Detecting novel low-abundant transcripts in Drosophila

Sanggyu Lee, Jingyue Bao, Guolin Zhou, Joshua Shapiro, Jinhua Xu, Zhang Shi Run, Xuemei Lu, Terry Clark, Deborah Johnson, Yeong C. Kim, Claudia Wing, Charles Tseng, Min Sun, Wei Lin, Jun Wang, Huanming Yang, Jian Wang, Wei Du, Chung I. Wu, Xiuqing ZhangMing Wang San

Research output: Contribution to journalArticlepeer-review

29 Scopus citations

Abstract

Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies.

Original languageEnglish (US)
Pages (from-to)939-946
Number of pages8
JournalRNA
Volume11
Issue number6
DOIs
StatePublished - Jun 2005

Keywords

  • Drosophila
  • EST
  • Genome
  • Low abundant
  • SAGE
  • Transcript

ASJC Scopus subject areas

  • Molecular Biology

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