CTCF Loop Anchors Disrupt MYC Enhancer-Promoter Interactions
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Solution Overview
Problem
Current understanding of enhancer-promoter interactions is limited, particularly regarding the mechanisms that ensure specific enhancers interact with specific promoters, and how these interactions are exploited in cancer cells to facilitate oncogenic expression of genes like MYC.
Innovation Solution
The discovery of conserved CTCF-bound sites at promoters that facilitate contacts with diverse cell-type specific enhancers, and the use of CRISPR-mediated deletion and targeted methylation to disrupt these interactions, particularly at the MYC enhancer-docking site, to reduce CTCF binding and super-enhancer interaction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Object-affected harmful factors
If CRISPR-mediated deletion is used to disrupt CTCF binding sites, then MYC gene expression and tumor cell proliferation are reduced, but the complexity of the therapeutic approach increases
Solution Approach 1:
The patent segments the therapeutic approach into distinct components: CRISPR-Cas9 system for genomic editing, methylation agents for epigenetic modification, and delivery vectors for targeted therapy. This segmentation allows each component to be optimized independently while working together to disrupt CTCF binding sites and reduce MYC expression.
Solution Approach 2:
The patent uses intermediaries such as guide RNAs that mediate between the CRISPR-Cas9 system and the target CTCF binding sites, and methylation agents that mediate between the delivery system and the DNA methylation modification. These intermediaries simplify the overall therapeutic approach by enabling precise and controllable disruption of enhancer-promoter interactions.
2Object-affected harmful factors
If targeted methylation is used to disrupt enhancer-promoter interactions, then CTCF binding and super-enhancer interaction are reduced, but the specificity and precision requirements increase
Solution Approach 1:
The patent applies local quality by using sequence-specific methylation agents that can distinguish between methylated and unmethylated cytosines at specific locations. The methylation activity is localized to the precise CTCF binding sites within the enhancer regions, allowing disruption of enhancer-promoter interactions without affecting other genomic regions. This local specificity is achieved through the combination of guide RNA targeting and sequence-specific methylation chemistry.
Data Source
AI summary
Disclosed are methods of altering expression of a gene with a promoter region CTCF binding site. Also disclosed are compositions and methods useful for treating a disease or condition involving over-expression or under-expression of a gene with a promoter region CTCF binding site. Further disclosed are cells and non-human animals with modified a promoter region CTCF binding site, as well as methods for screening for compounds that can modify the expression of a gene with a promoter region CTCF binding site.