SUV39H2
<table class="infobox infobox-gene">
<tr>
<th class="infobox-header" colspan="2">SUV39H2</th>
</tr>
<tr>
<td class="label">Full Name</td>
<td>Suppressor of Variegation 3-9 Homolog 2</td>
</tr>
<tr>
<td class="label">Gene Symbol</td>
<td>SUV39H2</td>
</tr>
<tr>
<td class="label">Aliases</td>
<td>KMT1B, SUV39H2L</td>
</tr>
<tr>
<td class="label">Chromosome</td>
<td>10p13</td>
</tr>
<tr>
<td class="label">Gene Type</td>
<td>Protein-coding</td>
</tr>
<tr>
<td class="label">OMIM</td>
<td>[606503](https://omim.org/entry/606503)</td>
</tr>
<tr>
<td class="label">UniProt</td>
<td>[Q9H5I1](https://www.uniprot.org/uniprot/Q9H5I1)</td>
</tr>
<tr>
<td class="label">HGNC</td>
<td>[17287](https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:17287)</td>
</tr>
<tr>
<td class="label">Entrez Gene</td>
<td>[79723](https://www.ncbi.nlm.nih.gov/gene/79723)</td>
</tr>
<tr>
<td class="label">Ensembl</td>
<td>[ENSG00000152455](https://ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000152455)</td>
</tr>
<tr>
<td class="label">Variant</td>
<td>Type</td>
</tr>
<tr>
<td class="label">rs78020275</td>
<td>Intronic</td>
</tr>
<tr>
<td class="label">SUV39H2 promoter methylation</td>
<td>Epigenetic</td>
</tr>
<tr>
<td class="label">KG Connections</td>
<td><a href="/atlas" style="color:#4fc3f7">1 edges</a></td>
</tr>
</table>
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SUV39H2
</div>
Overview
SUV39H2 is a human gene. Variants in SUV39H2 have been implicated in Alzheimer's Disease, Parkinson's Disease, Aging-Associated Neurodegeneration. This page covers the gene's normal function, disease associations, expression patterns, and key research findings relevant to neurodegeneration.
SUV39H2 (Suppressor of Variegation 3-9 Homolog 2), also designated KMT1B, encodes a histone lysine methyltransferase that catalyzes di- and trimethylation of histone H3 at lysine 9 (H3K9me2/3) at pericentromeric heterochromatin.<sup>[1]</sup> SUV39H2 is the autosomal paralog of [SUV39H1](/genes/suv39h1) (X-linked) and cooperates with it to establish constitutive heterochromatin. While both paralogs share the same catalytic activity, SUV39H2 has a unique N-terminal basic domain that provides additional chromatin-binding affinity and distinct expression patterns in the nervous system.<sup>[2]</sup> SUV39H2 maintains genomic stability, silences satellite repeats and retrotransposons, and protects against the heterochromatin erosion associated with aging and neurodegenerative diseases including [Alzheimer's disease](/diseases/alzheimers-disease) and [Parkinson's disease](/diseases/parkinsons-disease).
Function and Mechanism
SUV39H2 contains an N-terminal basic domain unique among SET domain proteins, a central chromodomain that reads pre-existing H3K9me marks, and a C-terminal SET domain that catalyzes methylation of H3K9. The basic domain provides DNA-binding capacity that enhances SUV39H2 chromatin association independently of the chromodomain.
Pericentromeric Heterochromatin Maintenance
SUV39H2 cooperates with [SUV39H1](/genes/suv39h1) to maintain H3K9me3 at pericentromeric satellite repeats. The two enzymes have partially redundant functions: single knockouts show mild heterochromatin defects, but double Suv39h1/h2 knockout mice exhibit severe pericentromeric heterochromatin loss, chromosome segregation errors, male-specific infertility, and genomic instability.<sup>[1]</sup> SUV39H2 compensates for SUV39H1 loss in many cell types, but this compensation is incomplete in [neurons](/entities/neurons).
HP1 Recruitment Loop
H3K9me3 deposited by SUV39H2 recruits [HP1α/CBX5](/genes/cbx5), HP1β, and HP1γ through their chromodomains. HP1 proteins in turn recruit additional SUV39H2 molecules through direct protein-protein interactions, establishing a self-reinforcing heterochromatin spreading mechanism. This positive feedback loop maintains stable heterochromatin domains across cell divisions.<sup>[3]</sup>
Retrotransposon Silencing
SUV39H2 silences LINE-1 (L1) and endogenous retroviral (ERV) elements through H3K9me3 deposition. In neurons, retrotransposon silencing is critical for genomic stability, as L1 retrotransposition has been detected in neural progenitor cells and may contribute to somatic mosaicism in the brain. Loss of SUV39H2-mediated silencing leads to increased L1 expression and retrotransposition.<sup>[4]</sup>
DNA Damage Response
SUV39H2 is recruited to DNA double-strand breaks where it deposits H3K9me3 to facilitate efficient DNA repair through the heterochromatin-associated DNA damage response (DDR). This function is particularly important in neurons, which accumulate oxidative DNA damage and rely on efficient repair mechanisms to maintain genomic integrity.<sup>[5]</sup>
Disease Associations
Alzheimer's Disease
In [Alzheimer's disease](/diseases/alzheimers-disease), global H3K9me3 levels decline in hippocampal and cortical neurons, reflecting impaired SUV39H1/H2 activity. This heterochromatin erosion leads to derepression of satellite repeats and retrotransposons, triggering innate immune responses through cytoplasmic DNA sensing pathways (cGAS-STING). The resulting neuroinflammation amplifies [amyloid-beta](/proteins/amyloid-beta) pathology and [tau](/proteins/tau) propagation.<sup>[6]</sup>
Parkinson's Disease
Dopaminergic neurons in [Parkinson's disease](/diseases/parkinsons-disease) show heterochromatin decondensation at pericentromeric regions. [Alpha-synuclein](/proteins/alpha-synuclein) oligomers bind to histones and disrupt SUV39H2-mediated H3K9me3 deposition, weakening heterochromatin integrity. This leads to reactivation of normally silenced repetitive elements and activation of inflammatory signaling.<sup>[7]</sup>
Aging-Associated Neurodegeneration
SUV39H2 expression declines with age in human brain tissue, contributing to the progressive heterochromatin erosion that characterizes brain aging. This age-dependent decline creates a permissive environment for retrotransposon reactivation and genomic instability, increasing vulnerability to neurodegenerative disease onset. Unlike SUV39H1, SUV39H2 shows more prominent age-related decline in cortical regions.<sup>[8]</sup>
Huntington's Disease
In [Huntington's disease](/diseases/huntington-disease), polyglutamine-expanded [huntingtin protein](/proteins/huntingtin) sequesters heterochromatin factors including SUV39H2, redistributing H3K9me3 from pericentromeric regions to ectopic genomic sites. This contributes to the global chromatin disorganization observed in HD striatal neurons.
Expression
SUV39H2 shows enrichment in the brain compared to many peripheral tissues, with particularly high expression in hippocampal CA1/CA3 pyramidal neurons, cortical layers II/III and V, cerebellar Purkinje cells, and substantia nigra dopaminergic neurons. During development, SUV39H2 is highly expressed in neural progenitor cells where it maintains heterochromatin through rapid cell divisions. Expression progressively declines with aging, particularly in brain regions vulnerable to neurodegeneration.
Common Variants
Therapeutic Implications
- SUV39H2 gene therapy: AAV-mediated overexpression to restore H3K9me3 at pericentromeric heterochromatin in vulnerable neurons
- Heterochromatin stabilizers: Small molecules that enhance HP1-H3K9me3 interaction to reinforce heterochromatin independently of SUV39H2 levels<sup>[9]</sup>
- Retrotransposon inhibitors: Nucleoside reverse transcriptase inhibitors (NRTIs) like lamivudine to block L1 retrotransposition downstream of SUV39H2 loss
- cGAS-STING antagonists: Blocking the innate immune response triggered by cytoplasmic DNA from derepressed retrotransposons
- SAM supplementation: Enhancing the methyl donor supply to boost residual SUV39H2 catalytic activity
See Also
- [SUV39H1](/genes/suv39h1) — Paralog (X-linked H3K9 methyltransferase)
- [CBX5](/genes/cbx5) — HP1α heterochromatin reader
- [SETDB1](/genes/setdb1) — Euchromatic H3K9 methyltransferase
- [EED](/genes/eed) — PRC2 core subunit
- [BMI1](/genes/bmi1) — PRC1 core subunit
External Links
- [NCBI Gene: SUV39H2](https://www.ncbi.nlm.nih.gov/gene/79723)
- [UniProt: Q9H5I1](https://www.uniprot.org/uniprot/Q9H5I1)
- [GeneCards: SUV39H2](https://www.genecards.org/cgi-bin/carddisp.pl?gene=SUV39H2)
References
[Peters et al., Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability (2001) (2001)](https://doi.org/10.1016/S0092-8674(01)
[O'Carroll et al., Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression (2000) (2000)](https://doi.org/10.1128/MCB.20.24.9423-9433.2000)
[Lachner et al., Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins (2001) (2001)](https://doi.org/10.1038/35065132)
[Bulut-Karslioglu et al., Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells (2014) (2014)](https://doi.org/10.1016/j.molcel.2014.05.029)
[Ayrapetov et al., DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin (2014) (2014)](https://doi.org/10.1073/pnas.1403565111)
[Frost et al., Tau promotes neurodegeneration through global chromatin relaxation (2014) (2014)](https://doi.org/10.1038/ncomms5595)
[Desplats et al., Alpha-synuclein sequesters Dnmt1 from the nucleus: a novel mechanism for epigenetic alterations in Lewy body diseases (2011) (2011)](https://doi.org/10.1074/jbc.C111.243015)
[Nativio et al., Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease (2018) (2018)](https://doi.org/10.1038/s41593-018-0101-9)
[Rea et al., Regulation of chromatin structure by site-specific histone H3 methyltransferases (2000) (2000)](https://doi.org/10.1038/35065138)
[Piao et al., The histone methyltransferase SUV39H2 is a novel component of the DNA damage response (2015) (2015)](https://doi.org/10.1016/j.cellsig.2015.08.010)