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


CONCLUSIONS
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.
Weile
Christian
C
Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Copenhagen N, Denmark. cweile@yahoo.dk <cweile@yahoo.dk>
Gardner
Paul P
PP
Hedegaard
Mads M
MM
Vinther
Jeppe
J
D000465:Algorithms; D001483:Base Sequence; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D022661:RNA, Untranslated / Q000302:isolation & purification*; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D014407:Tumor Cells, Cultured
D022661:RNA, Untranslated