Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure.

Abstract:

:It has become increasingly clear that large RNA molecules, especially long noncoding RNAs, function in almost all gene regulatory processes (Cech & Steitz, 2014). Many large RNAs appear to be structural scaffolds for assembly of important RNA/protein complexes. However, the structures of most large cellular RNA molecules are currently unknown (Hennelly & Sanbonmatsu, 2012). While chemical probing can reveal single-stranded regions of RNA, traditional approaches to identify sites of chemical modification are time consuming. Mod-seq is a high-throughput method used to map chemical modification sites on RNAs of any size, including complex mixtures of RNA. In this protocol, we describe preparation of Mod-seq high-throughput sequencing libraries from chemically modified RNA. We also describe a software package "Mod-seeker," which is a compilation of scripts written in Python, for the analysis of Mod-seq data. Mod-seeker returns statistically significant modification sites, which can then be used to aid in secondary structure prediction.

journal_name

Methods Enzymol

journal_title

Methods in enzymology

authors

Lin Y,May GE,Joel McManus C

doi

10.1016/bs.mie.2015.01.012

subject

Has Abstract

pub_date

2015-01-01 00:00:00

pages

125-152

eissn

0076-6879

issn

1557-7988

pii

S0076-6879(15)00025-7

journal_volume

558

pub_type

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