| Noncoding RNA genes are genes for which the RNA is the functional end product in the cell rather than a protein-coding messanger. Functional specificity is conferred upon many noncoding RNAs by secondary structure. How noncoding RNA genes can be identified in genomic sequences is an open problem that this dissertation addresses.; I performed a screen for noncoding RNA genes in the genomes of Methanocaldococcus (formerly Methanococcus) jannaschii and Pyrococcus furiosus by exploiting a bias in the GC content of their noncoding RNAs. I also screened for noncoding RNAs in P. furiosus using the comparative analysis program QRNA. Expression of nine of these predictions has been confirmed on Northern blots and through RACE reactions. One RNA, hgcC appears to be associated with transposition events. The gene hgcG from P. furiosus is homologous to the pseudouridylation guide RNA Afu-4 in Archaeoglobus fulgidus.; I then developed a program, RSEARCH, that finds homologs of a single, structured RNA in genomic sequences. To facilitate searching with RSEARCH, I also developed a series of matrices, called RIBOSUM matrices, for scoring alignments between RNA base pairs. RSEARCH finds previously unknown homologs of human RNase P in the eukaryotic genomes Ciona intestinalis, Caenorhabditis elegans, Drosophila melanogaster, Anopheles gambiae, and Encephalitozoon cuniculi.; I also mapped the ends of the previously identified noncoding RNAs tp2, t44, tpe7, tp1, tke1, tp8, tpk1, and tpk2 from Escherichia coli. Using predicted secondary structures, I found previously unknown homologs of several noncoding RNAs from E. coli in other gamma proteobacteria, including homologs of t44 in Yersinia pestis and Pseudomonas aeruginosa. I also proposed secondary structure models for t44 and tp1 (ryfA).; RSEARCH finds additional homologs of several of the RNAs I found in M. jannaschii and P. furiosus. It finds a homolog of hgcG in M. jannaschii that also appears to be a pseudouridylation guide RNA. It finds that hgcB from M. jannaschii is homologous to presumably transcribed sequence 5 ' of the small subunit ribosomal RNA gene in Pyrococcus . Finally, I found many additional homologs of hgcC adjacent to transposases, including several members of the IS605/ISC1316 transposon family. |
