5′-end SAGE for the analysis of transcriptional start sites

Abstract

Identification of the mRNA start site is essential in establishing the full-length cDNA sequence of a gene and analyzing its promoter region, which regulates gene expression. Here we describe the development of a 5′-end serial analysis of gene expression (5′ SAGE) that can be used to globally identify transcriptional start sites and the frequency of individual mRNAs. Of the 25,684 5′ SAGE tags in the HEK293 human cell library, 19,893 matched to the human genome. Among 15,448 tags in one locus of the genome, 85.8%–96.1% of the 5′ SAGE tags were assigned within −500 to +200 nt of mRNA start sites using the RefSeq, UniGene and DBTSS databases. This technique should facilitate 5′-end transcriptome analysis in a variety of cells and tissues.

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Figure 1
Figure 2: 5′ SAGE tags hit around the defined transcription start sites.

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Acknowledgements

This work was supported by Grant-in-Aid for Scientific Research on Priority Areas (C) “Medical Genome Science” from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

Author information

Correspondence to Kouji Matsushima.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Comparison of the novel 5′ ends of representative known genes between 5′SAGE and the directly sequenced data of the 5′ end of captured full length cDNAs in HEK293. (PDF 12 kb)

Supplementary Fig. 2

Scatter plot of the frequency of 5′SAGE and 3′SAGE tags. (PDF 115 kb)

Supplementary Table 1

Identification of uncharacterized candidate genes and exons. (PDF 6 kb)

Supplementary Table 2

Profile of the 5′-end transcripts in HEK293 cells. (PDF 10 kb)

Supplementary Note, part 1 (XLS 2543 kb)

Supplementary Note, part 2 (XLS 2240 kb)

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