Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray

@article{citeulike:1646957, abstract = {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. 10.1101/gr.6611807}, author = {He, Housheng and Wang, Jie and Liu, Tao and Liu, Shirley X. and Li, Tiantian and Wang, Yunfei and Qian, Zuwei and Zheng, Haixia and Zhu, Xiaopeng and Wu, Tao and Shi, Baochen and Deng, Wei and Zhou, Wei and Skogerbo, Geir and Chen, Runsheng }, citeulike-article-id = {1646957}, doi = {10.1101/gr.6611807}, journal = {Genome Res.}, keywords = {genomics, microarray, nematode, tiling, transcriptome}, month = {September}, pages = {gr.6611807+}, posted-at = {2007-12-27 01:13:23}, priority = {2}, title = {Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray}, url = {http://dx.doi.org/10.1101/gr.6611807}, year = {2007} }

TY - JOUR ID - citeulike:1646957 L3 - citeulike-article-id:1646957 TI - Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray JF - Genome Res. SP - gr.6611807 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. 10.1101/gr.6611807 KW - genomics KW - microarray KW - nematode KW - tiling KW - transcriptome AU - He, Housheng AU - Wang, Jie AU - Liu, Tao AU - Liu, Shirley AU - Li, Tiantian AU - Wang, Yunfei AU - Qian, Zuwei AU - Zheng, Haixia AU - Zhu, Xiaopeng AU - Wu, Tao AU - Shi, Baochen AU - Deng, Wei AU - Zhou, Wei AU - Skogerbo, Geir AU - Chen, Runsheng PY - 2007/09/04/ UR - http://dx.doi.org/10.1101/gr.6611807 ER -