Detecting novel low-abundant transcripts in Drosophila

Lee, Sanggyu, Bao, Jingyue, Zhou, Guolin, Shapiro, Joshua, Xu, Jinhua, Shi, Run Zhang, Lu, Xueme, Clark, Terry W., Johnson, Deborah, Kim, Yeong C., Wing, Claudia, Tseng, Charles, Sun , Min, Lin, Wei, Wang, Jun, Yang, Huanming, Wang, Jian, Du, Wei, Wu, Chung-I, Zhang, Xiuqing and Wang, San Ming (2005) Detecting novel low-abundant transcripts in Drosophila. RNA, 11 6: 939-946. doi:10.1261/rna.7239605

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Author Lee, Sanggyu
Bao, Jingyue
Zhou, Guolin
Shapiro, Joshua
Xu, Jinhua
Shi, Run Zhang
Lu, Xueme
Clark, Terry W.
Johnson, Deborah
Kim, Yeong C.
Wing, Claudia
Tseng, Charles
Sun , Min
Lin, Wei
Wang, Jun
Yang, Huanming
Wang, Jian
Du, Wei
Wu, Chung-I
Zhang, Xiuqing
Wang, San Ming
Title Detecting novel low-abundant transcripts in Drosophila
Journal name RNA   Check publisher's open access policy
ISSN 1355-8382
1469-9001
Publication date 2005-06-01
Sub-type Article (original research)
DOI 10.1261/rna.7239605
Open Access Status File (Publisher version)
Volume 11
Issue 6
Start page 939
End page 946
Total pages 8
Place of publication Woodbury, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Abstract ncreasing 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-a
Keyword Low-abundant transcripts
SAGE
EST
Drosophila
Genome
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Agriculture and Food Sciences
 
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