RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2024 
FD February 01 
VO 34 
IS 2 
SP 310 
OP 325 
DO 10.1101/gr.278101.123 
UL http://genome.cshlp.org/content/34/2/310.abstract 
AB 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.