Manipulating complex chromatin folding via CRISPR-guided bioorthogonal chemistry

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Understanding the 3D genome structure and its relationship with nuclear function is crucial.
• Current tools can manipulate single chromatin loops but lack the ability to control multiple loops concurrently.

Purpose of the Study:

• To engineer a novel CRISPR system capable of manipulating multiple chromatin contacts.
• To develop a method for independent and dynamic control of distinct chromatin loops within the same cell.

Main Methods:

• Development of the bioorthogonal reaction-mediated programmable chromatin loop (BPCL) system.
• Utilizing engineered single-guide RNAs and discrete bioorthogonal adaptors for targeted chromatin loop formation.
• Application of the BPCL system to juxtapose pluripotency gene promoters with enhancers.

Main Results:

• The BPCL system successfully manipulated multiple chromatin contacts without cross-talk.
• Independent and dynamic control over different chromatin loop formations was achieved.
• Endogenous expression of pluripotency genes was activated by juxtaposing promoters and enhancers.

Conclusions:

• The BPCL system offers unprecedented precision in engineering multiway chromatin contacts.
• This technology provides a powerful tool for dissecting the complexity and dynamics of chromatin folding.
• BPCL enables novel investigations into the functional implications of 3D genome organization.