A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum. Export

@article{citeulike:6081148, abstract = {Noncoding RNAs (ncRNAs) such as snRNAs, snoRNAs and microRNAs play important roles in transcription and translation control. These ncRNAs have yet to be discovered in the malarial parasite Plasmodium falciparum, an organism in which these basic biological processes are poorly understood. Inspired by a report by Klein et al., we initiated a bioinformatics screen to uncover several candidate ncRNAs from the parasite genome using two simple criteria: first, elevated GC content in the highly A-T rich intergenic regions of the P. falciparum genome and second, conservation of sequence homology between malaria parasite species. We show that all the annotated tRNAs can be successfully identified in our screen as well as several new candidates that show homology to snRNAs and snoRNAs, and ten candidate ncRNAs of unknown function. Three of the candidate snRNAs, a predicted selenocysteine tRNA and two candidates of unknown function are expressed in asexual stage parasites, further validating the screen. With these results, the biological processes underlying RNA-mediated regulation of transcription, translation and splicing can be studied in an important human pathogen.}, author = {Upadhyay, Roopam and Bawankar, Praveen and Malhotra, Deepti and Patankar, Swati}, citeulike-article-id = {6081148}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.molbiopara.2005.08.012}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16183147}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16183147}, doi = {10.1016/j.molbiopara.2005.08.012}, issn = {0166-6851}, journal = {Molecular and biochemical parasitology}, keywords = {malaria, ncrna}, month = {December}, number = {2}, pages = {149--158}, posted-at = {2009-11-06 16:08:47}, priority = {2}, title = {A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum.}, url = {http://dx.doi.org/10.1016/j.molbiopara.2005.08.012}, volume = {144}, year = {2005} }

TY - JOUR ID - citeulike:6081148 L3 - citeulike-article-id:6081148 N2 - Noncoding RNAs (ncRNAs) such as snRNAs, snoRNAs and microRNAs play important roles in transcription and translation control. These ncRNAs have yet to be discovered in the malarial parasite Plasmodium falciparum, an organism in which these basic biological processes are poorly understood. Inspired by a report by Klein et al., we initiated a bioinformatics screen to uncover several candidate ncRNAs from the parasite genome using two simple criteria: first, elevated GC content in the highly A-T rich intergenic regions of the P. falciparum genome and second, conservation of sequence homology between malaria parasite species. We show that all the annotated tRNAs can be successfully identified in our screen as well as several new candidates that show homology to snRNAs and snoRNAs, and ten candidate ncRNAs of unknown function. Three of the candidate snRNAs, a predicted selenocysteine tRNA and two candidates of unknown function are expressed in asexual stage parasites, further validating the screen. With these results, the biological processes underlying RNA-mediated regulation of transcription, translation and splicing can be studied in an important human pathogen. IS - 2 JF - Molecular and biochemical parasitology SN - 0166-6851 EP - 158 TI - A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum. VL - 144 SP - 149 KW - malaria KW - ncrna AU - Upadhyay, Roopam AU - Bawankar, Praveen AU - Malhotra, Deepti AU - Patankar, Swati PY - 2005/12// UR - http://dx.doi.org/10.1016/j.molbiopara.2005.08.012 ER -