Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

Xiao-Ning Zhu; Yu-Zhe Wang; Chong Li; Han-Yu Wu; Ran Zhang; Xiao-Xiang Hu

doi:10.24272/j.issn.2095-8137.2022.228

Volume 44 Issue 1

Jan. 2023

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Article Navigation > Zoological Research > 2023 > 44(1): 53-62

Xiao-Ning Zhu, Yu-Zhe Wang, Chong Li, Han-Yu Wu, Ran Zhang, Xiao-Xiang Hu. Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits. Zoological Research, 2023, 44(1): 53-62. doi: 10.24272/j.issn.2095-8137.2022.228

Citation:

Xiao-Ning Zhu, Yu-Zhe Wang, Chong Li, Han-Yu Wu, Ran Zhang, Xiao-Xiang Hu. Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits. Zoological Research, 2023, 44(1): 53-62. doi: 10.24272/j.issn.2095-8137.2022.228

Citation:

Xiao-Ning Zhu, Yu-Zhe Wang, Chong Li, Han-Yu Wu, Ran Zhang, Xiao-Xiang Hu. Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits. Zoological Research, 2023, 44(1): 53-62. doi: 10.24272/j.issn.2095-8137.2022.228

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Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

doi: 10.24272/j.issn.2095-8137.2022.228

Xiao-Ning Zhu¹,
Yu-Zhe Wang^{1, 2
,
,},
Chong Li¹,
Han-Yu Wu^{1, 2},
Ran Zhang¹,
Xiao-Xiang Hu^{1, 2
,
,}

1.
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
2.
National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China

All new sequence reads were deposited in the National Center for Biotechnology Information (NCBI) sequence read archive (SRA) under BioProjectID PRJNA847569, in the Genome Sequence Archive under Accession No. CRA008349, and in the Science Data Bank under DOI: 10.57760/sciencedb.02970. All data generated in this study are available within the article and its Supplementary Data files.
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
Y.Z.W. and X.X.H. conceived and designed the study and conducted the primary analyses. X.N.Z. collected samples and performed the experiments. C.L. carried out experimental verification. X.X.H., H.Y.W., and R.Z. helped analyze and interpret the data. Y.Z.W. wrote the initial manuscript. X.N.Z. and X.X.H. were responsible for statistical analyses and manuscript revision. All authors read and approved the final version of the manuscript.

Funds: This study was supported by the National Natural Science Foundation of China (U2002205, 32272862)

More Information

Corresponding author: E-mail: yuzhe891@cau.edu.cn; huxx@cau.edu.cn
Received Date: 2022-08-29
Accepted Date: 2022-10-26

Published Online: 2022-10-26

Publish Date: 2023-01-18

Abstract

Abstract

The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However, epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described. The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50 796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L (active in the duodenum), RCBTB1 (muscle and liver), and novel long non-coding RNA ENSGALG00000053256 (bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.
- Chicken,
- Chromatin accessibility atlas,
- ATAC-seq,
- Tissue-specific OCRs,
- GWAS,
- Growth traits

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References(54)

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