Cap analysis gene expression
Encyclopedia
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 20-21 nucleotide
s 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 and co-workers in 2003 .
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 an 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 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 .
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
(CAGE) is a technique used in molecular biology to produce a snapshot of the 5' end of the messenger RNA
Messenger RNA
Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein...
population in a biological sample. The small fragments (usually 20-21 nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s long) from the very beginnings of mRNAs (5' ends of capped
5' cap
The 5' cap is a specially altered nucleotide on the 5' end of precursor messenger RNA and some other primary RNA transcripts as found in eukaryotes. The process of 5' capping is vital to creating mature messenger RNA, which is then able to undergo translation...
transcripts) are extracted, reverse-transcribed to DNA, PCR amplified and sequenced
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
. CAGE was first published by Hayashizaki and co-workers in 2003 .
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
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
) 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
Serial Analysis of Gene Expression
Serial analysis of gene expression is a technique used by molecular biologists to produce a snapshot of the messenger RNA population in a sample of interest in the form of small tags that correspond to fragments of those transcripts. The original technique was developed by Dr. Victor Velculescu...
(SAGE, superSAGE) in which tags come from other parts of transcripts, CAGE is primarily used to locate an exact transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
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 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 .
External links
- CAGE homepage at the RIKENRIKENis a large natural sciences research institute in Japan. Founded in 1917, it now has approximately 3000 scientists on seven campuses across Japan, the main one in Wako, just outside Tokyo...
Omics Science Center.