TY  - JOUR
A1  - Lin, Yu
A1  - Li, Jing
A1  - Gu, Yiren
A1  - Jin, Long
A1  - Bai, Jingyi
A1  - Zhang, Jiaman
A1  - Wang, Yujie
A1  - Liu, Pengliang
A1  - Long, Keren
A1  - He, Mengnan
A1  - Li, Diyan
A1  - Liu, Can
A1  - Han, Ziyin
A1  - Zhang, Yu
A1  - Li, Xiaokai
A1  - Zeng, Bo
A1  - Lu, Lu
A1  - Kong, Fanli
A1  - Sun, Ying
A1  - Fan, Yongliang
A1  - Wang, Xun
A1  - Wang, Tao
A1  - Jiang, An'an
A1  - Ma, Jideng
A1  - Shen, Linyuan
A1  - Zhu, Li
A1  - Jiang, Yanzhi
A1  - Tang, Guoqing
A1  - Fan, Xiaolan
A1  - Liu, Qingyou
A1  - Li, Hua
A1  - Wang, Jinyong
A1  - Chen, Li
A1  - Ge, Liangpeng
A1  - Li, Xuewei
A1  - Tang, Qianzi
A1  - Li, Mingzhou
T1  - Haplotype-resolved 3D chromatin architecture of the hybrid pig
Y1  - 2024/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 310 
EP  - 325 
DO  - 10.1101/gr.278101.123 
VL  - 34 
IS  - 2 
UR  - http://genome.cshlp.org/content/34/2/310.abstract 
N2  - 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. 
ER  -