RPH1 Rph1p [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: RPH1
Official Full Name: Rph1p
Primary source: SGD:S000000971
Locus tag: YER169W
See related: AllianceGenome:SGD:S000000971; FungiDB:YER169W; VEuPathDB:YER169W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: KDM4
Summary: Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; histone H3 demethylase activity; and sequence-specific DNA binding activity. Involved in negative regulation of autophagy; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription elongation by RNA polymerase II. Predicted to be active in chromatin and nucleus. Human ortholog(s) of this gene implicated in several diseases, including autistic disorder; autosomal dominant intellectual developmental disorder 65; gastrointestinal system cancer (multiple); head and neck cancer; and withdrawal disorder. Orthologous to several human genes including KDM4A (lysine demethylase 4A); KDM4B (lysine demethylase 4B); and KDM4F (lysine demethylase 4F). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: all
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Genomic context

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See RPH1 in Genome Data Viewer

Location:: chromosome: V

Exon count:: 1

Sequence:: Chromosome: V; NC_001137.3 (523369..525759)

Chromosome V - NC_001137.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001137.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition.
Title: 2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition.
Rph1 coordinates transcription of ribosomal protein genes and ribosomal RNAs to control cell growth under nutrient stress conditions.
Title: Rph1 coordinates transcription of ribosomal protein genes and ribosomal RNAs to control cell growth under nutrient stress conditions.
RPH1 mutation partially suppresses DNA damage sensitivity. The suppression works through the loss of the Rpd3L histone deacetylase complex.
Title: Rpd3L Contributes to the DNA Damage Sensitivity of Saccharomyces cerevisiae Checkpoint Mutants.
led to the identification of Rph1 as a master transcriptional regulator of autophagy
Title: Rph1 mediates the nutrient-limitation signaling pathway leading to transcriptional activation of autophagy.
Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy.
Title: Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy.
activity of Rph1 is not essential for its role in the transcriptional response to nutrient signaling
Title: The histone demethylase activity of Rph1 is not essential for its role in the transcriptional response to nutrient signaling.
Our findings confirm the regulatory role of Rph1 as a transcriptional repressor and reveal that Rph1 might be a regulatory node connecting different signaling pathways responding to environmental stresses.
Title: Dissociation of the H3K36 demethylase Rph1 from chromatin mediates derepression of environmental stress-response genes under genotoxic stress in Saccharomyces cerevisiae.
these results show that of the JmjC-containing proteins, Rph1 is the demethylase that is specific for histone H3K36 trimethylation during transcription elongation in vivo.
Title: Role of yeast JmjC-domain containing histone demethylases in actively transcribed regions.
Results demonstrates that the histone demethylase Rph1 is associated with a specific chromatin locus and modulates histone modifications to repress a DNA damage responsive gene under control of damage checkpoint signaling.
Title: The histone H3K36 demethylase Rph1/KDM4 regulates the expression of the photoreactivation gene PHR1.
Jhd1 and Rph1 demethylate histone H3 Lys36 in transcribed regions to promote elongation
Title: Two Saccharomyces cerevisiae JmjC domain proteins demethylate histone H3 Lys36 in transcribed regions to promote elongation.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K36 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K36 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K36 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	HDA more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of autophagy	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription elongation by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IC Inferred by Curator more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Rph1p

NP_011096.1

JmjC domain-containing histone demethylase; targets tri- and dimethylated H3K36; associates with actively transcribed regions and promotes elongation; repressor of autophagy-related genes in nutrient-replete conditions; damage-responsive repressor of PHR1; phosphorylated by the Rad53p-dependent DNA damage checkpoint pathway and by a Rim1p-mediated event during starvation; target of stress-induced hormesis; RPH1 has a paralog, GIS1, that arose from the whole genome duplication

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001137.3 Reference assembly

Range

523369..525759

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179059.1 → NP_011096.1 TPA: Rph1p

See identical proteins and their annotated locations for NP_011096.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D3DM77, P39956

UniProtKB/TrEMBL

G2WD55, N1P5G0

Conserved Domains (4) summary

smart00545
Location:13 → 54

JmjN; Small domain found in the jumonji family of transcription factors

COG5048
Location:507 → 759

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:711 → 732

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam02373
Location:222 → 338

JmjC; JmjC domain, hydroxylase