
• W3040365013 cites W2026343134 @default.
• W3040365013 cites W2035746042 @default.
• W3040365013 cites W2037818631 @default.
• W3040365013 cites W2043805433 @default.
• W3040365013 cites W2045960652 @default.
• W3040365013 cites W2051288343 @default.
• W3040365013 cites W2059099579 @default.
• W3040365013 cites W2065487187 @default.
• W3040365013 cites W2069859329 @default.
• W3040365013 cites W2077053535 @default.
• W3040365013 cites W2077248943 @default.
• W3040365013 cites W2078498092 @default.
• W3040365013 cites W2084118479 @default.
• W3040365013 cites W2094722357 @default.
• W3040365013 cites W2095903180 @default.
• W3040365013 cites W2102868331 @default.
• W3040365013 cites W2104146295 @default.
• W3040365013 cites W2109340786 @default.
• W3040365013 cites W2114912562 @default.
• W3040365013 cites W2116463796 @default.
• W3040365013 cites W2121253798 @default.
• W3040365013 cites W2121654623 @default.
• W3040365013 cites W2127192982 @default.
• W3040365013 cites W2127431151 @default.
• W3040365013 cites W2131374955 @default.
• W3040365013 cites W2149206894 @default.
• W3040365013 cites W2152110866 @default.
• W3040365013 cites W2152642144 @default.
• W3040365013 cites W2153250619 @default.
• W3040365013 cites W2157009395 @default.
• W3040365013 cites W2157663132 @default.
• W3040365013 cites W2158519702 @default.
• W3040365013 cites W2159308963 @default.
• W3040365013 cites W2163327652 @default.
• W3040365013 cites W2168909179 @default.
• W3040365013 cites W2170546016 @default.
• W3040365013 cites W2178918065 @default.
• W3040365013 cites W2209288790 @default.
• W3040365013 cites W2275760250 @default.
• W3040365013 cites W2279483750 @default.
• W3040365013 cites W2529256946 @default.
• W3040365013 cites W2605303967 @default.
• W3040365013 cites W2769101421 @default.
• W3040365013 cites W2779335077 @default.
• W3040365013 cites W2797436707 @default.
• W3040365013 cites W2894501644 @default.
• W3040365013 cites W2917516255 @default.
• W3040365013 cites W2947153047 @default.
• W3040365013 cites W2952001873 @default.
• W3040365013 cites W2977265011 @default.
• W3040365013 cites W2981104463 @default.
• W3040365013 cites W2987733442 @default.
• W3040365013 cites W3000247917 @default.
• W3040365013 cites W3009615227 @default.
• W3040365013 cites W3011183076 @default.
• W3040365013 cites W3027341723 @default.
• W3040365013 cites W3040365013 @default.
• W3040365013 doi "https://doi.org/10.1186/s12915-020-00793-5" @default.
• W3040365013 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7339546" @default.
• W3040365013 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/32631327" @default.
• W3040365013 hasPublicationYear "2020" @default.

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