Document Type

Technical Report

Date of this Version

1-26-2012

Publication Source

Cell Reports

Volume

1

Issue

1

Start Page

69

Last Page

82

DOI

10.1016/j.celrep.2011.10.002

Abstract

The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.

Copyright/Permission Statement

Copyright © 2012 The Authors. Published by Elsevier Inc.

This article is published Open Access under a Creative Commons Attribution-NonCommerical-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) license.

 

Date Posted: 14 July 2017

This document has been peer reviewed.