5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

Abstract:

:Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows the regulatory inputs driving gene expression to be studied, which in turn enables the construction of transcriptional networks. Here we provide an optimized protocol for the construction of CAGE libraries on the basis of the preparation of 27-nt-long tags corresponding to initial bases at the 5' ends of capped RNAs. We have optimized the methods using simple steps based on filtration, which altogether takes 4 d to complete. The CAGE tags can be readily sequenced with Illumina sequencers, and upon modification they are also amenable to sequencing using other platforms.

journal_name

Nat Protoc

journal_title

Nature protocols

authors

Takahashi H,Lassmann T,Murata M,Carninci P

doi

10.1038/nprot.2012.005

subject

Has Abstract

pub_date

2012-02-23 00:00:00

pages

542-61

issue

3

eissn

1754-2189

issn

1750-2799

pii

nprot.2012.005

journal_volume

7

pub_type

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