A Split Luciferase Biosensing Platform for Detection and Imaging of Chromatin Loops in Individual Live Cells

Eukaryotic cells regulate higher-order chromatin architecture, gene expression, and gene recombination via compaction of the genome into chromatin loops and topologically associating domains (TADs). While chromatin architecture has been thoroughly characterized for many eukaryotic genomes using cell-destructive techniques such as 3C-based methods, live-cell biosensing tools that can probe three-dimensional chromatin contacts in real-time are lacking. Using a dual dCas9 DNA biosensor based on a split NanoLuc luciferase reporter, we directly detected chromatin loops in live cells using luminescence quantification in a luminometer. We were able to see signal above background ratios of up to 10-fold. In addition, we directly visualized chromatin looping at the MYC TAD in live cells using high-resolution, low light live-cell imaging. Our biosensing platform therefore provides a useful methodology for live-cell, real-time detection of known or novel loops and for monitoring looping dynamics upon alterations in cell state. Overall design: 4C-seq of cell-type specific chromatin loops in WT HCT116 cells, WT K562 cells, HCT116 E7 enhancer deletion cells, and HCT116 RAD21-mAC cells treated with either 1 uM DMSO or 1 uM auxin for 120 min using a non-blind viewpoint centered on the conserved CTCF binding site upstream of the MYC promoter with three replicates per cell type.