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Series GSE71728 Query DataSets for GSE71728
Status Public on Aug 05, 2015
Title Function and regulation of Cph2 in Candida albicans [ChIP-Seq]
Organism Candida albicans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Candida albicans is associated with humans as both a harmless commensal organism and a pathogen. Cph2 is a transcription factor whose DNA binding domain is similar to mammalian sterol response element binding proteins (SREBPs). SREBPs are master regulators of cellular cholesterol levels, and are highly conserved from fungi to mammals. However, ergosterol biosynthesis is regulated by the zinc finger transcription factor Upc2 in C. albicans and several other yeasts. Cph2 is not necessary for ergosterol biosynthesis, but important for colonization in the murine gastrointestinal tract. Here we demonstrate that Cph2 is a membrane-associated transcription factor that is processed to release the N-terminal DNA binding domain like SREBPs; but its cleavage is not regulated by cellular levels of ergosterol or oxygen. ChIP-Seq shows that Cph2 binds to the promoters of HMS1 and other components of the regulatory circuit for GI tract colonization. In addition, 50% of Cph2 targets are also bound by Hms1 and other factors of the regulatory circuit. Several common targets function at the head of the glycolysis pathway. Thus, Cph2 is an integral part of the regulatory circuit for GI colonization that regulates glycolytic flux. RNA-seq shows a significant overlap in genes differentially regulated by Cph2 and hypoxia, and Cph2 is important for optimal expression of some hypoxia-responsive genes in glycolysis and the citric acid cycle. We suggest that Cph2 and Upc2 regulate hypoxia-responsive expression in different pathways, consistent with a synthetic lethal defect of the cph2 upc2 double mutant in hypoxia.
 
Overall design Genome binding/occupancy profiling by high throughput sequencing. ChIP-seq of Cph2 was carried out in a wild-type strain carrying N-terminal myc-tagged Cph2 under the MAL2 promoter (MAL2-myc-Cph2N). IP and INPUT samples from 2 independent experiments, as well as a sample of untagged wild-type control, were sequenced.
 
Contributor(s) Lane S, Di Lena P, Baldi P, Liu H
Citation(s) 26342020
Submission date Aug 04, 2015
Last update date May 15, 2019
Contact name Haoping Liu
E-mail h4liu@uci.edu
Phone 949-824-1137
Organization name University of California
Department Dept. of Biological Chemistry
Street address Med. Sci. I, Rm D234
City Irvine
State/province CA
ZIP/Postal code 926197
Country USA
 
Platforms (1)
GPL19036 Illumina HiSeq 2500 (Candida albicans)
Samples (6)
GSM1843887 IP rep 1
GSM1843888 IP rep 2
GSM1843889 Input rep 1
This SubSeries is part of SuperSeries:
GSE71904 Function and regulation of Cph2 in Candida albicans
Relations
BioProject PRJNA291924
SRA SRP062028

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71728_Cph2_bound_genes.txt.gz 2.6 Kb (ftp)(http) TXT
GSE71728_QUEST_IP1-IN1_recommended.txt.gz 10.9 Kb (ftp)(http) TXT
GSE71728_QUEST_IP2-IN2_recommended.txt.gz 1.4 Kb (ftp)(http) TXT
GSE71728_QUEST_WTIP-WTIN_recommended.txt.gz 14.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data is available on Series record

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