SRNAtoolbox: an integrated collection of small RNA research tools.

Antonio Rueda,Michael Hackenberg,Cristina Gómez-Martín,Ángel Alganza,Guillermo Barturen,José L Oliver,Ricardo Lebrón

doi:10.1093/nar/gkv555

Abstract

Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates. Given the general broad interest in small RNAs, and in particular microRNAs, a large number of bioinformatics aided analysis types are needed by the scientific community. To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual exploration in a genome context as a function of read length, gene list analysis and blast search of unmapped reads. All tools can be used independently or for the exploration and downstream analysis of sRNAbench results. Workflows like the prediction of consensus target genes of parasite microRNAs in the host followed by the detection of enriched pathways can be easily established. The web-interface interconnecting all these tools is available at http://bioinfo5.ugr.es/srnatoolbox

Highlights

Over the last years, high-throughput sequencing (HTS) technologies changed notably our understanding of the biogenesis and function of small RNA molecules
Small interfering RNAs, trans-acting RNAs and heterochromatic small interfering RNAs (siRNA) are involved in the regulation of gene expression and the chromatin state by depositing repressive marks (DNA methylation and histone marks) [3]
Reproducibly processed small RNA fragments of yRNA, tRNA and snoRNA origin have been identified [6] and especially tRNA fragments might be functional by regulating translation [7]

Summary

Introduction

High-throughput sequencing (HTS) technologies changed notably our understanding of the biogenesis and function of small RNA molecules. Given the increasing interest in studying microbe-host interactions, one frequently needed analysis type would be to estimate the impact of parasite secreted microRNAs on the host genes, i.e. which genes and which pathways might be regulated by those exogenous microRNAs. Another example could be the visual exploration of small RNA differential expression in a genome context as a function of read length, given that at least in plants 24 nt long reads have clearly different functions than 21/22 nt long reads.

Results

Conclusion