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

Sellam A, Hogues H, Askew C, Tebbji F, van Het Hoog M, Lavoie H, Kumamoto CA, Whiteway M, Nantel A - Genome Biol. (2010)

Bottom Line: Furthermore, we found that genomic regions adjacent to telomeres harbor a cluster of expressed ncRNAs.This comprehensive approach allowed the identification of different families of ncRNAs.In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montréal, Québec, H4P 2R2, Canada. Adnane.Sellam@cnrc-nrc.gc.ca

ABSTRACT

Background: 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.

Results: 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 2,000 novel transcriptional segments, including new ORFs and exons, non-coding RNAs (ncRNAs) as well as convincing cases of antisense gene transcription. We also characterized the 5' and 3' UTRs 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 ncRNAs.

Conclusions: In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements.

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Functional gene categories differentially regulated in hyphae, biofilm and caecum-grown cells. GO functional categories of (a) up- and (b) down-regulated genes are shown. P-values were calculated using hypergeometric distribution.
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Figure 5: Functional gene categories differentially regulated in hyphae, biofilm and caecum-grown cells. GO functional categories of (a) up- and (b) down-regulated genes are shown. P-values were calculated using hypergeometric distribution.

Mentions: As an opportunistic fungus, C. albicans must activate numerous transcriptional outputs to promote host colonization or virulence [71]. To elucidate the transcriptional patterns of annotated features in the different tested conditions, signal intensities of transfrags detected in cells growing as hyphae, biofilms and in the mouse caecum were compared to their counterparts in yeast cells (the control condition). GO analysis was used to assess the average expression levels of genes encoding specific classes of proteins in the three tested conditions (Figure 5; Additional files 11 and 12). In general, our results demonstrated a large overlap in transcripts present in hyphae or biofilms that were found in other studies. For instance, many differentially expressed genes in the three tested conditions encode adhesins and fungal cell wall proteins, consistent with their described roles during the interaction with the host and biofilm formation [71-73]. Unexpectedly, classes of genes involved in ncRNA metabolic processes, such as small nucleolar ribonucleoprotein (snoRNP) assembly complexes, were found differentially expressed in hyphae and in cells recovered from the caecum (Figure 5). Similarly, several genes that had never been detected before in C. albicans biofilms, including genes encoding tRNAs (GO term 'translation elongation'; P = 1.57e-59), were found to be significantly consistently repressed with the repression of ribosomal genes, as reported in other biofilm models [74,75].


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

Sellam A, Hogues H, Askew C, Tebbji F, van Het Hoog M, Lavoie H, Kumamoto CA, Whiteway M, Nantel A - Genome Biol. (2010)

Functional gene categories differentially regulated in hyphae, biofilm and caecum-grown cells. GO functional categories of (a) up- and (b) down-regulated genes are shown. P-values were calculated using hypergeometric distribution.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2926782&req=5

Figure 5: Functional gene categories differentially regulated in hyphae, biofilm and caecum-grown cells. GO functional categories of (a) up- and (b) down-regulated genes are shown. P-values were calculated using hypergeometric distribution.
Mentions: As an opportunistic fungus, C. albicans must activate numerous transcriptional outputs to promote host colonization or virulence [71]. To elucidate the transcriptional patterns of annotated features in the different tested conditions, signal intensities of transfrags detected in cells growing as hyphae, biofilms and in the mouse caecum were compared to their counterparts in yeast cells (the control condition). GO analysis was used to assess the average expression levels of genes encoding specific classes of proteins in the three tested conditions (Figure 5; Additional files 11 and 12). In general, our results demonstrated a large overlap in transcripts present in hyphae or biofilms that were found in other studies. For instance, many differentially expressed genes in the three tested conditions encode adhesins and fungal cell wall proteins, consistent with their described roles during the interaction with the host and biofilm formation [71-73]. Unexpectedly, classes of genes involved in ncRNA metabolic processes, such as small nucleolar ribonucleoprotein (snoRNP) assembly complexes, were found differentially expressed in hyphae and in cells recovered from the caecum (Figure 5). Similarly, several genes that had never been detected before in C. albicans biofilms, including genes encoding tRNAs (GO term 'translation elongation'; P = 1.57e-59), were found to be significantly consistently repressed with the repression of ribosomal genes, as reported in other biofilm models [74,75].

Bottom Line: Furthermore, we found that genomic regions adjacent to telomeres harbor a cluster of expressed ncRNAs.This comprehensive approach allowed the identification of different families of ncRNAs.In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montréal, Québec, H4P 2R2, Canada. Adnane.Sellam@cnrc-nrc.gc.ca

ABSTRACT

Background: 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.

Results: 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 2,000 novel transcriptional segments, including new ORFs and exons, non-coding RNAs (ncRNAs) as well as convincing cases of antisense gene transcription. We also characterized the 5' and 3' UTRs 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 ncRNAs.

Conclusions: In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements.

Show MeSH
Related in: MedlinePlus