Open AccessTranscriptome‐Wide Identification of Pseudouridine Modifications Using Pseudo‐seq
Author(s) -
Carlile Thomas M.,
RojasDuran Maria F.,
Gilbert Wendy V.
Publication year - 2015
Publication title -
current protocols in molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.533
H-Index - 42
eISSN - 1934-3647
pISSN - 1934-3639
DOI - 10.1002/0471142727.mb0425s112
Subject(s) - pseudouridine , computational biology , rna , identification (biology) , transcriptome , rna seq , biology , small nucleolar rna , genome , genetics , non coding rna , gene , transfer rna , gene expression , botany
A diverse array of post‐transcriptional modifications is found in RNA molecules from all domains of life. While the locations of RNA modifications are well characterized in abundant noncoding RNAs, modified sites in less abundant mRNAs are just beginning to be discovered. Recent work has revealed hundreds of previously unknown and dynamically regulated pseudouridines (Ψ) in mRNAs from diverse organisms. This unit describes Pseudo‐seq, an efficient, high‐resolution method for identification of Ψs genome‐wide. This unit includes methods for isolation of RNA from S. cerevisiae , preparation of Pseudo‐seq libraries from RNA samples, and identification of sites of pseudouridylation from the sequencing data. Pseudo‐seq is applicable to any organism or cell type, facilitating rapid identification of novel pseudouridylation events. © 2015 by John Wiley & Sons, Inc.