Wiser Gene Annotations with 5' SAGE?

THE KEYS TO CAGE© 2003 National Academy of Sciencesand its competitors are a 5' cap-trapping step and a class II restriction enzyme (MmeI), which cleaves DNA 20/18 bp downstream of the recognition site to create the sequence tag. (Reprinted from T. Shiraki, Proc Nat Acad Sci, 100:15776–81, 2003.)Serial analysis of gene expression (SAGE) has been used extensively to map and quantify transcripts in different tissues. But the technique, which extracts short oligos (14–21 bp long) f

Written byCathy Holding

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and its competitors are a 5' cap-trapping step and a class II restriction enzyme (MmeI), which cleaves DNA 20/18 bp downstream of the recognition site to create the sequence tag. (Reprinted from T. Shiraki, Proc Nat Acad Sci, 100:15776–81, 2003.)

Serial analysis of gene expression (SAGE) has been used extensively to map and quantify transcripts in different tissues. But the technique, which extracts short oligos (14–21 bp long) from the 3' ends of pooled mRNAs, offers no insight into transcription start points. Three recent papers describe SAGE variants that can.

First, Piero Carninci's group at the RIKEN Genomic Sciences Center in Japan described a "cap analysis gene expression" (CAGE) method that uses "cap-trapping" to isolate an mRNA's 5' end.1 Next, a team at the Genome Institute of Singapore used 5' and 3' "LongSAGE" approaches to separately map both ends of a transcript.2 Finally, Kouji ...

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