RT Journal
A1 Wang, Jingyao
A1 Xue, Yue
A1 He, Yueying
A1 Quan, Hui
A1 Zhang, Jun
A1 Gao, Yi Qin
T1 Characterization of network hierarchy reflects cell state specificity in genome organization
JF Genome Research 
JO Genome Research 
YR 2023 
FD February 01 
VO 33 
IS 2 
SP 247 
OP 260 
DO 10.1101/gr.277206.122 
UL http://genome.cshlp.org/content/33/2/247.abstract 
AB Dynamic chromatin structure acts as the regulator of transcription program in crucial processes including cancer and cell development, but a unified framework for characterizing chromatin structural evolution remains to be established. Here, we performed graph inferences on Hi-C data sets and derived the chromatin contact networks. We discovered significant decreases in information transmission efficiencies in chromatin of colorectal cancer (CRC) and T-cell acute lymphoblastic leukemia (T-ALL) compared to corresponding normal controls through graph statistics. Using network embedding in the Poincaré disk, the hierarchy depths of chromatin from CRC and T-ALL patients were found to be significantly shallower compared to their normal controls. A reverse trend of change in chromatin structure was observed during early embryo development. We found tissue-specific conservation of hierarchy order in chromatin contact networks. Our findings reveal the top-down hierarchy of chromatin organization, which is significantly attenuated in cancer.