Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer.
3D genome
TADs
cancer
gene regulation
loop
Journal
Frontiers of medicine
ISSN: 2095-0225
Titre abrégé: Front Med
Pays: China
ID NLM: 101549428
Informations de publication
Date de publication:
Feb 2024
Feb 2024
Historique:
received:
14
11
2022
accepted:
05
05
2023
pubmed:
18
9
2023
medline:
18
9
2023
entrez:
18
9
2023
Statut:
ppublish
Résumé
Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer. However, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited. Here, by taking advantage of in situ Hi-C, RNA-sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq), we investigated structural reorganization and functional changes in chromosomal compartments, topologically associated domains (TADs), and CCCTC binding factor (CTCF)-mediated loops in gallbladder cancer (GBC) tissues and cell lines. We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes. Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls. Furthermore, the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial-mesenchymal transition activation were enriched in cancer compared with their control counterparts. Cancer-specific enhancer-promoter loops, which contain multiple transcription factor binding motifs, acted as a central element to regulate aberrant gene expression. Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions. Collectively, our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.
Identifiants
pubmed: 37721643
doi: 10.1007/s11684-023-1008-8
pii: 10.1007/s11684-023-1008-8
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
109-127Informations de copyright
© 2023. Higher Education Press.
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