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MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

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Published on: February 23, 2021

Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing.

Qi Liu¹, Changjun Ding¹, Xiaoqiang Lang²

¹State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China.

Briefings in Bioinformatics

|December 31, 2019

Summary

This summary is machine-generated.

sRNAtools is a new bioinformatics platform for comprehensive analysis of small noncoding RNAs (sncRNAs). It identifies and annotates diverse sncRNA types, including tRNA-derived small RNA fragments (tRFs) and phased, secondary, small-interfering RNAs (phasiRNAs).

Keywords:

24-nt siRNA phasiRNA small noncoding RNA software tRF wood formation

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Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Small noncoding RNAs (sncRNAs) regulate crucial biological processes like gene expression and cell proliferation.
Next-generation sequencing (NGS) enables discovery and quantification of diverse sncRNAs, including tRFs, phasiRNAs, piRNAs, and 24-nt siRNAs.
Existing web tools lack comprehensive analysis capabilities for these varied sncRNA types.

Purpose of the Study:

To introduce sRNAtools, a novel integrated platform for the identification and functional annotation of diverse sncRNAs.
To provide a user-friendly tool for analyzing various sncRNA classes, including microRNAs, piRNAs, tRNAs, and newly discovered types like isomiRs and phasiRNAs.
To support the analysis of sncRNA data from up to 21 model organisms.

Main Methods:

Development of a novel integrated bioinformatics platform, sRNAtools.
Implementation of distinct analytical modules (single case, batch case, group case, target case) for flexible sncRNA studies.
Support for various data uploading methods and interactive queue systems, with local versions available (program package/Docker/virtureBox).

Main Results:

sRNAtools enables comprehensive profiling of microRNAs, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs, and rRNAs.
The platform facilitates the discovery of isomiRs, tRFs, phasiRNAs, and plant-specific 24-nt siRNAs.
sRNAtools supports flexible analysis across multiple modules and data input formats.

Conclusions:

sRNAtools offers a powerful, integrated solution for the comprehensive analysis of diverse sncRNAs.
The platform enhances the ability to identify and functionally annotate various sncRNA classes using high-throughput sequencing data.
sRNAtools is expected to significantly benefit the scientific community in sncRNA research.