Pan-genome isolation of low abundance transcripts using SAGE tag

Yeong Cheol Kim, Yong Chul Jung, Zhenyu Xuan, Hui Dong, Michael Q. Zhang, San Ming Wang

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

The SAGE (serial analysis of gene expression) method is sensitive at detecting the lower abundance transcripts. More than a third of human SAGE tags identified are novel representing the low abundance unknown transcripts. Using the GLGI method (generation of longer 3′ EST from SAGE tag for gene identification), we converted 1009 low-copy, human X chromosome-specific SAGE tags into 10210 3′ ESTs. We identified 3418 unique 3′ ESTs, 46% of which are novel and originated from the lower abundance transcripts. However, nearly all 3′ ESTs were mapped to various regions across the genome but not X chromosome. Detailed analysis indicates that those 3′ ESTs were isolated by SAGE tag mis-priming to the non-parent transcripts. Replacing SAGE tags with non-transcribed genomic DNA tags resulted in poor amplification, indicating that the sequence similarity between different transcripts contributed to the amplification. Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through SAGE tags mis-priming.

Original languageEnglish (US)
Pages (from-to)6721-6729
Number of pages9
JournalFEBS Letters
Volume580
Issue number28-29
DOIs
StatePublished - Dec 11 2006

Keywords

  • 3′ EST
  • Low abundance
  • SAGE tag
  • Transcript

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology

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