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An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics.

Zhangyuan PanYing WangMing-Shan WangYuzhe WangXiaoning ZhuShenwen GuConghao ZhongLiqi AnMingzhu ShanJoana DamasMichelle M HalsteadDai-Lu GuanNares TrakooljulKlaus WimmersYe BiShang WuMary E DelanyXuechen BaiHans H ChengCongjiao SunNing YangXiaoxiang HuHarris A LewinLingzhao FangHuaijun Zhou
Published in: Science advances (2023)
A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements in the chicken genome by integrating 377 genome-wide sequencing datasets from 23 adult tissues. In total, we annotated 1.57 million regulatory elements, representing 15 distinct chromatin states, and predicted about 1.2 million enhancer-gene pairs and 7662 super-enhancers. This functional annotation of the chicken genome should have wide utility on identifying regulatory elements accounting for gene regulation underlying domestication, selection, and complex trait regulation, which we explored. In short, this comprehensive atlas of regulatory elements provides the scientific community with a valuable resource for chicken genetics and genomics.
Keyphrases
  • genome wide
  • transcription factor
  • single cell
  • dna methylation
  • gene expression
  • healthcare
  • young adults
  • mental health
  • copy number
  • oxidative stress
  • dna damage
  • genome wide identification
  • binding protein