title: In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs.
abstract: BACKGROUND
  Noncoding RNAs (ncRNAs) play important roles in a variety of cellular processes. Characterizing the transcriptional activity of ncRNA promoters is therefore a critical step toward understanding the complex cellular roles of ncRNAs.
  
  
  RESULTS
  Here we present an in vivo transcriptional analysis of three C. elegans ncRNA upstream motifs (UM1-3). Transcriptional activity of all three motifs has been demonstrated, and mutational analysis revealed differential contributions of different parts of each motif. We showed that upstream motif 1 (UM1) can drive the expression of green fluorescent protein (GFP), and utilized this for detailed analysis of temporal and spatial expression patterns of 5 SL2 RNAs. Upstream motifs 2 and 3 do not drive GFP expression, and termination at consecutive T runs suggests transcription by RNA polymerase III. The UM2 sequence resembles the tRNA promoter, and is actually embedded within its own short-lived, primary transcript. This is a structure which is also found at a few plant and yeast loci, and may indicate an evolutionarily very old dicistronic transcription pattern in which a tRNA serves as a promoter for an adjacent snoRNA.
  
  
  CONCLUSIONS
  The study has demonstrated that the three upstream motifs UM1-3 have promoter activity. The UM1 sequence can drive expression of GFP, which allows for the use of UM1::GFP fusion constructs to study temporal-spatial expression patterns of UM1 ncRNA loci. The UM1 loci appear to act in concert with other upstream sequences, whereas the transcriptional activities of the UM2 and UM3 are confined to the motifs themselves.
authors.affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101, PR China. litiantian_222@hotmail.com
authors.forename: Tiantian
authors.initials: T
authors.lastname: Li
authors.forename: Housheng
authors.initials: H
authors.lastname: He
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Wang
authors.forename: Haixia
authors.initials: H
authors.lastname: Zheng
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D005786:Gene Expression Regulation; D049452:Green Fluorescent Proteins / Q000235:genetics; D016297:Mutagenesis, Site-Directed; D011401:Promoter Regions, Genetic / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D022661:RNA, Untranslated; D049452:Green Fluorescent Proteins