title: Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression.
abstract: Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created controversy over whether these transcripts are functional. Applying a novel cloning strategy, we have cloned 100 novel and 61 known or predicted Caenorhabditis elegans full-length ncRNAs. Studying the genomic environment and transcriptional characteristics have shown that two-thirds of all ncRNAs, including many intronic snoRNAs, are independently transcribed under the control of ncRNA-specific upstream promoter elements. Furthermore, the transcription levels of at least 60% of the ncRNAs vary with developmental stages. We identified two new classes of ncRNAs, stem-bulge RNAs (sbRNAs) and snRNA-like RNAs (snlRNAs), both featuring distinct internal motifs, secondary structures, upstream elements, and high and developmentally variable expression. Most of the novel ncRNAs are conserved in Caenorhabditis briggsae, but only one homolog was found outside the nematodes. Preliminary estimates indicate that the C. elegans transcriptome contains approximately 2700 small non-coding RNAs, potentially acting as regulatory elements in nematode development.
authors.affiliation: Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Fu
authors.forename: Yudong
authors.initials: Y
authors.lastname: Wang
authors.forename: Housheng
authors.initials: H
authors.lastname: He
authors.forename: Lun
authors.initials: L
authors.lastname: Cai
authors.forename: Hong
authors.initials: H
authors.lastname: Sun
authors.forename: Changning
authors.initials: C
authors.lastname: Liu
authors.forename: Biao
authors.initials: B
authors.lastname: Li
authors.forename: Baoyan
authors.initials: B
authors.lastname: Bai
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Dong
authors.initials: D
authors.lastname: Jia
authors.forename: Shiwei
authors.initials: S
authors.lastname: Sun
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.forename: Yan
authors.initials: Y
authors.lastname: Cui
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000196:embryology / Q000235:genetics*; D049751:Genome, Helminth / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018510:RNA, Helminth / Q000145:classification / Q000235:genetics*; D022661:RNA, Untranslated / Q000145:classification / Q000235:genetics*
chemical_list: D018510:RNA, Helminth; D022661:RNA, Untranslated