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Haplotype-resolved 3D chromatin architecture of the hybrid pig.
Lin, Yu; Li, Jing; Gu, Yiren; Jin, Long; Bai, Jingyi; Zhang, Jiaman; Wang, Yujie; Liu, Pengliang; Long, Keren; He, Mengnan; Li, Diyan; Liu, Can; Han, Ziyin; Zhang, Yu; Li, Xiaokai; Zeng, Bo; Lu, Lu; Kong, Fanli; Sun, Ying; Fan, Yongliang; Wang, Xun; Wang, Tao; Jiang, An'an; Ma, Jideng; Shen, Linyuan; Zhu, Li; Jiang, Yanzhi; Tang, Guoqing; Fan, Xiaolan; Liu, Qingyou; Li, Hua; Wang, Jinyong; Chen, Li; Ge, Liangpeng; Li, Xuewei; Tang, Qianzi; Li, Mingzhou.
Affiliation
  • Lin Y; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Li J; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; lijing_2020@sicau.edu.cn tangqianzi@sicau.edu.cn mingzhou.li@sicau.edu.cn.
  • Gu Y; College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.
  • Jin L; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China.
  • Bai J; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Zhang J; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Wang Y; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Liu P; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Long K; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • He M; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Li D; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Liu C; School of Pharmacy, Chengdu University, Chengdu 610106, China.
  • Han Z; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Zhang Y; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Li X; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Zeng B; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Lu L; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Kong F; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Sun Y; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Fan Y; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Wang X; Institute of Geriatric Health, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China.
  • Wang T; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Jiang A; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Ma J; School of Pharmacy, Chengdu University, Chengdu 610106, China.
  • Shen L; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Zhu L; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Jiang Y; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Tang G; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Fan X; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Liu Q; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Li H; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
  • Wang J; Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China.
  • Chen L; Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China.
  • Ge L; Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China.
  • Li X; National Center of Technology Innovation for Pigs, Chongqing 402460, China.
  • Tang Q; Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China.
  • Li M; National Center of Technology Innovation for Pigs, Chongqing 402460, China.
Genome Res ; 34(2): 310-325, 2024 03 20.
Article in En | MEDLINE | ID: mdl-38479837
ABSTRACT
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Chromatin / Chromosomes Limits: Animals Language: En Journal: Genome Res Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2024 Document type: Article Affiliation country: China
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Chromatin / Chromosomes Limits: Animals Language: En Journal: Genome Res Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2024 Document type: Article Affiliation country: China