Please use this identifier to cite or link to this item: https://biore.bio.bg.ac.rs/handle/123456789/2483
Title: A Simple Criterion for Inferring CRISPR Array Direction
Authors: Milicevic, Ognjen
Repac, Jelena 
Božić, Bojan 
Djordjevic, Magdalena
Djordjevic, Marko 
Keywords: cas gene orientation;CRISPR array orientation;CRISPR/Cas;large-scale analysis;non-canonical functions
Issue Date: 4-Sep-2019
Rank: M21
Journal: Frontiers in Microbiology
Abstract: 
© Copyright © 2019 Milicevic, Repac, Bozic, Djordjevic and Djordjevic. Inferring transcriptional direction (orientation) of the CRISPR array is essential for many applications, including systematically investigating non-canonical CRISPR/Cas functions. The standard method, CRISPRDirection (embedded within CRISPRCasFinder), fails to predict the orientation (ND predictions) for ∼37% of the classified CRISPR arrays (>2200 loci); this goes up to >70% for the II-B subtype where non-canonical functions were first experimentally discovered. Alternatively, Potential Orientation (also embedded within CRISPRCasFinder), has a much smaller frequency of ND predictions but might have significantly lower accuracy. We propose a novel simple criterion, where the CRISPR array direction is assigned according to the direction of its associated cas genes (Cas Orientation). We systematically assess the performance of the three methods (Cas Orientation, CRISPRDirection, and Potential Orientation) across all CRISPR/Cas subtypes, by a mutual crosscheck of their predictions, and by comparing them to the experimental dataset. Interestingly, CRISPRDirection agrees much better with Cas Orientation than with Potential Orientation, despite CRISPRDirection and Potential Orientation being mutually related – Potential Orientation corresponding to one of six (heterogeneous) predictors employed by CRISPRDirection – and being unrelated to Cas Orientation. We find that Cas Orientation has much higher accuracy compared to Potential Orientation and comparable accuracy to CRISPRDirection – while accurately assigning an orientation to ∼95% of the CRISPR arrays that are non-determined by CRISPRDirection. Cas Orientation is, at the same time, simple to employ, requiring only (routine for prokaryotes) the prediction of the associated protein coding gene direction.
URI: https://biore.bio.bg.ac.rs/handle/123456789/2483
ISSN: 1664-302X
DOI: 10.3389/fmicb.2019.02054
Appears in Collections:Journal Article

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