# OptoLoop – an optogenetic tool to probe the functional role of genome organization

## TL;DR

OptoLoop is a light-controlled tool that allows researchers to study how genome structure affects gene regulation by creating chromatin loops.

## Contribution

OptoLoop introduces a novel optogenetic system to manipulate chromatin contacts with light, enabling precise study of genome structure-function relationships.

## Key findings

- OptoLoop can bring together distant DNA loci to form chromatin loops.
- Looping at the TERT gene is associated with repression of telomerase expression.
- The tool allows individual allele analysis of chromatin looping and RNA production.

## Abstract

The genome folds inside the cell nucleus into hierarchical architectural features, such as chromatin loops and domains. If and how this genome organization influences the regulation of gene expression remains only partially understood. The structure–function relationship of genomes has traditionally been probed by population-wide measurements after mutation of crucial DNA elements or by perturbation of chromatin-associated proteins. To circumvent possible pleiotropic effects of such approaches, we have developed OptoLoop, an optogenetic system that allows direct manipulation of chromatin contacts by light in a controlled fashion. OptoLoop is based on the fusion between a nuclease-dead SpCas9 protein and the light-inducible oligomerizing protein CRY2. We demonstrate that OptoLoop can bring together genomically distant, repetitive DNA loci. As a proof-of-principle application of OptoLoop, we probed the functional role of DNA looping in the regulation of the human telomerase gene TERT. By analyzing the extent of chromatin looping and nascent RNA production at individual alleles, we find evidence for looping-mediated repression of TERT. In sum, OptoLoop represents a novel means for the interrogation of structure–function relationships in the genome.

Summary: The development of OptoLoop – an optogenetic tool to induce chromatin looping in a controlled fashion using light and how this tool can be applied to study genome structure–function relationship.