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

Zhangyuan Pan; Ying Wang; Mingshan Wang; Yuzhe Wang; Xiaoning Zhu; Shenwen Gu; Conghao Zhong; Liqi An; Mingzhu Shan; Joana Damas; Michelle M. Halstead; Dailu Guan; Nares Trakooljul; Klaus Wimmers; Ye Bi; Shang Wu; Mary E. Delany; Xuechen Bai; Hans H. Cheng; Congjiao Sun; Ning Yang; Xiaoxiang Hu; Harris A. Lewin; Lingzhao Fang; Huaijun Zhou

doi:10.1126/sciadv.ade1204

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

Zhangyuan Pan, Ying Wang, Mingshan Wang, Yuzhe Wang, Xiaoning Zhu, Shenwen Gu, Conghao Zhong, Liqi An, Mingzhu Shan, Joana Damas, Michelle M. Halstead, Dailu Guan, Nares Trakooljul, Klaus Wimmers, Ye Bi, Shang Wu, Mary E. Delany, Xuechen Bai, Hans H. Cheng, Congjiao SunNing Yang, Xiaoxiang Hu, Harris A. Lewin, Lingzhao Fang, Huaijun Zhou

Center for Quantitative Genetics and Genomics

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

13 Citations (Scopus)

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.

Original language	English
Article number	eade1204
Journal	Science Advances
Volume	9
Issue	18
Number of pages	14
ISSN	2375-2548
DOIs	https://doi.org/10.1126/sciadv.ade1204
Publication status	Published - May 2023

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Pan, Z., Wang, Y., Wang, M., Wang, Y., Zhu, X., Gu, S., Zhong, C., An, L., Shan, M., Damas, J., Halstead, M. M., Guan, D., Trakooljul, N., Wimmers, K., Bi, Y., Wu, S., Delany, M. E., Bai, X., Cheng, H. H., ... Zhou, H. (2023). An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. Science Advances, 9(18), Article eade1204. https://doi.org/10.1126/sciadv.ade1204

@article{73c0d55c9dac44689c37be2df8db9215,

title = "An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics",

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.",

author = "Zhangyuan Pan and Ying Wang and Mingshan Wang and Yuzhe Wang and Xiaoning Zhu and Shenwen Gu and Conghao Zhong and Liqi An and Mingzhu Shan and Joana Damas and Halstead, {Michelle M.} and Dailu Guan and Nares Trakooljul and Klaus Wimmers and Ye Bi and Shang Wu and Delany, {Mary E.} and Xuechen Bai and Cheng, {Hans H.} and Congjiao Sun and Ning Yang and Xiaoxiang Hu and Lewin, {Harris A.} and Lingzhao Fang and Huaijun Zhou",

year = "2023",

month = may,

doi = "10.1126/sciadv.ade1204",

language = "English",

volume = "9",

journal = "Science Advances",

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number = "18",

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Pan, Z, Wang, Y, Wang, M, Wang, Y, Zhu, X, Gu, S, Zhong, C, An, L, Shan, M, Damas, J, Halstead, MM, Guan, D, Trakooljul, N, Wimmers, K, Bi, Y, Wu, S, Delany, ME, Bai, X, Cheng, HH, Sun, C, Yang, N, Hu, X, Lewin, HA, Fang, L & Zhou, H 2023, 'An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics', Science Advances, vol. 9, no. 18, eade1204. https://doi.org/10.1126/sciadv.ade1204

TY - JOUR

T1 - An atlas of regulatory elements in chicken

T2 - A resource for chicken genetics and genomics

AU - Pan, Zhangyuan

AU - Wang, Ying

AU - Wang, Mingshan

AU - Wang, Yuzhe

AU - Zhu, Xiaoning

AU - Gu, Shenwen

AU - Zhong, Conghao

AU - An, Liqi

AU - Shan, Mingzhu

AU - Damas, Joana

AU - Halstead, Michelle M.

AU - Guan, Dailu

AU - Trakooljul, Nares

AU - Wimmers, Klaus

AU - Bi, Ye

AU - Wu, Shang

AU - Delany, Mary E.

AU - Bai, Xuechen

AU - Cheng, Hans H.

AU - Sun, Congjiao

AU - Yang, Ning

AU - Hu, Xiaoxiang

AU - Lewin, Harris A.

AU - Fang, Lingzhao

AU - Zhou, Huaijun

PY - 2023/5

Y1 - 2023/5

N2 - 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.

AB - 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.

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SN - 2375-2548

VL - 9

JO - Science Advances

JF - Science Advances

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

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