title: Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.
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 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.
authors.affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Housheng
authors.initials: H
authors.lastname: He
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
authors.forename: Tiantian
authors.initials: T
authors.lastname: Li
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Wang
authors.forename: Zuwei
authors.initials: Z
authors.lastname: Qian
authors.forename: Haixia
authors.initials: H
authors.lastname: Zheng
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.forename: Baochen
authors.initials: B
authors.lastname: Shi
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: 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