TY  - JOUR
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
Y1  - 2007/10/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 000 
EP  - 000 
DO  - 10.1101/gr.6611807 
VL  - 17 
IS  - 10 
UR  - http://genome.cshlp.org/content/early/2007/09/04/gr.6611807.abstract 
N2  - 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. 
ER  -