Location: Endemic Poultry Viral Diseases ResearchTitle: An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics
|PAN, ZHANGYUAN - University Of California, Davis|
|WANG, YING - University Of California, Davis|
|WANG, MINGSHAN - Kunming Institute Of Botany|
|WANG, ZUZHE - China Agricultural University|
|ZHU, XIAONING - China Agriculture University|
|GU, SHENWEN - University Of California, Davis|
|ZHONG, CONGHAO - China Agriculture University|
|AN, LIQI - University Of California, Davis|
|DAMAS, JOANA - University Of California, Davis|
|HALSTED, MICHELLE - University Of California, Davis|
|ZHOU, HUAIJUN - University Of California, Davis|
Submitted to: Science Advances
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2023
Publication Date: 5/3/2023
Citation: Pan, Z., Wang, Y., Wang, M., Wang, Z., Zhu, X., Gu, S., Zhong, C., An, L., Damas, J., Halsted, M., Cheng, H.H., Zhou, H. 2023. An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. Science Advances. 9:eade1204. https://www.science.org/doi/10.1126/sciadv.ade1204.
Interpretive Summary: Since the advent of whole genome assemblies like in chicken, a primary research focus has been to translate this information. This task has proven to be very challenging especially in identifying what are known as regulatory elements, which control when specific genes are turned on or off in a specific tissue, developmental age, response to an infectious pathogen, etc. In this study, using a variety of genomic screens followed by computational analyses, the most current annotation of the chicken genome was released. There are a number of key findings including which enhancers regulate which gene, how enhancers are implicated in chicken domestication or response to selection for muscle growth or number of eggs produced. In closing, this regulatory element atlas of the chicken genome represents a major advancement for scientists that want to understand chicken biology or evolutionary biology and, more importantly, for the poultry industry, information that can be leverage to more precisely breed for superior chickens.
Technical Abstract: 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.