RT Journal
A1 He, Housheng
A1 Wang, Jie
A1 Liu, Tao
A1 Liu, X. Shirley
A1 Li, Tiantian
A1 Wang, Yunfei
A1 Qian, Zuwei
A1 Zheng, Haixia
A1 Zhu, Xiaopeng
A1 Wu, Tao
A1 Shi, Baochen
A1 Deng, Wei
A1 Zhou, Wei
A1 Skogerbø, Geir
A1 Chen, Runsheng
T1 Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray
JF Genome Research 
JO Genome Research 
YR 2007 
FD October 01 
VO 17 
IS 10 
SP 000 
OP 000 
DO 10.1101/gr.6611807 
UL http://genome.cshlp.org/content/early/2007/09/04/gr.6611807.abstract 
AB 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 ∼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 ∼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.