Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations
文献类型： 外文期刊
作者： Fang, Lingzhao 1 ; Liu, Shuli 1 ; Liu, Mei 1 ; Kang, Xiaolong 1 ; Lin, Shudai 1 ; Li, Bingjie 1 ; Connor, Erin E. 1 ; Bal 1 ;
作者机构： 1.ARS, Anim Genom & Improvement Lab, BARC, USDA, Beltsville, MD 20705 USA
2.Univ Maryland, Dept Anim & Avian Sci, College Pk, MD 20742 USA
3.China Agr Univ, Coll Anim Sci & Technol, Beijing 100193, Peoples R China
4.Northwest A&F Univ, Shaanxi Key Lab Agr Mol Biol, Coll Anim Sci & Technol, Yangling 712100, Shaanxi, Peoples R China
5.Ningxia Univ, Coll Agr, Yinchuan 750021, Peoples R China
6.South China Agr Univ, Coll Anim Sci, Minist Agr, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou 510642, Guangdong, Peoples R China
7.South China Agr Univ, Coll Anim Sci, Minist Agr, Key Lab Chicken Genet Breeding & Reprod, Guangzhou 510642, Guangdong, Peoples R China
8.Univ Edinburgh, Roslin Inst, Edinburgh EH4 2XU, Midlothian, Scotland
关键词： Cattle genome; Functional annotation; Chromatin states; Butyrate; Rumen development
期刊名称：BMC BIOLOGY （ 影响因子：7.431； 五年影响因子：8.182 ）
ISSN：
年卷期： 2019 年 17 卷 1 期
页码：
收录情况： SCI
摘要： Background The functional annotation of genomes, including chromatin accessibility and modifications, is important for understanding and effectively utilizing the increased amount of genome sequences reported. However, while such annotation has been well explored in a diverse set of tissues and cell types in human and model organisms, relatively little data are available for livestock genomes, hindering our understanding of complex trait variation, domestication, and adaptive evolution. Here, we present the first complete global landscape of regulatory elements in cattle and explore the dynamics of chromatin states in rumen epithelial cells induced by the rumen developmental regulator-butyrate. Results We established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle, through genome-wide profiling for six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial primary cells (REPC), rumen tissues, and Madin-Darby bovine kidney epithelial cells (MDBK). We demonstrated that each chromatin state exhibited specific enrichment for sequence ontology, transcription, methylation, trait-associated variants, gene expression-associated variants, selection signatures, and evolutionarily conserved elements, implying distinct biological functions. After butyrate treatments, we observed that the weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states, occurred concomitantly with significant alterations in gene expression and DNA methylation, which was significantly associated with heifer conception rate and stature economic traits. Conclusion Our results demonstrate the crucial role of functional genome annotation for understanding genome regulation, complex trait variation, and adaptive evolution in livestock. Using butyrate to induce the dynamics of the epigenomic landscape, we were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.
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