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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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General features of transcribed regions in the C. albicans genome. Representative genes illustrating different transcriptional architectures are shown. (a) Nested genes. (b) Detection of INO4 intron. (c) Unannotated ORF. (d, e) CRH12 and CCW14 AS transcripts. (f) Intron-hosted snoRNA (snR18). (g) Putative conserved upstream ORF (uORF) of CLN3. (h) Unannotated 5' and 3' UTRs of ZCF37.
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Figure 2: General features of transcribed regions in the C. albicans genome. Representative genes illustrating different transcriptional architectures are shown. (a) Nested genes. (b) Detection of INO4 intron. (c) Unannotated ORF. (d, e) CRH12 and CCW14 AS transcripts. (f) Intron-hosted snoRNA (snR18). (g) Putative conserved upstream ORF (uORF) of CLN3. (h) Unannotated 5' and 3' UTRs of ZCF37.

Mentions: As shown in Figure 1, a clear correlation can be seen between the annotated ORFs and the signal intensities of probes. In general, the obtained data are in agreement with the current Candida Genome Database (CGD) annotation [27]. At the gene level, our data allowed us to confirm the presence of introns in a number of ORFs, as shown for INO4 (ORF19.837.1) and EFB1 (ORF19.3838) (Figure 2b, f). Although the resolution of our tiling array was not high enough to delimit precisely intron boundaries, we were able to confirm the introns previously annotated in the C. albicans genome [28]. Moreover, extensions of transcripts corresponding to potential upstream ORFs (for example, CLN3; Figure 2g) or 5' and 3' UTRs (for example, ZCF37; Figure 2h) were identified in several locations. Genetic elements displaying complex transcriptional architectures, such as nested genes (TLO34 and ORF9.2662; Figure 2a; Additional file 3) or intronic nested genes (snR18 hosted by the EFB1 intron; Figure 2f), were identified. Additionally, a large number of sense-AS transcript pairs have been detected (PFK1 and EFB1; Figure 2d, f). Intriguingly, in some cases, AS transcription was found on the opposite strand rather than the annotated strands (CRH12 and CCW14; Figure 2d, e). Previously unannotated ORFs and ncRNAs were also uncovered (ORF19.6853.1 and snR18; Figure 2c, f). To illustrate the annotation concept, some of the most relevant C. albicans genome features will be highlighted throughout the manuscript.


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)

General features of transcribed regions in the C. albicans genome. Representative genes illustrating different transcriptional architectures are shown. (a) Nested genes. (b) Detection of INO4 intron. (c) Unannotated ORF. (d, e) CRH12 and CCW14 AS transcripts. (f) Intron-hosted snoRNA (snR18). (g) Putative conserved upstream ORF (uORF) of CLN3. (h) Unannotated 5' and 3' UTRs of ZCF37.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: General features of transcribed regions in the C. albicans genome. Representative genes illustrating different transcriptional architectures are shown. (a) Nested genes. (b) Detection of INO4 intron. (c) Unannotated ORF. (d, e) CRH12 and CCW14 AS transcripts. (f) Intron-hosted snoRNA (snR18). (g) Putative conserved upstream ORF (uORF) of CLN3. (h) Unannotated 5' and 3' UTRs of ZCF37.
Mentions: As shown in Figure 1, a clear correlation can be seen between the annotated ORFs and the signal intensities of probes. In general, the obtained data are in agreement with the current Candida Genome Database (CGD) annotation [27]. At the gene level, our data allowed us to confirm the presence of introns in a number of ORFs, as shown for INO4 (ORF19.837.1) and EFB1 (ORF19.3838) (Figure 2b, f). Although the resolution of our tiling array was not high enough to delimit precisely intron boundaries, we were able to confirm the introns previously annotated in the C. albicans genome [28]. Moreover, extensions of transcripts corresponding to potential upstream ORFs (for example, CLN3; Figure 2g) or 5' and 3' UTRs (for example, ZCF37; Figure 2h) were identified in several locations. Genetic elements displaying complex transcriptional architectures, such as nested genes (TLO34 and ORF9.2662; Figure 2a; Additional file 3) or intronic nested genes (snR18 hosted by the EFB1 intron; Figure 2f), were identified. Additionally, a large number of sense-AS transcript pairs have been detected (PFK1 and EFB1; Figure 2d, f). Intriguingly, in some cases, AS transcription was found on the opposite strand rather than the annotated strands (CRH12 and CCW14; Figure 2d, e). Previously unannotated ORFs and ncRNAs were also uncovered (ORF19.6853.1 and snR18; Figure 2c, f). To illustrate the annotation concept, some of the most relevant C. albicans genome features will be highlighted throughout the manuscript.

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