WebPORD: a web-based pipeline of RNA degradome. (29th June 2019)

• Record Type: Journal Article
• Authors: Won, Jung-Im; Lee, JunBeom; Lee, HeonWoo; Shin, JaeMoon; Yoon, JeeHee; Jeong, Dong-Hoon
• Is Part Of: International journal of data mining and bioinformatics. Volume 22:Number 3(2019)
• Page Start: 216
• Page End: 230
• Publication Date: 2019-06-29
• Subjects: web-based pipeline -- next-generation sequencing -- RNA degradome -- parallel analysis of RNA ends; Data mining -- Periodicals; Bioinformatics -- Periodicals; 006.312
• Languages: English
• ISSNs: 1748-5673

Abstract

The advent of high-throughput Next-Generation Sequencing (NGS) technology has brought in a new genomics era. It is widely utilised not only for genomic but also for transcriptome sequencing. NGS-based transcriptomic methods, including RNA-seq, are widely used to study gene expression regulation. Recently, post-transcriptional gene regulation has been studied by several RNA degradome sequencing methods that differ from RNA-seq and directly profile degraded RNAs. Parallel Analysis of RNA Ends (PARE) sequencing is one of these methods. It is widely used for identifying microRNA targets and nonsense-mediated mRNA decay events as well as for global analysis of RNA degradation. We have developed WebPORD, a user-friendly web-based pipeline for analysing the PARE sequencing data. This pipeline trims and applies several filters to PARE sequencing. In addition, this pipeline provides a degradome table and degradome-plots for users to further analyse RNA degradation at a genomic scale. This is the first web-based pipeline for global analysis of RNA degradation using PARE data from animals and plants, which provides mechanistic insights into post-transcriptional gene regulation.