Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

Hu, Guangan; Llinás, Manuel; Li, Jingguang; Preiser, Peter R.; Bozdech, Zbynek

doi:10.1186/1471-2105-8-350

Cited by 54 publications

(75 citation statements)

References 35 publications

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“…These synchronous, monoclonal, erythrocytic isolates were cultured ex vivo from the early ring stage to the schizont stage (see Table S1) (12,14). Transcriptional analysis using a genome-wide long oligonucleotide microarray designed by the recently established algorithm OligoRankPick (15) showed that during the P. vivax IDC, each gene is activated at a particular developmental stage analogous to P. falciparum ( Fig. 1) (6).…”

Section: Resultsmentioning

confidence: 99%

“…From these, 5,063 are represented by a single oligonucleotide, whereas 272 genes (typically long ORFs) are represented by two or more oligonucleotide elements. The P. vivax microarray oligonucleotide set was designed by OligoRankPick (15). Sequences of all oligonucleotides and further information are available online at http:// zblab.sbs.ntu.edu.sg/vivax/index.html.…”

Section: Methodsmentioning

confidence: 99%

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The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites

Bozdech

Mok

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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244

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Plasmodium vivax causes over 100 million clinical infections each year. Primarily because of the lack of a suitable culture system, our understanding of the biology of this parasite lags significantly behind that of the more deadly species P. falciparum. Here, we present the complete transcriptional profile throughout the 48-h intraerythrocytic cycle of three distinct P. vivax isolates. This approach identifies strain specific patterns of expression for subsets of genes predicted to encode proteins associated with virulence and host pathogen interactions. Comparison to P. falciparum revealed significant differences in the expression of genes involved in crucial cellular functions that underpin the biological differences between the two parasite species. These data provide insights into the biology of P. vivax and constitute an important resource for the development of therapeutic approaches.comparative genomics ͉ Plasmodium falciparum I t is now increasingly recognized that P. vivax infections contribute significantly to the burden of malaria (1, 2). In all endemic areas except for Africa, P. vivax is often the dominant species, and at least 100 million cases are reported annually (2, 3). Although vivax malaria is clinically less likely than P. falciparum to develop into a life threatening disease, it exerts a substantial toll on the individual's health and economic well being. The chronic, long-lasting nature of the infection contributes substantially to morbidity. Chronicity is because of hypnozoites, dormant liver stages from which fresh blood infection or relapses originate up to 2 years after the infectious bite (4). The presence of hypnozoites make infections by P. vivax difficult to cure radically and pose a serious obstacle to the control and eventual eradication of this parasite.The description of the P. falciparum genome (5) and staged erythrocytic transcriptome (6, 7) has provided an invaluable resource for the study of this important species. It would be of fundamental and practical interest to do the same for P. vivax because there are important biological and clinical differences between this species and P. falciparum, whose basis is currently unknown (8). For example, the presence of circulating mature erythrocytic stages of P. vivax would suggest that multigene families and processes implicated in antigenic variation and immune evasion are quite different to P. falciparum, whose mature asexual red cell stages generally sequester. Unlike P. falciparum, P. vivax has a selective preference for infecting reticulocytes (9), strongly suggesting an alternate red cell attachment invasion mechanism. In contrast to the rigid, sticky and knobby P. falciparum infected red cell, P. vivax remodels the host-cell membranes to produce a highly deformable erythrocyte characterized by numerous caveola-vesicle complexes (10-12). Finally, the kinetics of gametocyte production in P. vivax is also different than P. falciparum, with P. vivax gametocytes appearing much earlier and being relatively short lived (8). Aside ...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites

Bozdech

Mok

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

244

272

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show abstract

“…The five parasite lines were tightly synchronized to a 0-to 5-h window, and RNA was obtained at seven time points along the asexual blood cycle. Relative transcript levels were determined by hybridizing samples against a common reference pool in a long-oligonucleotides microarray (Hu et al 2007). Principal component analysis (PCA) revealed clustering of samples collected at the same time point, as expected for wellsynchronized samples.…”

Section: Identification Of Genes Under Clonally Variant Expressionmentioning

confidence: 99%

“…The microarray used in this study is based on long oligonucleotides (70 nt) designed against the PlasmoDB 4.4 release of the 3D7 reference P. falciparum genome (Hu et al 2007). We reannotated the microarray against the 3D7 PlasmoDB 7.0 genome release, which resulted in changes in more than 700 probes, including removal of cross-reactive probes.…”

Section: Microarray Experimentsmentioning

confidence: 99%

Transcriptional variation in the malaria parasitePlasmodium falciparum

Rovira-Graells¹,

Gupta²,

Planet³

et al. 2012

Genome Res.

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Malaria genetic variation has been extensively characterized, but the level of epigenetic plasticity remains largely unexplored. Here we provide a comprehensive characterization of transcriptional variation in the most lethal malaria parasite, Plasmodium falciparum, based on highly accurate transcriptional analysis of isogenic parasite lines grown under homogeneous conditions. This analysis revealed extensive transcriptional heterogeneity within genetically homogeneous clonal parasite populations. We show that clonally variant expression controlled at the epigenetic level is an intrinsic property of specific genes and gene families, the majority of which participate in host-parasite interactions. Intrinsic transcriptional variability is not restricted to genes involved in immune evasion, but also affects genes linked to lipid metabolism, protein folding, erythrocyte remodeling, or transcriptional regulation, among others, indicating that epigenetic variation results in both antigenic and functional variation. We observed a general association between heterochromatin marks and clonally variant expression, extending previous observations for specific genes to essentially all variantly expressed gene families. These results suggest that phenotypic variation of functionally unrelated P. falciparum gene families is mediated by a common mechanism based on reversible formation of H3K9me3-based heterochromatin. In changing environments, diversity confers fitness to a population. Our results support the idea that P. falciparum uses a bethedging strategy, as an alternative to directed transcriptional responses, to adapt to common fluctuations in its environment. Consistent with this idea, we found that transcriptionally different isogenic parasite lines markedly differed in their survival to heat-shock mimicking febrile episodes and adapted to periodic heat-shock with a pattern consistent with natural selection of pre-existing parasites.

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“…Numerous publications and software tools are currently available for designing DNA microarray probes (8)(9)(10)(11). However there are no software packages or even design rules published so far specifically for DNA barcode probes.…”

mentioning

confidence: 99%

Design of 240,000 orthogonal 25mer DNA barcode probes

Schlabach

Hannon

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

157

120

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DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.A DNA barcode is a short DNA sequence that uniquely identifies a certain linked feature such as a gene or a mutation. Linking features to DNA barcodes of homogenous length and melting temperature (T m ) allows experiments to be performed on the features in a pooled format, with subsequent deconvolution by PCR followed by microarray hybridization or high throughput sequencing. DNA barcode technology greatly improves the throughput of genetic screens, making possible experiments that would otherwise be quite time-consuming or laborious. For example, DNA barcodes built into the yeast deletion collection have facilitated identification of genes whose mutants are depleted or enriched under various growth conditions or drug treatments (1-4).For the construction of large libraries of short hairpin RNAs (5) or open-reading frames (6), it is desirable to have the libraries linked with barcodes with superior microarray hybridization characteristics. Although the DNA barcodes in the yeast deletion collection have performed well, there are only about 16,000 unique barcodes in the TAG4 set (7), which are too few for barcoding large mammalian libraries. Using random barcodes for these large libraries is less than optimal, because of the frequent off-target hybridization that occurs with random barcodes.Numerous publications and software tools are currently available for designing DNA microarray probes (8-11). However there are no software packages or even design rules published so far specifically for DNA barcode probes. Regular probe design procedures do not fit the purpose of barcode probes very well because of one major difference in target sequence constraints. For current DNA probe design procedures, there is a fixed set of long DNA sequences (such as all yeast open-reading frames or all human RefSeq sequences) that constrain target sequences. One or more short tags (probes) are then picked that uniquely identify each target sequence and display reduced crosshybridization to regions of other targets. In the case of barcode designs, however, the set of target sequences is not fixed. Instead, we are free to select optimal probes from the enormous space of short oligos of the same length. Also, because the probes and targets are the same sequences in the barcode case, cross...

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Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

Cited by 54 publications

References 35 publications

The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites

The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites

Transcriptional variation in the malaria parasitePlasmodium falciparum

Design of 240,000 orthogonal 25mer DNA barcode probes

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