Improved Definition of the Mouse Transcriptome Via Targeted RNA Sequencing

Overview

Journal Genome Res

Specialty Genetics

Date 2016 May 20

PMID 27197243

Citations 19

Authors

Giovanni Bussotti

Tommaso Leonardi

Michael B Clark

Tim R Mercer

Joanna Crawford

Lorenzo Malquori

Cedric Notredame

Marcel E Dinger

John S Mattick

Anton J Enright

Affiliations

Soon will be listed here.

Abstract

Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.

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