A new approach to the discovery of rna structural elements in the human genome

Analysis of a large number of RNA molecules indicates that variations in their nucleotide sequences do not necessarily convey differences in their secondary structures. Numerous methods have been developed to find patterns in RNA molecules, including the detection of structural motifs in families of noncoding RNAs (ncRNAs). When almost identical sequences render similar structures, these methods work well. However, when given structures differ from each other, there may not exist a motif common to all of them. In such cases, it is desirable to find out if such motifs are indeed present and if not, to determine the extent to which they are shared by the structures under study. We present here a novel tool to be used in finding common patterns among RNAs. In particular, we describe the use of this tool to find RNA structural elements in the human genome. Many of the RNA structures found by our method overlap with human genomic regions that have been previously found through other genome-wide studies aimed to discover conserved structured RNAs. Our method thus provides a complementary tool to the currently used approaches for mining conserved structured RNAs in the human genome.