News from the RNA world

CREATED: 200902100303 Speaker: Peter F. Stadler, Bioinformatics Group, CS Dept, University of Leipzig ** Annotation of ncRNA

• transcriptiome complexity of the Hox A cluster
• novel small RNA families, promoter and termini associated RNAS, Science 316:1484-1488 (2007)
• annotation of ncRNAs: homology search based on sequence and/or structure, clustering
• finding ncRNA on the genome: known ncRNAs are more stable than genomic background, certain base pairings must be conserved to preserve the secondary structure
• structure conservation index, z-score, sequence alignment score can be used to search for structured ncRNA
• machine learning approaches for specific families: micro RNAs, snoRNAs
• structure-based clustering ** Evolution of microRNA
• protein coding genes are old, few new transcription factor were invented through vertebrate evolution, whereas small RNAs, in particular microRNAs, are new
• link between ncRNA innovation and novelty at the organismal level
• expansion of the Metazoan microRNA repertoire during evolution