Cap analysis gene expression (CAGE) is a technique used in molecular biology to produce a snapshot of the 5′ end of the messenger RNA population in a biological sample. The small fragments (usually 27 nucleotides long) from the very beginnings of mRNAs (5' ends of capped transcripts) are extracted, reverse-transcribed to DNA, PCR amplified and sequenced. CAGE was first published by Hayashizaki, Carninci and co-workers in 2003. CAGE has been extensively used within the FANTOM research projects.
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Analysis
The output of CAGE is a set of short nucleotide sequences (often called tags) with their observed counts. Using a reference genome a researcher can usually determine, with some confidence, the original mRNA (and therefore which gene) the tag was extracted from. Copy numbers of CAGE tags provide an easy way of digital quantification of the RNA transcript abundances in biological samples.
Unlike a similar technique Serial Analysis of Gene Expression (SAGE, superSAGE) in which tags come from other parts of transcripts, CAGE is primarily used to locate exact transcription start sites in the genome. This knowledge in turn allows a researcher to investigate promoter structure necessary for gene expression.
However, the CAGE protocol has a known bias with a nonspecific guanine (G) at the most 5′ end of the CAGE tags, which is attributed to the template-free 5′-extension during the first-strand cDNA synthesis. This would induce erroneous mapping of CAGE tags, for instance to nontranscribed pseudogenes.
History
The original CAGE method (Shiraki et al., 2003) was using CAP Trapper for capturing the 5′ ends, oligo-dT primers for synthesizing the cDNAs, the type IIs restriction enzyme MmeI for cleaving the tags, and the Sanger method for sequencing them.
Random reverse-transcription primers were introduced in 2006 by Kodzius et al. to better detect the non-polyadenylated RNAs.
In DeepCAGE (Valen et al., 2008), the tag concatemers were sequenced at a higher throughput on the 454 “next-generation” sequencing platform.
In 2008, barcode multiplexing was added to the DeepCAGE protocol (Maeda et al., 2008).
In nanoCAGE (Plessy et al., 2010), the 5′ ends or RNAs were captured with the template-switching method instead of CAP Trapper, in order to analyze smaller starting amounts of total RNA. Longer tags were cleaved with the type III restriction enzyme EcoP15I and directly sequenced on the Solexa (then Illumina) platform without concatenation.
The CAGEscan methodology (Plessy et al., 2010), where the enzymatic tag cleavage is skipped, and the 5′ cDNAs sequenced paired-end, was introduced in the same article to connect novel promoters to known annotations.
With HeliScopeCAGE (Kanamori-Katayama et al., 2011), the CAP-trapped CAGE protocol was changed to skip the enzymatic tag cleavage and sequence directly the capped 5′ ends on the HeliScope platform, without PCR amplification. It was then automated by Itoh et al. in 2012.
In 2012, the standard CAGE protocol was updated by Takahashi et al. to cleave tags with EcoP15I and sequence them on the Illumina-Solexa platform.
In 2013, Batut et al. combined CAP trapper, template switching, and 5′-phosphate-dependent exonuclease digestion in RAMPAGE to maximize promoter specificity.
In 2014, Murata et al. published the nAnTi-CAGE protocol, where capped 5′ ends are sequenced on the Illumina platform with no PCR amplification and no tag cleavage.