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The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
- Source :
- Computational and Structural Biotechnology Journal, Vol 19, Iss, Pp 1684-1693 (2021), Computational and Structural Biotechnology Journal
- Publication Year :
- 2021
- Publisher :
- Elsevier BV, 2021.
-
Abstract
- Graphical abstract<br />Highlights • The hierarchical levels of TAD boundaries were tissue- and cell type-specific. • The TAD nesting level of genes in tumors is different from that in normal tissue. • Hierarchical TAD level of genes is related to abnormal transcription and prognosis in cancers.<br />Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a “TAD hierarchical score (TH score)” for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. We demonstrated that the TAD nesting levels of genes in a tumor differ from those in normal tissue. Furthermore, the hierarchical TAD level dynamics were related to transcriptional changes in cancer, and some of the genes in which the hierarchical level was altered were significantly related to the prognosis of cancer patients. Overall, the results of this study suggest that the folding dynamics of TADs are closely related to transcriptional abnormalities in cancers, emphasizing that the function of hierarchical chromatin organization goes beyond simple chromatin packaging efficiency.
- Subjects :
- Biophysics
Normal tissue
Computational biology
Biology
Biochemistry
03 medical and health sciences
Transcriptional regulation
0302 clinical medicine
Hi-C
Structural Biology
Genetics
medicine
TH score
Gene
ComputingMethodologies_COMPUTERGRAPHICS
030304 developmental biology
0303 health sciences
Dynamics (mechanics)
Cancer
medicine.disease
Colorectal cancer
Computer Science Applications
Chromatin
Folding (chemistry)
Hierarchical TAD
030220 oncology & carcinogenesis
Cancers
TP248.13-248.65
Function (biology)
Research Article
Biotechnology
Subjects
Details
- ISSN :
- 20010370
- Volume :
- 19
- Database :
- OpenAIRE
- Journal :
- Computational and Structural Biotechnology Journal
- Accession number :
- edsair.doi.dedup.....ba7d382c8aee5d0ae8db3c40f6a68628