Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis
Xue, Y.; Yang, Y.; Tian, H.; Quan, H.; Liu, S.; Zhang, L.; Gao, Y. Q.
Show abstract
The three-dimensional (3D) chromatin structure, together with DNA methylation and other epigenetic marks, profoundly affects gene expression and displays abnormal behaviors in cancer cells. We elucidated the chromatin architecture remodeling in carcinogenesis from the perspective of spatial interactions between CGI forest and prairie domains, which are two types of megabase-sized domains defined by different sequence features but show distinct epigenetic and transcriptional patterns. DNA sequence strongly affects chromosome spatial interaction, DNA methylation and gene expression. Globally, forests and prairies show enhanced spatial segregation in cancer cells and such structural changes are accordant with the alteration of CGI interactions and domain boundary insulation, which could affect vital cancer-related properties. As the cancer progresses, a gradual increase of the DNA methylation difference between the two types of DNA domains is also observed for many different types of cancers. These observations are consistent with the change of transcriptional level differences of genes in these two domains, suggesting a highly-connected global structural, epigenetic and transcriptional activity changes in carcinogenesis.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- DORGE: Discovery of Oncogenes and Tumor SuppressoR Genes Using Genetic and Epigenetic Features 95%
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation 94%
- The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA 94%
Similar papers in this journal
- Regulation associated modules reflect 3D genome modularity associated with chromatin activity 97%
- A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb targets 95%
- H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions 94%
Similar papers in this journal
- Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers 96%
- Functional characteristics and computational model of abundant hyperactive loci in the human genome 94%
- Artificially inserted G-quadruplex DNA secondary structures induce long-distance chromatin activation 94%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.