Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-05-07

AUTHORS

Luca Fiorillo, Francesco Musella, Mattia Conte, Rieke Kempfer, Andrea M. Chiariello, Simona Bianco, Alexander Kukalev, Ibai Irastorza-Azcarate, Andrea Esposito, Alex Abraham, Antonella Prisco, Ana Pombo, Mario Nicodemi

ABSTRACT

Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled, framework against known 3D structures of polymer models of murine and human loci, which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed fluorescence in situ hybridization (FISH) single-molecule conformations. We find that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D structures whereas single-cell data reflect strong variability among single molecules. The minimal number of cells required in replicate experiments to return statistically similar contacts is different across the technologies, being lowest in SPRITE and highest in GAM under the same conditions. Noise-to-signal levels follow an inverse power law with detection efficiency and grow with genomic distance differently among the three methods, being lowest in GAM for genomic separations >1 Mb. More... »

PAGES

482-490

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41592-021-01135-1

    DOI

    http://dx.doi.org/10.1038/s41592-021-01135-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1137806101

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/33963348


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