title: Detecting novel low-abundant transcripts in Drosophila.
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.
authors.affiliation: Department of Medicine, University of Chicago, IL 60637, USA.
authors.forename: Sanggyu
authors.initials: S
authors.lastname: Lee
authors.forename: Jingyue
authors.initials: J
authors.lastname: Bao
authors.forename: Guolin
authors.initials: G
authors.lastname: Zhou
authors.forename: Joshua
authors.initials: J
authors.lastname: Shapiro
authors.forename: Jinhua
authors.initials: J
authors.lastname: Xu
authors.forename: Run Zhang
authors.initials: RZ
authors.lastname: Shi
authors.forename: Xuemei
authors.initials: X
authors.lastname: Lu
authors.forename: Terry
authors.initials: T
authors.lastname: Clark
authors.forename: Deborah
authors.initials: D
authors.lastname: Johnson
authors.forename: Yeong C
authors.initials: YC
authors.lastname: Kim
authors.forename: Claudia
authors.initials: C
authors.lastname: Wing
authors.forename: Charles
authors.initials: C
authors.lastname: Tseng
authors.forename: Min
authors.initials: M
authors.lastname: Sun
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Du
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.forename: San Ming
authors.initials: SM
authors.lastname: Wang
mesh_terms: 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
chemical_list: D012333:RNA, Messenger