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Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis 认领 引用 被引量：5
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作者 Jie Cheng Xiukai Cao +8 位作者 Xiaogang Wang Jian Wang Binglin Yue Wei Sun Yongzhen Huang Xianyong Lan Gang Ren Chuzhao Lei Hong Chen 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2023年第4期1344-1362,共19页
Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China.Three-dimensional genome structure is confirmed to be an important layer of transcription regulation... Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China.Three-dimensional genome structure is confirmed to be an important layer of transcription regulation.Although genome-wide interaction data of several livestock species have already been produced,the genome structure states and its regulatory rules in cattle muscle are still limited.Results Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle(Bos taurus).We showed that compartments,topologically associating domains(TADs),and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development.Furthermore,we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps.We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.Conclusions Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology,which will benefit the progress of genetic improvement of beef cattle. 展开更多
关键词 Cattle Cis-regulatory elements Muscle Selection sweep 3D genome
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3D genome organization and its study in livestock breeding 认领 引用 被引量：1
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作者 Jie Cheng Xiukai Cao +7 位作者 Shengxuan Wang Jiaqiang Zhang Binglin Yue Xiaoyan Zhang Yongzhen Huang Xianyong Lan Gang Ren Hong Chen 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2024年第1期39-58,共20页
Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associati... Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding. 展开更多
关键词 3D genome organization 3D genomic methodology regulatory mechanisms muscle development livestock breeding
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An atlas of CNV maps in cattle, goat and sheep 认领 引用 被引量：11
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作者 Yongzhen Huang Yunjia Li +21 位作者 Xihong Wang Jiantao Yu Yudong Cai Zhuqing Zheng Ran Li Shunjin Zhang Ningbo Chen Hojjat Asadollahpour Nanaei Quratulain Hanif Qiuming Chen Weiwei Fu Chao Li Xiukai Cao Guangxian Zhou Shudong Liu Sangang He Wenrong Li Yulin Chen Hong Chen Chuzhao Lei Mingjun Liu Yu Jiang 《Science China(Life Sciences)》 SCIE CAS CSCD 2021年第10期1747-1764,共18页
Copy number variation(CNV)is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans,animals and plants.However,the mechanisms underlyi... Copy number variation(CNV)is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans,animals and plants.However,the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown.Here,we generated CNV region(CNVR)datasets which were diverged or shared among cattle,goat,and sheep,including 886 individuals from 171 diverse populations.Using 9 environmental factors for genome-wide association study(GWAS),we identified a series of candidate CNVRs,including genes relating to immunity,tick resistance,multi-drug resistance,and muscle development.The number of CNVRs shared between species is significantly higher than expected(P<0.00001),and these CNVRs may be more persist than the single nucleotide polymorphisms(SNPs)shared between species.We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes.This study provides the evidence that balancing selection might be more common in mammals than previously considered,and might play an important role in the daily activities of these ruminant species. 展开更多
关键词 copy number variation species-shared balancing selection ruminant livestock
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