Research article

Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

Christian Weile , Paul P Gardner , Mads M Hedegaard and Jeppe Vinther

Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Ole Maaløes Vej 5, Building 4.1.27, DK-2200 Copenhagen N, Denmark

author email corresponding author email

BMC Genomics 2007, 8:244doi:10.1186/1471-2164-8-244

Published:	23 July 2007

Abstract

Background

Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human genome. Moreover, genome wide transcription profiling with tiling arrays indicate that the majority of the genome is transcribed.

Results

We have combined tiling array data with genome wide structural RNA predictions to search for novel noncoding and structural RNA genes that are expressed in the human neuroblastoma cell line SK-N-AS. Using this strategy, we identify thousands of human candidate RNA genes. To further verify the expression of these genes, we focused on candidate genes that had a stable hairpin structures or a high level of covariance. Using northern blotting, we verify the expression of 2 out of 3 of the hairpin structures and 3 out of 9 high covariance structures in SK-N-AS cells.

Conclusion

Our results demonstrate that many human noncoding, structured and conserved RNA genes remain to be discovered and that tissue specific tiling array data can be used in combination with computational predictions of sequences encoding structural RNAs to improve the search for such genes.