Genetic regulation of gene expression across multiple tissues in chickens

文献类型： 外文期刊

第一作者： Guan, Dailu

作者： Guan, Dailu;Wang, Ying;Zhou, Huaijun;Bai, Zhonghao;Zhu, Di;Li, Houcheng;Buitenhuis, Albert Johannes;Sahana, Goutam;Lund, Mogens Sando;Fang, Lingzhao;Zhu, Xiaoning;Zhu, Di;Wang, Yuzhe;Hu, Xiaoxiang;Zhong, Conghao;Lan, Fangren;Li, Xiaochang;Sun, Congjiao;Yang, Ning;Zhong, Conghao;Lan, Fangren;Li, Xiaochang;Sun, Congjiao;Yang, Ning;Hou, Yali;Pan, Zhangyuan;Si, Wei;Diao, Shuqi;Gao, Yahui;Teng, Jinyan;Xu, Zhiting;Lin, Qing;Li, Zhenhui;Nie, Qinghua;Zhang, Xiquan;Zhang, Zhe;Yao, Yuelin;Yao, Yuelin;Zhao, Bingru;Gao, Yahui;Liu, George E.;Gao, Yahui;Zou, Dong;Wang, Ruizhen;Xu, Tianyi;Zhang, Zhang;Zou, Dong;Wang, Ruizhen;Xu, Tianyi;Zhang, Zhang;Wang, Ruizhen;Zhang, Zhang;Yin, Hongwei;Shi, Shourong;Shao, Dan;Degalez, Fabien;Lagarrigue, Sandrine;Wang, Mingshan;Peng, Minsheng;Wang, Mingshan;Peng, Minsheng;Rocha, Dominique;Charles, Mathieu;Smith, Jacqueline;Watson, Kellie;Warren, Wesley;Frantz, Laurent;Frantz, Laurent;Larson, Greger;Lamont, Susan J.;Si, Wei;Zhao, Xin;Li, Bingjie;Zhang, Haihan;Luo, Chenglong;Shu, Dingming;Qu, Hao;Luo, Wei;Li, Zhenhui;Nie, Qinghua;Zhang, Xiquan;Li, Zhenhui;Nie, Qinghua;Zhang, Xiquan;Xiang, Ruidong;Xiang, Ruidong;Xiang, Ruidong;Liu, Shuli;Cheng, Hans

作者机构：

期刊名称：NATURE GENETICS （ 影响因子：29.0； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2025 年 57 卷 5 期

页码：

收录情况： SCI

摘要： The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3 '-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits.

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