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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 and boundaries in pairwise distance matrices. FISHnet uncovers cell type-specific domain-like folding patterns on single alleles, thus enabling future studies aiming to elucidate the role for single-cell folding variation on genome function.

SUBMITTER: Patel R

PROVIDER: S-EPMC11212945 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature

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

Patel Rohan R Pham Kenneth K Chandrashekar Harshini H Phillips-Cremins Jennifer E JE

bioRxiv : the preprint server for biology 20240618

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 and boundaries in pairwise distance matrices. FISHnet uncovers cell type-specific domain-like folding patterns ...[more]

PMID: 38948824

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