Benchmark of software tools for prokaryotic chromosomal interaction domain identification

Magnitov, M.D.; Kuznetsova, V.S.; Ulianov, S.V.; Razin, S.V.; Tyakht, A.V.

Авторы: Magnitov Mikhail D., Kuznetsova Veronika S., Ulianov Sergey V., Razin Sergey V., Tyakht Alexander V.
Журнал: Bioinformatics
Год издания: 2020
Издательство: Oxford University Press
Местоположение издательства: United Kingdom
DOI: 10.1093/bioinformatics/btaa555
Аннотация: Motivation: The application of genome-wide chromosome conformation capture (3C) methods to prokaryotes provided insights into the spatial organization of their genomes and identified patterns conserved across the tree of life, such as chromatin compartments and contact domains. Prokaryotic genomes vary in GC content and the density of restriction sites along the chromosome, suggesting that these properties should be taken into consideration when planning experiments and choosing appropriate software for data processing. Diverse algorithms are available for the analysis of eukaryotic chromatin contact maps, but their potential application to prokaryotic data has not yet been evaluated.Results: Here we present a comparative analysis of domain calling algorithms using available single-microbe experimental data. We evaluated the algorithms’ intra-dataset reproducibility, concordance with other tools, and sensitivity to coverage and resolution of contact maps. Using RNA-seq as an example, we showed how orthogonal biological data can be utilized to validate the reliability and significance of annotated domains. We also suggest that in silico simulations of contact maps can be used to choose optimal restriction enzymes and estimate theoretical map resolutions before the experiment. Our results provide guidelines for researchers investigating microbes and microbial communities using high-throughput 3C assays such as Hi-C and 3C-seq.
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Benchmark of software tools for prokaryotic chromosomal interaction domain identificationстатья Исследовательская статья

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