Abstract
MicroRNAs (miRNAs) are small noncoding 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 robustsmallchimeric RNAanalysispipeline for the bioinformatic processing of chimeric sncRNA:target RNA sequencing data. SCRAP consists of two parts, each of which is 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 data sets 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 annotations to broaden accessibility for processing small chimeric RNA sequencing data and enable insights into the targets of small noncoding RNAs in regulating diverse biological systems.
Funder
Braude Foundation award
Maryland Stem Cell Research Fund Launch Program
Blaustein Endowment for Pain Research and Education
National Institutes of Health
Publisher
Cold Spring Harbor Laboratory
Reference84 articles.
1. Predicting effective microRNA target sites in mammalian mRNAs
2. Andrews S . 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed March 17, 2022).
3. Gene Ontology: tool for the unification of biology
4. Auwera GAV , O'Connor BD . 2020. Genomics in the cloud: using Docker, GATK, and WDL in Terra, 1st ed. O'Reilly Media, Sebastopol, CA.
Cited by
3 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献