FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data.

ABSTRACT: Sequential Oligopaints DNA FISH is an imaging technique that measures higher-order genome folding at single-allele resolution via multiplexed, probe-based tracing. Currently there is a paucity of algorithms to identify 3D genome features in sequential Oligopaints data. Here, we present FISHnet, a graph theory method based on optimization of network modularity to detect chromatin domains in pairwise distance matrices. FISHnet sensitively and specifically identifies domains and boundaries in both simulated and real single-allele imaging data and provides statistical tests for the identification of cell-type-specific domains-like folding patterns. Application of FISHnet across multiple published Oligopaints datasets confirms that nested domains consistent with TADs and subTADs are not an emer

SUBMITTER: Patel R 

PROVIDER: S-EPMC12165856 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature