CRISPR-FOIL: A Programmable CRISPR Tool to Engineer and Illuminate Chromatin Folding in Live Human Cells

Abstract

Chromatin organization plays a critical role in regulating gene expression. Chromatin compaction represses gene expression by physically restricting the access of the transcriptional machinery to DNA, while spatial proximity between enhancers and promoters, often mediated by chromatin loops, is essential for gene activation. To investigate the regulatory mechanisms underlying loop formation and chromatin compaction, as well as their effects on gene expression, we developed CRISPR-FOIL (utilizing CRISPR to FOld and ILluminate chromosomal DNA), a novel programmable platform for engineering chromatin loops and inducing chromatin compaction in live cells. CRISPR-FOIL anchors pairs of genomic loci in proximity by engineered single-guide RNAs (sgRNAs), resulting in an artificial chromatin loop. The fused two CRISPR-Sirius gRNAs enable genomic loci to be visualized through fluorescent RNA coat proteins in various colors. In addition, multiple CRISPR-FOIL complexes can act cooperatively to drive chromatin compaction. These results establish CRISPR-FOIL as a powerful tool for engineering chromatin organization in live cells and highlight its potential as a therapeutic platform for gene regulation and disease control.