Version: 8.1.0
Date: Fri Apr 18 2025
34 results for PHO4

PHO4

(Saccharomyces cerevisiae)
Gene
Name: PHOsphate metabolism
Synonyms: YFR034C, phoD
Source: SGD:S000001930
Biotype: protein coding gene
Symbol: PHO4 (Sce)
Symbol: PHO4
Alleles: pho4-Δ (Sce)...pho4-4 (Sce)

pho4-Δ

(Saccharomyces cerevisiae)
Allele/Variant
Source: SGD:S000281151
Genes: PHO4 (Sce)
Synonyms: Not Available
Variant Type: unreported
Molecular Consequence: Not Available
Diseases: Not Available
Variant Name: Not Available
Symbol: pho4-Δ (Sce)
Genes: PHO4 (Sce)
Symbol: pho4-Δ

pho4-4

(Saccharomyces cerevisiae)
Allele/Variant
Source: SGD:S000286878
Genes: PHO4 (Sce)
Synonyms: Not Available
Variant Type: unreported
Molecular Consequence: Not Available
Diseases: Not Available
Variant Name: Not Available
Symbol: pho4-4 (Sce)
Genes: PHO4 (Sce)
Symbol: pho4-4

Pho4 binding to JokerCAKE 8-mer library

HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE99723
Tags: bioinformatics and computational biology
Summary: MITOMI 2.0 fluorescence intensity data for C-terminally 6xHis-tagged S. cerevisae Pho4 protein interacting with a JokerCAKE 8mer library containing joker characters.
Symbol: Pho4 binding to JokerCAKE 8-mer library
Name: Pho4 binding to JokerCAKE 8-mer library

PHO4 target expression for yeast S. cerevisiae under phosphate perturbation

(Saccharomyces cerevisiae)
HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE26770
Tags: phosphorus utilization
Summary: In this study, we determined the expression profiles of Pho4 and Cbf1 targeted genes in phosphate perturbation.
Symbol: PHO4 target expression for yeast S. cerevisiae under phosphate perturbation
Name: PHO4 target expression for yeast S. cerevisiae under phosphate perturbation

positive regulation of phosphate metabolic process

Gene Ontology
Source: GO:0045937
Synonyms:
  • activation of phosphate metabolic process
  • positive regulation of phosphate metabolism
Branch: biological process
Genes: PHO4 (Sce)

PHO5

(Saccharomyces cerevisiae)
Gene
Name: PHOsphate metabolism
Synonyms: YBR093C, phoE
Source: SGD:S000000297
Biotype: protein coding gene
Gene Synopsis: pathway derived cell surface glycoprotein; induced by phosphate starvation and coordinately regulated by PHO4

DIP-chip from Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5

HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE13751
Tags: chromatin organization
Summary: DNA Immunoprecipitation was performed using purified, naked, genomic DNA and purified recombinant DNA binding domains for S. cerevisiae transcription factors (Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5) and then competitively hybridized against input DNA on NimbleGen 385k whole-genome, 32bp, tiling arrays to identify the consensus sequence for each transcription factor as a whole in the genome.
Symbol: DIP-chip from Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5

cellular response to phosphate starvation

Gene Ontology
Source: GO:0016036
Synonyms: Not Available
Branch: biological process
Genes: PHO4 (Sce)

PHO11

(Saccharomyces cerevisiae)
Gene
Name: PHOsphate metabolism
Synonyms: YAR071W
Source: SGD:S000000094
Biotype: protein coding gene
Gene Synopsis: cell surface by the secretory pathway; induced by phosphate starvation and coordinately regulated by PHO4

Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer RNA-seq]

(Saccharomyces cerevisiae)
HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE97799
Tags: transcriptional regulation, phosphorus utilization
Summary: In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. We used RNA-seq to profile the transcriptome of wild type and mutants of Pho4 / Pho2, or Pho4 ortholog swap in S. cerevisiae, to identify genes induced by Pho4 or its orthologs in S. cerevisiae background.

Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4

HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE29506
Tags: transcription, phosphorus utilization
Summary: Binding of transcription factors to DNA is a key regulatory step in the control of gene expression
Symbol: Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4
Name: Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4

Role of the Pho4p transcription factor in the transcriptional response associated to AICAR and SAICAR accumulation

(Saccharomyces cerevisiae)
HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE13186
Tags: amino acid metabolism
Summary: We investigated the role of Pho4p in the transcriptional response associated to AICAR and SAICAR accumulation
Symbol: Role of the Pho4p transcription factor in the transcriptional response associated to AICAR and SAICAR

Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer ChIP-seq]

HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE97797
Tags: transcriptional regulation, phosphorus utilization
Summary: In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. We used Biotin-assisted Chromatin-ImmunoPrecipitation followed by high-throughput sequencing (BioChIP-seq) to identify the binding locations of Pho4 from both S. cerevisiae and C. glabrata in the S. cerevisiae background lacking the negative regulator Pho80, and either with or without Pho2.

PHO92

(Saccharomyces cerevisiae)
Gene
Name: PHOsphate metabolism
Synonyms: MRB1, YDR374C
Source: SGD:S000002782
Biotype: protein coding gene
Gene Synopsis: subsequent decay of m6A modified transcripts, resulting in timely meiotic recombination; regulates PHO4

Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [titration]

HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE163511
Tags: transcription
Summary: Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e. paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are co-expressed in the cell, and thus can compete for target sites across the genome. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data shows that Cbf1 and Pho4 greatly influence each other’s occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs' expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.

Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [competition]

HTP Dataset Index
High-Throughput (HTP) Dataset Index metadata provided by SGD
ID: GEO:GSE163509
Tags: transcription, genetic interaction
Summary: Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e. paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are co-expressed in the cell, and thus can compete for target sites across the genome. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data shows that Cbf1 and Pho4 greatly influence each other’s occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs' expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.

protein dimerization activity

Gene Ontology
Source: GO:0046983
Synonyms: Not Available
Branch: molecular function
Genes: PHO4 (Sce)

sequence-specific DNA binding

Gene Ontology
Source: GO:0043565
Synonyms:
  • sequence specific DNA binding
Branch: molecular function
Genes: PHO4 (Sce)

chromatin remodeling

Gene Ontology
Source: GO:0006338
Synonyms:
  • ATP-dependent chromatin remodeling
  • ATP-dependent chromatin remodelling
Branch: biological process
Genes: PHO4 (Sce)

DNA-binding transcription factor activity

Gene Ontology
Source: GO:0003700
Synonyms:
  • DNA binding transcription factor activity
  • bacterial-type DNA binding transcription factor activity
Branch: molecular function
Genes: PHO4 (Sce)

negative regulation of transcription by RNA polymerase II

Gene Ontology
Source: GO:0000122
Synonyms:
  • down regulation of global transcription from RNA polymerase II promoter
  • down regulation of transcription from RNA polymerase II promoter
Branch: biological process
Genes: PHO4 (Sce)

positive regulation of transcription by RNA polymerase II

Gene Ontology
Source: GO:0045944
Synonyms:
  • activation of global transcription from RNA polymerase II promoter
  • activation of transcription from RNA polymerase II promoter
Branch: biological process
Genes: PHO4 (Sce)

DNA binding

Gene Ontology
Source: GO:0003677
Synonyms:
  • microtubule/chromatin interaction
  • plasmid binding
Branch: molecular function
Genes: PHO4 (Sce)

nucleus

Gene Ontology
Source: GO:0005634
Synonyms:
  • cell nucleus
  • horsetail nucleus
Branch: cellular component
Genes: PHO4 (Sce)

cytoplasm

Gene Ontology
Source: GO:0005737
Synonyms: Not Available
Branch: cellular component
Genes: PHO4 (Sce)

(R64-2-1)chrVI:225352C>T

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225352C>T
Genes: PHO4 (Sce), QCR6 (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: missense_variant, intergenic_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225352C>T

(R64-2-1)chrVI:225428A>G

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225428A>G
Genes: PHO4 (Sce), QCR6 (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: intergenic_variant, synonymous_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225428A>G

(R64-2-1)chrVI:225899G>A

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225899G>A
Genes: PHO4 (Sce), YFR034W-A (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: intergenic_variant, synonymous_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225899G>A

(R64-2-1)chrVI:225130T>C

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225130T>C
Genes: PHO4 (Sce), QCR6 (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: missense_variant, intergenic_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225130T>C

(R64-2-1)chrVI:225313C>T

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225313C>T
Genes: PHO4 (Sce), QCR6 (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: missense_variant, intergenic_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225313C>T

(R64-2-1)chrVI:225030A>C

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225030A>C
Genes: PHO4 (Sce), QCR6 (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: missense_variant, intergenic_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225030A>C

(R64-2-1)chrVI:225913G>A

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225913G>A
Genes: PHO4 (Sce), YFR034W-A (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: intergenic_variant, synonymous_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225913G>A

(R64-2-1)chrVI:225457T>C

(Saccharomyces cerevisiae)
Allele/Variant
Source: NC_001138.5:g.225457T>C
Genes: PHO4 (Sce), QCR6 (Sce)
Synonyms: Not Available
Variant Type: SNP
Molecular Consequence: missense_variant, intergenic_variant
Diseases: Not Available
Variant Name: (R64-2-1)chrVI:225457T>C