Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of Candida albicans Hda1 complex mutants (hda1∆∆, hda2∆∆ and hda3∆∆) and wildtype SN152 in yeast and hyphae inducing conditions

ABSTRACT: Candida albicans is a normally commensal yeast which becomes pathogenic to human hosts under some conditions and specifically in immune compromised individuals. This contributes to a global health crisis of fungal disease. This yeast can morphologically adapt to the environment by reversibly developing hyphae which allows for traversing of tissue. Histone deacetylase 1 (Hda1) is involved in this transition as it is established that the deletion of the associated gene stunts this morphological switch. In Saccharomyces cerevisiae this protein complexes with two similarly named proteins: Hda2 and Hda3. Here we evaluate Candida albicans strains with mutations in the genes that code for these proteins. The strains are grown in yeast (YPD 30 °C) and hyphae (RPMI 37 °C) -inducing conditions for 90 minutes prior to RNA extraction. After alignment by HISAT2, the homozygous mutants are then individually compared to wildtype (matching growth conditions) using DESeq2.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Candida albicans

SUBMITTER: Alessia Buscaino

PROVIDER: E-MTAB-6920 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description: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).

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Dataset Information

RNA-seq of Candida albicans Hda1 complex mutants (hda1∆∆, hda2∆∆ and hda3∆∆) and wildtype SN152 in yeast and hyphae inducing conditions

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