Detecting novel low-abundant transcripts in Drosophila.
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.
Lee
Sanggyu
S
Department of Medicine, University of Chicago, IL 60637, USA.
Bao
Jingyue
J
Zhou
Guolin
G
Shapiro
Joshua
J
Xu
Jinhua
J
Shi
Run Zhang
RZ
Lu
Xuemei
X
Clark
Terry
T
Johnson
Deborah
D
Kim
Yeong C
YC
Wing
Claudia
C
Tseng
Charles
C
Sun
Min
M
Lin
Wei
W
Wang
Jun
J
Yang
Huanming
H
Wang
Jian
J
Du
Wei
W
Wu
Chung-I
CI
Zhang
Xiuqing
X
Wang
San Ming
SM
D000818:Animals; D002874:Chromosome Mapping; D004331:Drosophila melanogaster / Q000235:genetics*; D020224:Expressed Sequence Tags; D015698:Genomic Library; D012333:RNA, Messenger / Q000032:analysis*; D014158:Transcription, Genetic
D012333:RNA, Messenger