Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging.

ABSTRACT: Genome-wide chromosome conformation capture (Hi-C) has revealed the organization of chromatin into topologically associating domains (TADs) and loops, which are thought to help regulate genome functions. TADs and loops are understood as the result of DNA extrusion mediated by the cohesin complex. However, despite recent efforts, direct visualization and quantification of this process in single cells remains an open challenge. Here, we use polymer simulations and dedicated analysis methods to explore if, and under which conditions, DNA loop extrusion can be detected and quantitatively characterized by imaging pairs of fluorescently labeled loci located near loop or TAD anchors in fixed or living cells. We find that under realistic conditions, extrusion can be detected and the frequency of l

SUBMITTER: Sabate T 

PROVIDER: S-EPMC10085712 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature