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

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Title A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A–T rich genome of Plasmodium falciparum
 
Creator UPADHYAY, ROOPAM
BAWANKAR, PRAVEEN
MALHOTRA, DEEPTI
PATANKAR, SWATI
 
Subject biological materials-rna
bioinformatics
intermediate
 
Description 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.
 
Publisher Elsevier
 
Date 2009-04-23T11:40:51Z
2011-12-08T06:25:21Z
2011-12-26T13:01:32Z
2011-12-27T05:45:05Z
2009-04-23T11:40:51Z
2011-12-08T06:25:21Z
2011-12-26T13:01:32Z
2011-12-27T05:45:05Z
2005
 
Type Article
 
Identifier Molecular and Biochemical Parasitology 144(2), 149-158
0166-6851
10.1016/j.molbiopara.2005.08.012
http://hdl.handle.net/10054/1215
http://dspace.library.iitb.ac.in/xmlui/handle/10054/1215
 
Language en