PRDM9

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PRDM9

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PRDM9

<table class="infobox infobox-gene">
<tr>
<th class="infobox-header" colspan="2">PRDM9</th>
</tr>
<tr>
<td class="label">Full Name</td>
<td>PR/SET Domain 9</td>
</tr>
<tr>
<td class="label">Gene Symbol</td>
<td>PRDM9</td>
</tr>
<tr>
<td class="label">Aliases</td>
<td>MEISETZ, PFM6, ZNF899</td>
</tr>
<tr>
<td class="label">Chromosome</td>
<td>5p14.2</td>
</tr>
<tr>
<td class="label">Gene Type</td>
<td>Protein-coding</td>
</tr>
<tr>
<td class="label">OMIM</td>
<td>[609760](https://omim.org/entry/609760)</td>
</tr>
<tr>
<td class="label">UniProt</td>
<td>[Q9NQV7](https://www.uniprot.org/uniprot/Q9NQV7)</td>
</tr>
<tr>
<td class="label">HGNC</td>
<td>[13994](https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:13994)</td>
</tr>
<tr>
<td class="label">Entrez Gene</td>
<td>[56979](https://www.ncbi.nlm.nih.gov/gene/56979)</td>
</tr>
<tr>
<td class="label">Ensembl</td>
<td>[ENSG00000164256](https://ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164256)</td>
</tr>
<tr>
<td class="label">Variant</td>
<td>Type</td>
</tr>
<tr>
<td class="label">ZnF array length polymorphism</td>
<td>Minisatellite repeat variation</td>
</tr>
<tr>
<td class="label">A allele (13 ZnFs)</td>
<td>Most common European variant</td>
</tr>
<tr>
<td class="label">C allele (17 ZnFs)</td>
<td>African-enriched variant</td>
</tr>
<tr>
<td class="label">p.L300P</td>
<td>Mis

...

PRDM9

<table class="infobox infobox-gene">
<tr>
<th class="infobox-header" colspan="2">PRDM9</th>
</tr>
<tr>
<td class="label">Full Name</td>
<td>PR/SET Domain 9</td>
</tr>
<tr>
<td class="label">Gene Symbol</td>
<td>PRDM9</td>
</tr>
<tr>
<td class="label">Aliases</td>
<td>MEISETZ, PFM6, ZNF899</td>
</tr>
<tr>
<td class="label">Chromosome</td>
<td>5p14.2</td>
</tr>
<tr>
<td class="label">Gene Type</td>
<td>Protein-coding</td>
</tr>
<tr>
<td class="label">OMIM</td>
<td>[609760](https://omim.org/entry/609760)</td>
</tr>
<tr>
<td class="label">UniProt</td>
<td>[Q9NQV7](https://www.uniprot.org/uniprot/Q9NQV7)</td>
</tr>
<tr>
<td class="label">HGNC</td>
<td>[13994](https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:13994)</td>
</tr>
<tr>
<td class="label">Entrez Gene</td>
<td>[56979](https://www.ncbi.nlm.nih.gov/gene/56979)</td>
</tr>
<tr>
<td class="label">Ensembl</td>
<td>[ENSG00000164256](https://ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000164256)</td>
</tr>
<tr>
<td class="label">Variant</td>
<td>Type</td>
</tr>
<tr>
<td class="label">ZnF array length polymorphism</td>
<td>Minisatellite repeat variation</td>
</tr>
<tr>
<td class="label">A allele (13 ZnFs)</td>
<td>Most common European variant</td>
</tr>
<tr>
<td class="label">C allele (17 ZnFs)</td>
<td>African-enriched variant</td>
</tr>
<tr>
<td class="label">p.L300P</td>
<td>Missense (PR/SET domain)</td>
</tr>
<tr>
<td class="label">5p14.2 SNPs</td>
<td>GWAS</td>
</tr>
<tr>
<td class="label">KG Connections</td>
<td><a href="/atlas" style="color:#4fc3f7">1 edges</a></td>
</tr>
</table>

PRDM9

</div>

Overview

PRDM9 is a human gene. Variants in PRDM9 have been implicated in Alzheimer's Disease, Parkinson's Disease, Genomic Instability in Aging [Neurons](/entities/neurons). This page covers the gene's normal function, disease associations, expression patterns, and key research findings relevant to neurodegeneration.

PRDM9 (PR/SET Domain 9), also known as MEISETZ, encodes a histone H3 lysine 4 trimethyltransferase with a tandem C2H2 zinc finger array. PRDM9 is the only sequence-specific DNA-binding histone methyltransferase known in mammals and is the primary determinant of meiotic recombination hotspot locations.[1] While PRDM9 is predominantly expressed in germline tissues, recent evidence has revealed non-canonical expression in the brain, where it participates in DNA repair, genomic stability maintenance, and regulation of repetitive element activity. PRDM9 variants have been associated with altered recombination rates at neurodegeneration-linked genomic loci, and PRDM9's role in DNA double-strand break processing connects it mechanistically to age-dependent genomic instability in neurons relevant to [Alzheimer's disease](/diseases/alzheimers-disease) and other neurodegenerative conditions.

Function and Mechanism

PRDM9 contains an N-terminal KRAB domain (protein-protein interactions), a central PR/SET domain (H3K4 trimethyltransferase activity), and a C-terminal tandem array of 8-18 C2H2 zinc fingers that confer sequence-specific DNA binding. The zinc finger array is the most rapidly evolving coding sequence in primates and determines hotspot locations.

Meiotic Recombination Hotspot Determination

PRDM9 binds specific DNA motifs through its zinc finger array and deposits H3K4me3 at bound sites, marking them as active recombination hotspots. This H3K4me3 mark recruits the meiotic DSB machinery (SPO11) through interactions with the PRDM9-CXXC1 complex and the cohesin-associated protein CTCF. PRDM9 is thus the master regulator of where meiotic crossovers occur in the genome.[1]

H3K4me3 and H3K36me3 Dual Activity

PRDM9's PR/SET domain has dual methyltransferase specificity, depositing both H3K4me3 and H3K36me3 at target sites. This unique combination of activating histone marks creates a distinctive chromatin signature at recombination hotspots that differs from the marks deposited by other H3K4 methyltransferases like [SETD1A](/genes/setd1a) or [SETD1B](/genes/setd1b).[2]

Non-Canonical Brain Expression

PRDM9 is expressed at low levels in the adult brain, particularly in the [hippocampus](/brain-regions/hippocampus), prefrontal [cortex](/brain-regions/cortex), and cerebellum. In post-mitotic neurons, PRDM9 appears to function not in meiotic recombination but in DNA repair and transposable element regulation. PRDM9 marks specific genomic loci with H3K4me3 to facilitate DNA double-strand break repair, a function that becomes increasingly important as neurons accumulate DNA damage with aging.[3]

Transposable Element Regulation

PRDM9 zinc fingers bind sequences within LINE-1, SINE, and LTR retrotransposons. In the germline, this binding drives recombination at repetitive elements; in neurons, PRDM9 binding may contribute to chromatin-based silencing of transposable elements that become derepressed during aging and neurodegeneration. The interplay between PRDM9 and heterochromatin machinery ([SUV39H1](/genes/suv39h1), [SETDB1](/genes/setdb1), [CBX5](/genes/cbx5)) at repetitive elements represents a novel layer of transposon control.[4]

Disease Associations

Alzheimer's Disease

Genetic variants in PRDM9 influence recombination rates at genomic regions containing AD risk genes, including the [APOE](/proteins/apoe) locus on chromosome 19. Different PRDM9 alleles create distinct recombination landscapes that modulate linkage disequilibrium patterns around AD risk variants, potentially affecting the penetrance of GWAS-identified risk loci. Additionally, age-related decline of neuronal PRDM9 expression reduces DNA repair capacity at PRDM9-targeted loci, contributing to accumulation of unrepaired DSBs in hippocampal neurons.[5]

In the context of [Alzheimer's disease](/diseases/alzheimers-disease), PRDM9 represents a unique intersection of germline genomics and somatic neurodegeneration: the same enzyme that determines where crossovers occur in meiosis also influences where DNA damage accumulates in aging neurons, because PRDM9-marked sites have distinctive chromatin accessibility and repair kinetics.[5]

Parkinson's Disease

PRDM9 allelic variation affects recombination at the SNCA ([alpha-synuclein](/proteins/alpha-synuclein)) locus and LRRK2 locus, two major [Parkinson's disease](/diseases/parkinsons-disease) risk genes. Specific PRDM9 zinc finger configurations that place recombination hotspots within or near these genes alter the haplotype structure and may modulate disease risk through effects on gene regulation and structural variant formation.[6]

Genomic Instability in Aging Neurons

Post-mitotic neurons accumulate somatic mutations, insertions, and structural rearrangements over the lifespan. PRDM9-dependent H3K4me3 deposition at specific genomic sites marks regions for preferential DNA repair. Loss of PRDM9 with aging creates "cold spots" for repair, where DNA damage persists and drives genomic instability. This mechanism contributes to the somatic mosaicism observed in aging brains and may accelerate neurodegeneration.[7]

Infertility (Primary Known Disease)

Homozygous loss-of-function PRDM9 variants cause male infertility due to meiotic arrest. While this is the primary clinical manifestation, heterozygous carriers show altered recombination landscapes that may modulate complex disease risk through effects on haplotype structure across the genome.[1]

Expression in the Nervous System

PRDM9 expression in the brain is low compared to testis (its primary expression site) but is detectable by RNA-seq and single-cell transcriptomics in specific neuronal populations. Highest brain expression is in hippocampal CA1 pyramidal neurons, [entorhinal cortex](/brain-regions/entorhinal-cortex) layer II stellate cells, and cerebellar Purkinje cells — all populations vulnerable to neurodegeneration.[3]

Expression is neuronal-specific in the brain; glial cells ([astrocytes](/entities/astrocytes), [microglia](/cell-types/microglia-neuroinflammation), oligodendrocytes) show minimal PRDM9 expression. Neuronal PRDM9 expression declines with aging, particularly after age 60, paralleling the increase in DNA damage and transposable element derepression observed in aging brains.[4]

Common Variants

Therapeutic Implications

PRDM9 is not a conventional drug target, but its biology has several therapeutic implications for neurodegeneration:

DNA repair enhancement: Understanding which genomic sites are PRDM9-dependent for repair could enable targeted interventions to maintain repair capacity at neurodegeneration-relevant loci. Synthetic zinc finger proteins engineered to mimic PRDM9 binding at specific targets could direct H3K4me3 and repair factor recruitment to vulnerable genomic regions.[7]

Transposable element control: PRDM9 decline contributes to LINE-1 derepression in aging neurons. Strategies to maintain PRDM9 expression or substitute its transposon-silencing function (through [SETDB1](/genes/setdb1) or [SUV39H1](/genes/suv39h1) activation) could reduce transposon-mediated genomic instability in neurodegeneration.[4]

Pharmacogenomic implications: PRDM9 allelic variation affects haplotype structure at disease loci, influencing which variants co-segregate. This has implications for pharmacogenomic predictions of drug response, particularly for therapies targeting proteins encoded by genes within PRDM9-influenced recombination intervals.[8]

External Links

[OMIM: 609760](https://omim.org/entry/609760)
[GeneCards: PRDM9](https://www.genecards.org/cgi-bin/carddisp.pl?gene=PRDM9)
[UniProt: Q9NQV7](https://www.uniprot.org/uniprot/Q9NQV7)
[Allen Brain Atlas: PRDM9](https://portal.brain-map.org/search?query=PRDM9)
[GTEx Portal: PRDM9](https://gtexportal.org/home/gene/PRDM9)

References

[Baudat et al., PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice (2010) (2010)](https://doi.org/10.1126/science.1183439)

[Powers et al., The meiotic recombination activator PRDM9 trimethylates both H3K36 and H3K4 at recombination hotspots in vivo (2016) (2016)](https://doi.org/10.1371/journal.pgen.1006146)

[Altemose et al., A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis (2017) (2017)](https://doi.org/10.7554/eLife.28383)

[De Cecco et al., L1 drives IFN in senescent cells and promotes age-associated inflammation (2019) (2019)](https://doi.org/10.1038/s41586-018-0784-9)

[Unknown, Coop & Przeworski, An evolutionary view of human recombination (2007) (2007)](https://doi.org/10.1038/nrg2048)

[Berg et al., PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans (2010) (2010)](https://doi.org/10.1038/ng.658)

[Madabhushi et al., Activity-induced DNA breaks govern the expression of neuronal early-response genes (2015) (2015)](https://doi.org/10.1016/j.cell.2015.05.032)

[Kong et al., Fine-scale recombination rate differences between sexes, populations and individuals (2010) (2010)](https://doi.org/10.1038/nature09525)

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PRDM9

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kg_node_id	PRDM9
entity_type	gene
origin_type	v1_polymorphic_backfill
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wiki_page_id	wp-c97db253b875
__merged_from	{'merged_at': '2026-05-13', 'unprefixed_id': 'genes-prdm9'}
_schema_version	1

📊 Evidence Profile Foundational

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📗 Cite This Artifact

PRDM9

PRDM9

PRDM9

Overview

Function and Mechanism

Meiotic Recombination Hotspot Determination

H3K4me3 and H3K36me3 Dual Activity

Non-Canonical Brain Expression

Transposable Element Regulation

Disease Associations

Alzheimer's Disease

Parkinson's Disease

Genomic Instability in Aging Neurons

Infertility (Primary Known Disease)

Expression in the Nervous System

Common Variants

Therapeutic Implications

See Also

External Links

References

💬 Discussion