Machine learning for design of degenerate Cas13a crRNAs using lassa virus as a model of highly variable RNA target

The design of minimum CRISPR RNA (crRNA) sets for detection of diverse RNA targets using sequence degeneracy has not been systematically addressed. We tested candidate degenerate Cas13a crRNA sets designed for detection of diverse RNA targets (Lassa virus). A decision tree machine learning (ML) algo...

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Bibliographic Details
Published in:Scientific reports 2023-04, Vol.13 (1), p.6506-6506, Article 6506
Main Authors: Leski, T. A., Spangler, J. R., Wang, Z., Schultzhaus, Z., Taitt, C. R., Dean, S. N., Stenger, D. A.
Format: Article
Language:English
Subjects:
631/114
631/1647
631/326
631/337
Algorithms
CRISPR
CRISPR-Cas Systems - genetics
Design
Humanities and Social Sciences
Lassa virus - genetics
Learning algorithms
Machine learning
multidisciplinary
Nuclease
Nucleotide sequence
Ribonucleic acid
RNA
RNA - metabolism
RNA Processing, Post-Transcriptional
RNA viruses
Science
Science (multidisciplinary)
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Summary:The design of minimum CRISPR RNA (crRNA) sets for detection of diverse RNA targets using sequence degeneracy has not been systematically addressed. We tested candidate degenerate Cas13a crRNA sets designed for detection of diverse RNA targets (Lassa virus). A decision tree machine learning (ML) algorithm (RuleFit) was applied to define the top attributes that determine the specificity of degenerate crRNAs to elicit collateral nuclease activity. Although the total number of mismatches (0–4) is important, the specificity depends as well on the spacing of mismatches, and their proximity to the 5’ end of the spacer. We developed a predictive algorithm for design of candidate degenerate crRNA sets, allowing improved discrimination between “included” and “excluded” groups of related target sequences. A single degenerate crRNA set adhering to these rules detected representatives of all Lassa lineages. Our general ML approach may be applied to the design of degenerate crRNA sets for any CRISPR/Cas system.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-023-33494-4