biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsAdnane SellamCell line - Two-color microarrayCandida albicansCandida albicanshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-10882So far, there is no known regulatory circuits that mediate filamentation of the pathogenic yeast Candida albicans exclusively in response to hypoxia. In this study, we performed a quantitative analysis of gene deletion mutants from different collections of protein kinases and transcriptional regulators to identify specific regulator of the hypoxic filamentation. Our work uncovered two transcription factors, Ahr1 and Tye7, that act as prominent regulators of C. albicans filamentation specifically under hypoxia. In summary, we used genome-wide transcriptional profiling and promoter occupancy to characterize both Ahr1 and Tye7 regulons associated with the hypoxic filamentation in C. albicans.biostudies-arrayexpressScaning - Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 5-µm resolution for tiling arrays and 10-µm for expression arrays. ChIP-Chip data was normalized as described by Lavoie et al. (2010) PLoS Biol 8(3): e1000329. Expression array data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).Hybridization - The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with 1X SSC-0.2% SDS and 3 times with 0.1X SSC.Nucleic Acid Extraction - ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. Chromatin immunoprecipitation was performed by following the protocol available at http://www.ircm.qc.ca/microsites/francoisrobert/en/317.html with the following exceptions: chromatin was sonicated to an average 300 bp, and 700 μl of whole-cell extract (WCE) were incubated with IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01beads). RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174–1183, using RNeasy Mini kit (Qiagen).Sample Collection - For the transcriptional profiling experiments using 2-channels microarrays, all Cy5-labelled cDNA were from cells under hypoxia while Cy3-labelled control cDNA were grown under normoxia. For both microarray and ChIP-chip experiments, cells were collected directly from agar plates with a cell scraper after growing for 48 h at 37°C under either normoxia (21% O2) or hypoxia (1% O2). Growth under hypoxic conditions was achieved by incubating agar plates in an anaerobic chamber (Oxoid; HP0011A) flushed daily with nitrogen to remove oxygen and any gaseous by-products.Labeling - Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen). For expression profiling experiment, 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsAdnane SellamfalseTranscriptional control of hypoxic hyphal growth in the fungal pathogen Candida albicansSo far, there is no known regulatory circuits that mediate filamentation of the pathogenic yeast Candida albicans exclusively in response to hypoxia. In this study, we performed a quantitative analysis of gene deletion mutants from different collections of protein kinases and transcriptional regulators to identify specific regulator of the hypoxic filamentation. Our work uncovered two transcription factors, Ahr1 and Tye7, that act as prominent regulators of C. albicans filamentation specifically under hypoxia. In summary, we used genome-wide transcriptional profiling and promoter occupancy to characterize both Ahr1 and Tye7 regulons associated with the hypoxic filamentation in C. albicans.2021-08-18T00:00:00Z2022-02-23T18:45:05.973Z2022-02-23T18:45:05.973ZE-MTAB-10882E-MTAB-10883EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003815