Research article

In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs

Tiantian Li^1,4* , Housheng He^1,4* , Yunfei Wang^1,4 , Haixia Zheng^1,5 , Geir Skogerbø¹ and Runsheng Chen^1,2,3

¹  Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101, PR China

²  Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Science, Beijing 100080, PR China

³  Chinese National Human Genome Center, Beijing 100176, PR China

⁴  Graduate School of the Chinese Academy of Science, Beijing 100080, PR China

⁵  Shanxi Agricultural University, Taigu, Shanxi, 030801, PR China

author email corresponding author email* Contributed equally

BMC Molecular Biology 2008, 9:71doi:10.1186/1471-2199-9-71

Published:	5 August 2008

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.

Conclusion

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.