首页|CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

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The genetic information coded in DNA leads to trait innovation via a gene regulatory net-work(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ru-minant multi-chambered stomach innovation.We generated paired expression and chromatin acces-sibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminant-specific conserved non-coding elements(active-RSCNEs).To interpret the function of these active-RSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to under-standing how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

Trait innovationGene regulatory networkConserved non-coding elementToolkit transcription factorRuminant

Xiangyu Pan、Zhaoxia Ma、Xinqi Sun、Hui Li、Tingting Zhang、Chen Zhao、Nini Wang、Rasmus Heller、Wing Hung Wong、Wen Wang、Yu Jiang、Yong Wang

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Key Laboratory of Animal Genetics,Breeding and Reproduction of Shaanxi Province,College of Animal Science and Technology,Northwest A&F University,Yangling 712100,China

Department of Medical Research,Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences,Guangzhou 510080,China

Guangdong Cardiovascular Institute,Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences,Guangzhou 510080,China

Academy of Mathematics and Systems Science,Chinese Academy of Sciences,Beijing 100190,China

School of Mathematics,University of Chinese Academy of Sciences,Beijing 100049,China

State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,College of Animal Science and Technology,Guangxi University,Nanning 530005,China

Section for Computational and RNA Biology,Department of Biology,University of Copenhagen,Copenhagen DK-2100,Denmark

Department of Statistics,Department of Biomedical Data Science,Bio-X Program,Stanford University,Stanford,CA 94305,USA

Center for Ecological and Environmental Sciences,Northwestern Polytechnical University,Xi'an 710072,China

State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China

Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming 650223,China

Key Laboratory of Systems Health Science of Zhejiang Province,School of Life Science,Hangzhou Institute for Advanced Study,University of Chinese Academy of Sciences,Hangzhou 310024,China

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National Key R&D Program of ChinaStrategic Priority Research Program of the Chinese Academy of SciencesCAS Project for Young Scientists in Basic ResearchNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaNational Thousand Youth Talents Plan,and the CAS"Light of West China"Program,China

2020YFA0712402XDPB17YSBR-07712025107118714631168810161621003xbzgzdsys-201913

2023

10.1016/j.gpb.2022.11.007

基因组蛋白质组与生物信息学报(英文版)
中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报(英文版)

CSTPCDCSCD
影响因子：0.495
ISSN：1672-0229
年,卷(期)：2023.21(3)
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