Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.
The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein-coding transcriptome remains unknown. Expression profiling on whole-genome tiling microarrays applied to a mixed-stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11%) of the polyadenylated transcription is non-annotated and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). Almost half (44%) of the detected transcriptional output is non-polyadenylated and probably not protein coding, and of this, 70% overlaps the boundaries of protein-coding genes in a complex manner. Specific analysis of small non-polyadenylated transcripts verified 97% of all annotated small ncRNAs and suggested that the transcriptome contains approximately 1200 small (<500 nt) unannotated noncoding loci. After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed.
He
Housheng
H
Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Wang
Jie
J
Liu
Tao
T
Liu
X Shirley
XS
Li
Tiantian
T
Wang
Yunfei
Y
Qian
Zuwei
Z
Zheng
Haixia
H
Zhu
Xiaopeng
X
Wu
Tao
T
Shi
Baochen
B
Deng
Wei
W
Zhou
Wei
W
Skogerbø
Geir
G
Chen
Runsheng
R
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D005091:Exons; D020869:Gene Expression Profiling; D049751:Genome, Helminth; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D018510:RNA, Helminth / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D014158:Transcription, Genetic