Phf2 PHD finger protein 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Phf2provided by MGI
Official Full Name: PHD finger protein 2provided by MGI
Primary source: MGI:MGI:1338034
See related: Ensembl:ENSMUSG00000038025 AllianceGenome:MGI:1338034
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: GRC5
Summary: Enables histone H4-methyl-lysine-20 demethylase activity. Involved in epigenetic maintenance of chromatin in transcription-competent conformation; histone H3-K9 demethylation; and histone H4-K20 demethylation. Predicted to be located in kinetochore; nucleolus; and nucleoplasm. Is expressed in several structures, including alimentary system; eye; genitourinary system; nervous system; and respiratory system. Orthologous to human PHF2 (PHD finger protein 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 29.7), limb E14.5 (RPKM 14.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 A5; 13 24.96 cM

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (48955226..49024361, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (48801750..48870885, complement)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The H3K9 demethylase plant homeodomain finger protein 2 regulates interleukin 4 production in CD4[+] T cells.
Title: The H3K9 demethylase plant homeodomain finger protein 2 regulates interleukin 4 production in CD4(+) T cells.
PHF2 depletion induces R-loop accumulation that leads to extensive DNA damage and cell cycle arrest. These data reveal a role of PHF2 as a guarantor of genome stability that allows proper expansion of neural progenitors during development.
Title: PHF2 histone demethylase prevents DNA damage and genome instability by controlling cell cycle progression of neural progenitors.
The paper's findings establish a downstream epigenetic checkpoint, whereby Phf2, through facilitating H3K9me2 demethylation at specific gene promoters, protects liver from the pathogenesis progression of Non-alcoholic Fatty Liver Disease.
Title: The histone demethylase Phf2 acts as a molecular checkpoint to prevent NAFLD progression during obesity.
these results demonstrate that PHF2 histone demethylase controls adipogenic gene expression during differentiation.
Title: The histone demethylase PHF2 promotes fat cell differentiation as an epigenetic activator of both C/EBPα and C/EBPδ.
PHF2 enhances osteoblast differentiation by demethylating Runx2, while suppressor of variegation 3-9 homolog 1 (SUV39H1) inhibits bone formation by methylating it.
Title: Plant homeodomain finger protein 2 promotes bone formation by demethylating and activating Runx2 for osteoblast differentiation.
Arid5b recruits Phf2 to the promoter region of Sox9 target genes and stimulates H3K9me2 demethylation of these genes.
Title: Arid5b facilitates chondrogenesis by recruiting the histone demethylase Phf2 to Sox9-regulated genes.
Data from PHF2 knockout mice suggest that PHF2 plays roles in both adipogenesis and neonatal growth/weight gain; PHF2 interacts with promoter region of CEBPA (CCAAT-enhancer binding protein alpha) gene and demethylates histones in chromatin.
Title: Epigenetic regulation of adipogenesis by PHF2 histone demethylase.
histone H3K4 trimethylation by a homeodomain of PHF2 modulates histone demethylation
Title: Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Phf2 (e-PCR), detects polymorphism
- UniSTS:547286

D13Mit120 (e-PCR), detects polymorphism
- UniSTS:126946

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9 demethylase activity	TAS Traceable Author Statement more info	PubMed
enables histone H4K20 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables iron ion binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of rDNA heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in protein demethylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein demethylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription initiation-coupled chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
located_in kinetochore	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lysine-specific demethylase PHF2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_011078.3 → NP_035208.2 lysine-specific demethylase PHF2

See identical proteins and their annotated locations for NP_035208.2

Status: VALIDATED

Source sequence(s)

AC109249

Consensus CDS

CCDS26496.1

UniProtKB/Swiss-Prot

Q6A023, Q80WA8, Q9WTU0

Related

ENSMUSP00000047308.8, ENSMUST00000035540.9

Conserved Domains (3) summary

pfam02373
Location:236 → 336

JmjC; JmjC domain, hydroxylase

smart00558
Location:201 → 264

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cd15554
Location:7 → 53

PHD_PHF2_like; PHD finger found in PHF2, PHF8 and KDM7