Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. Export

@article{citeulike:1719172, abstract = {As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts.}, address = {1Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA.}, author = {Chakrabarti, Kausik and Pearson, Michael and Grate, Leslie and Sterne-Weiler, Timothy and Deans, Jonathan and Donohue, John Paul P. and Ares, Manuel}, citeulike-article-id = {1719172}, citeulike-linkout-0 = {http://dx.doi.org/10.1261/rna.751807}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17901154}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17901154}, day = {27}, doi = {10.1261/rna.751807}, issn = {1355-8382}, journal = {RNA (New York, N.Y.)}, keywords = {malaria, ncrna}, month = {November}, number = {11}, pages = {1923--1939}, posted-at = {2009-11-05 23:30:43}, priority = {2}, title = {Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis.}, url = {http://dx.doi.org/10.1261/rna.751807}, volume = {13}, year = {2007} }

TY - JOUR ID - citeulike:1719172 L3 - citeulike-article-id:1719172 N2 - As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts. IS - 11 JF - RNA (New York, N.Y.) SN - 1355-8382 AD - 1Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA. EP - 1939 TI - Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. VL - 13 SP - 1923 KW - malaria KW - ncrna AU - Chakrabarti, Kausik AU - Pearson, Michael AU - Grate, Leslie AU - Sterne-Weiler, Timothy AU - Deans, Jonathan AU - Donohue, John Paul AU - Ares, Manuel PY - 2007/11/27/ UR - http://dx.doi.org/10.1261/rna.751807 ER -