dsRID: in silico identification of dsRNA regions using long-read RNA-seq data.
Bioinformatics 2023;
39:btad649. [PMID:
37871161 PMCID:
PMC10628436 DOI:
10.1093/bioinformatics/btad649]
[Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023] Open
Abstract
MOTIVATION
Double-stranded RNAs (dsRNAs) are potent triggers of innate immune responses upon recognition by cytosolic dsRNA sensor proteins. Identification of endogenous dsRNAs helps to better understand the dsRNAome and its relevance to innate immunity related to human diseases.
RESULTS
Here, we report dsRID (double-stranded RNA identifier), a machine-learning-based method to predict dsRNA regions in silico, leveraging the power of long-read RNA-sequencing (RNA-seq) and molecular traits of dsRNAs. Using models trained with PacBio long-read RNA-seq data derived from Alzheimer's disease (AD) brain, we show that our approach is highly accurate in predicting dsRNA regions in multiple datasets. Applied to an AD cohort sequenced by the ENCODE consortium, we characterize the global dsRNA profile with potentially distinct expression patterns between AD and controls. Together, we show that dsRID provides an effective approach to capture global dsRNA profiles using long-read RNA-seq data.
AVAILABILITY AND IMPLEMENTATION
Software implementation of dsRID, and genomic coordinates of regions predicted by dsRID in all samples are available at the GitHub repository: https://github.com/gxiaolab/dsRID.
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