RT Journal
A1 He, Yueying
A1 Xue, Yue
A1 Wang, Jingyao
A1 Huang, Yupeng
A1 Liu, Lu
A1 Huang, Yanyi
A1 Gao, Yi Qin
T1 Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
JF Genome Research 
JO Genome Research 
YR 2023 
FD August 01 
VO 33 
IS 8 
SP 1354 
OP 1368 
DO 10.1101/gr.277737.123 
UL http://genome.cshlp.org/content/33/8/1354.abstract 
AB The interactome networks at the DNA, RNA, and protein levels are crucial for cellular functions, and the diverse variations of these networks are heavily involved in the establishment of different cell states. We have developed a diffusion-based method, Hi-C to geometry (CTG), to obtain reliable geometric information on the chromatin from Hi-C data. CTG produces a consistent and reproducible framework for the 3D genomic structure and provides a reliable and quantitative understanding of the alterations of genomic structures under different cellular conditions. The genomic structure yielded by CTG serves as an architectural blueprint of the dynamic gene regulatory network, based on which cell-specific correspondence between gene–gene and corresponding protein–protein physical interactions, as well as transcription correlation, is revealed. We also find that gene fusion events are significantly enriched between genes of short CTG distances and are thus close in 3D space. These findings indicate that 3D chromatin structure is at least partially correlated with downstream processes such as transcription, gene regulation, and even regulatory networking through affecting protein–protein interactions.