Transcriptomics

Dataset Information

3

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high resolution tiling arrays


ABSTRACT: Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. Here we have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to C. albicans pathogenicity, including biofilm, lab-grown yeast and serum-induced hyphae as well as cells isolated from the mouse caecum. This work provides a genome-wide experimental validation for a large number of predicted ORFs for which transcription had not been detected by other approaches. Additionally, we identified more than 2000 novel transcriptional segments, including new ORFs and exons, non-coding RNAs (ncRNA) as well as convincing cases of antisense gene transcription. We also characterized the 5’- and 3’-untranslated regions (UTR) of expressed ORFs, and established that genes with long 5’UTRs are significantly enriched in regulatory functions controlling filamentous growth. Furthermore, we found that genomic regions adjacent to telomeres harbor a cluster of expressed ncRNAs. To validate and confirm new ncRNA candidates, we adapted an iterative strategy combining both genome-wide occupancy of the different subunits of RNA polymerases I, II and III, and expression data. This comprehensive approach allowed the identification of different families of ncRNA. In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to a discovery of new ORF and non-coding genetic elements. We have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to Candida albicans pathogenicity, including biofilm, lab-grown yeast and serum-induced hyphae as well as cells isolated from the mouse caecum. We also adapted a strategy in which genome-wide occupancy of different subunits of RNA polymerases (RNAP) I, II and III, is combined with expression data to annotate ncRNAs resulting from real transcriptional events. For this purpose we have performed ChIP-chip of subunits that represent the three RNAP machines in C. albicans cells growing in rich media (YPD) at 30°C. In this study, we performed peak detection only for RNA Polymerase III (Rpc82p). All detected peaks and their genomic features are included as a supplementary file on the Sample record (GSM561024).

ORGANISM(S): Candida albicans  

SUBMITTER: Hugo Lavoie   Carol A Kumamoto  Malcolm Whiteway  André Nantel  Marco vanhetHoog  Hervé Hogues  Adnane Sellam  Christopher Askew  Faiza Tebbji 

PROVIDER: E-GEOD-22625 | ArrayExpress | 2010-07-07

SECONDARY ACCESSION(S): GSE22625PRJNA128203

REPOSITORIES: GEO, ArrayExpress

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Publications

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays.

Sellam Adnane A   Hogues Hervé H   Askew Christopher C   Tebbji Faiza F   van Het Hoog Marco M   Lavoie Hugo H   Kumamoto Carol A CA   Whiteway Malcolm M   Nantel André A  

Genome Biology 20100709 7


Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation.We have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to C. albicans pa  ...[more]

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