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Data from: Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

dataset
posted on 2024-02-13, 13:56 authored by Lingzhao Fang, Shuli Liu, Mei Liu, Xiaolong Kang, Shudai Lin, Bingjie Li, Erin E. Connor, Ransom L. Baldwin, Albert Tenesa, Li Ma, George E. Liu, Cong-jun Li

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: 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.


Resources in this dataset:

Funding

USDA-NIFA: 2013-67015-20951

USDA-NIFA: 2016-67015-24886

USDA-NIFA: 2019-67015-29321

United States - Israel Binational Agricultural Research and Development Fund: US-4997-17

USDA-ARS: 8042-31000-001-00-D

USDA-ARS: 8042-31310-078-00-D

History

Data contact name

Li, Cong-jun

Data contact email

congjun.li@usda.gov

Publisher

BMC Biology

Intended use

To obtain a complete global landscape of regulatory elements in cattle and to explore the dynamics of chromatin states in rumen epithelial cells induced by butyrate (a key regulator for rumen development and an HDAC inhibitor) at early developmental stages. These datasets will serve as a valuable resource for interpreting the biological and genetic datasets in cattle, such as GWAS of diverse complex phenotypes, and thereby benefiting their genomic improvements.

Temporal Extent Start Date

2019-08-16

Theme

  • Not specified

Geographic Coverage

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ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

histones; binding sites; cattle; rumen; epithelium; butyrates; regulatory sequences; genome; genomics; epigenetics; data collection; binding proteins; methylation; acetylation; experimental design; guidelines; metabolism; humans; chromatin; tissues; models; domestication; evolutionary adaptation; epithelial cells; DNA-directed RNA polymerase; DNA; DNA methylation; transcriptome; kidneys; genes; transcription (genetics); heifers; conception rate; nutrient content; phenotype

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Fang, Lingzhao; Liu, Shuli; Liu, Mei; Kang, Xiaolong; Lin, Shudai; Li, Bingjie; Connor, Erin E.; Baldwin, Ransom L.; Tenesa, Albert; Ma, Li; Liu, George E.; Li, Cong-jun (2019). Data from: Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations. BMC Biology.

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