Chromatin Loop Engineering via CTCF Motif Targeting
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Solution Overview
Problem
Current methods lack the capability to effectively alter chromatin three-dimensional (3D) structure in cells, particularly for altering chromatin loop formation and structure, which is crucial for regulating gene expression and treating diseases like cancer or genetic disorders, and existing techniques are limited in assessing the spatial co-localization of multiple genomic loci.
Innovation Solution
The method involves interfering with the function of CTCF and cohesin during chromatin extrusion to engineer chromatin loops and contact domains by targeting CTCF or cohesin binding motifs, using CRISPR/Cas systems, zinc finger proteins, or other sequence-specific DNA targeting agents to introduce, remove, or modify chromatin loops, allowing for the creation of new loops or domains.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If existing techniques are used to assess chromatin structure, then basic chromatin organization can be observed, but spatial co-localization of multiple genomic loci cannot be effectively assessed
Solution Approach 1:
The patent transitions from traditional 2D chromatin conformation capture to 3D spatial mapping by introducing a third dimension through sequential imaging of multiple genomic loci. This enables precise assessment of spatial co-localization in three-dimensional nuclear space, resolving the limitation of existing techniques that could only observe basic chromatin organization without accurate multi-locus spatial relationships
2Adaptability or versatility
If chromatin loop formation is not altered, then natural gene expression patterns are maintained, but the ability to treat diseases like cancer or genetic disorders is limited
Solution Approach 1:
The patent applies parameter changes by modifying chromatin architectural parameters through targeted disruption or formation of chromatin loops using engineered proteins. This allows dynamic control of chromatin 3D structure to alter gene expression patterns, enabling disease treatment while maintaining controllable stability through reversible or conditional modifications rather than permanent structural changes
3Manufacturing precision
If chromatin loops are engineered to control gene expression, then disease treatment capability is improved, but precision and control over chromatin 3D structure are currently lacking
Solution Approach 1:
The patent segments chromatin architecture into discrete, addressable units by targeting specific chromatin loops and domains individually. This segmentation enables precise engineering of specific chromatin structures without affecting global chromatin organization, allowing controlled modification of gene expression in specific genomic regions while maintaining overall chromatin integrity and function
Data Source
AI summary
Chromatin 3D structure modulating agents in the context of the present invention are intended to interfere or manipulate the function of loop anchor motifs, such as CTCF motifs. In certain example embodiments, the present invention may block formation of an loop anchor or chromatin domain or induce formation of a loop anchor or chromatin domain at a targeted genomic location. For instance, a loop anchor motif can be altered, such as by mutating (including inverting) a binding motif so as to remove such a motif, or by adding new binding motifs in new locations within a loop domain, so as to reduce the size of an existing loop, so as to modify the size of an existing loop, or combinations thereof. Alternatively, the chromatin 3D structure modulating agent may bind a target region and mask a loop anchor motif, thereby preventing a loop anchor or chromatin domain from forming. The chromatin 3D structure modulating agent may bind a target region and cause a loop anchor of chromatin domain to form.