SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data

• Published in: RNA (Cambridge) Vol. 29; no. 1; pp. 1 - 17
• Main Authors: Mills, 4th, William T, Eadara, Sreenivas, Jaffe, Andrew E, Meffert, Mollie K
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.01.2023
• Subjects: Bioinformatics; Gene regulation; MicroRNAs; miRNA; Next-generation sequencing; Post-transcription; RNA processing; RNA-induced silencing complex; RNA-mediated interference; microRNA; bioinformatic pipeline; noncoding RNA; Ago CLIP; chimeric RNA
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1261/rna.079240.122

MicroRNAs (miRNAs) are small non-coding RNAs (sncRNAs) that function in post-transcriptional gene regulation through imperfect base pairing with mRNA targets which results in inhibition of translation and typically destabilization of bound transcripts. Sequence-based algorithms historically used to predict miRNA targets face inherent challenges in reliably reflecting in vivo interactions. Recent strategies have directly profiled miRNA-target interactions by crosslinking and ligation of sncRNAs to their targets within the RNA-induced silencing complex (RISC), followed by high throughput sequencing of the chimeric sncRNA:target RNAs. Despite the strength of these direct profiling approaches, standardized pipelines for effectively analyzing the resulting chimeric sncRNA:target RNA sequencing data are not readily available. Here we present SCRAP, a robust Small Chimeric RNA Analysis Pipeline for the bioinformatic processing of chimeric sncRNA:target RNA sequencing data. SCRAP consists of two parts, each of which are specifically optimized for the distinctive characteristics of chimeric small RNA sequencing reads: first, read processing and alignment and second, peak calling and annotation. We apply SCRAP to benchmark chimeric sncRNA:target RNA sequencing datasets generated by distinct molecular approaches, and compare SCRAP to existing chimeric RNA analysis pipelines. SCRAP has minimal hardware requirements, is cross-platform, and contains extensive annotation to broaden accessibility for processing small chimeric RNA sequencing data and enable insights about the targets of small non-coding RNAs in regulating diverse biological systems.