A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH.

ABSTRACT: Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from

SUBMITTER: Jia BB 

PROVIDER: S-EPMC10344783 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature