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

Upadhyay, Roopam; Bawankar, Praveen; Malhotra, Deepti; Patankar, Swati

doi:10.1016/j.molbiopara.2005.08.012

Cited by 29 publications

(27 citation statements)

References 28 publications

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“…Only one of those novel candidates was verified as transcribed by Upadhyay et al (2005), and our microarray analysis confirms expression of this candidate (our candidate 3370). This comparison indicates the difficulty posed by identifying noncoding RNA genes in P. falciparum.…”

Section: Discussionsupporting

confidence: 53%

“…Eighteen noncoding RNA genes have previously been reported in the P. falciparum genome (Upadhyay et al 2005); 11 of these candidates are present in our alignments, and six are found among our RNA predictions (Supplemental Table S8). Only one of those novel candidates was verified as transcribed by Upadhyay et al (2005), and our microarray analysis confirms expression of this candidate (our candidate 3370).…”

Section: Discussionmentioning

confidence: 94%

“…A significant proportion of these noncoding transcripts map to structured ncRNA candidates, predicted in the ENCODE region (Washietl et al 2007) and thus shedding further light on the widespread occurrence of structured RNAs and their potential roles in shaping the functional landscape of the human genome. However, in the P. falciparum genome, only a minimal set of tRNAs and a small set of ribosomal and spliceosomal RNAs have been identified by sequence annotation (Gardner et al 2002;Upadhyay et al 2005). An in silico comparison based on the identification of homologous GC rich regions across several Plasmodium species sequences identified a total of 18 different potential RNA types present in all, of which nine had homology with known noncoding RNAs (Upadhyay et al 2005).…”

mentioning

confidence: 99%

“…However, in the P. falciparum genome, only a minimal set of tRNAs and a small set of ribosomal and spliceosomal RNAs have been identified by sequence annotation (Gardner et al 2002;Upadhyay et al 2005). An in silico comparison based on the identification of homologous GC rich regions across several Plasmodium species sequences identified a total of 18 different potential RNA types present in all, of which nine had homology with known noncoding RNAs (Upadhyay et al 2005). Transcripts were detected in asexual parasites' RNA for six of the 18 candidates, but only one of these six was a novel RNA.…”

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confidence: 99%

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Genome-wide discovery and verification of novel structured RNAs inPlasmodium falciparum

et al. 2007

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We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp. genome sequences. By using Northern blot analysis for 76 high-scoring predictions and microarray analysis for the majority of candidates, we have verified the expression of 33 novel ncRNA transcripts including four members of a ncRNA family in the asexual blood stage. These transcripts represent novel structured ncRNAs in P. falciparum and are not represented in any RNA databases. We provide supporting evidence for purifying selection acting on the experimentally verified ncRNAs by comparing the nucleotide substitutions in the predicted ncRNA candidate structures in P. falciparum with the closely related chimp malaria parasite P. reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism's life cycle.

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Section: Discussionsupporting

confidence: 53%

Section: Discussionmentioning

confidence: 94%

mentioning

confidence: 99%

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confidence: 99%

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Genome-wide discovery and verification of novel structured RNAs inPlasmodium falciparum

et al. 2007

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“…Although the sequences of P. falciparum and the related rodent parasite P. yoelii yoelii are essentially complete, those of the other Plasmodium species are nearing completion (Coppel et al 2004;Kooij et al 2006). Initial attempts have been made to predict and annotate RNA coding genes of the parasite (Upadhyay et al 2005); however more comprehensive efforts using whole genome comparisons and experimental validation are necessary to complete this process.…”

Section: Introductionmentioning

confidence: 99%

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

Chakrabarti¹,

Pearson²,

Grate³

et al. 2007

RNA

115

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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.

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Resetting var Gene Transcription in Plasmodium falciparum

Mitesser¹,

Dzikowski²

2022

Methods in Molecular Biology

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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

Cited by 29 publications

References 28 publications

Genome-wide discovery and verification of novel structured RNAs inPlasmodium falciparum

Genome-wide discovery and verification of novel structured RNAs inPlasmodium falciparum

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

Resetting var Gene Transcription in Plasmodium falciparum

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