TY  - JOUR
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
Y1  - 2023/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 247 
EP  - 260 
DO  - 10.1101/gr.277206.122 
VL  - 33 
IS  - 2 
UR  - http://genome.cshlp.org/content/33/2/247.abstract 
N2  - 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. 
ER  -