Linking Promoters to Functional Transcripts in Small Samples with NanoCAGE and CAGEscan

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2010 Jun 15

PMID 20543846

Citations 83

Authors

Charles Plessy

Nicolas Bertin

Hazuki Takahashi

Roberto Simone

Md Salimullah

Timo Lassmann

Morana Vitezic

Jessica Severin

Signe Olivarius

Dejan Lazarevic

Nadine Hornig

Valerio Orlando

Ian Bell

Hui Gao

Jacqueline Dumais

Philipp Kapranov

Huaien Wang

Carrie A Davis

Thomas R Gingeras

Jun Kawai

Carsten O Daub

Yoshihide Hayashizaki

Stefano Gustincich

Piero Carninci

Affiliations

Soon will be listed here.

Abstract

Large-scale sequencing projects have revealed an unexpected complexity in the origins, structures and functions of mammalian transcripts. Many loci are known to produce overlapping coding and noncoding RNAs with capped 5' ends that vary in size. Methods to identify the 5' ends of transcripts will facilitate the discovery of new promoters and 5' ends derived from secondary capping events. Such methods often require high input amounts of RNA not obtainable from highly refined samples such as tissue microdissections and subcellular fractions. Therefore, we developed nano-cap analysis of gene expression (nanoCAGE), a method that captures the 5' ends of transcripts from as little as 10 ng of total RNA, and CAGEscan, a mate-pair adaptation of nanoCAGE that captures the transcript 5' ends linked to a downstream region. Both of these methods allow further annotation-agnostic studies of the complex human transcriptome.

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