SUV39H1

Summary

SUV39H1 (SUV39H1 histone lysine methyltransferase, HGNC:11479) is a protein-coding gene on chromosome Xp11.23, encoding Histone-lysine N-methyltransferase SUV39H1 (O43463). Histone methyltransferase that specifically mediates trimethylation of ‘Lys-9’ of histone H3 (H3K9me3) using monomethylated H3 ‘Lys-9’ (H3K9me1) as substrate.

This gene encodes an evolutionarily-conserved protein containing an N-terminal chromodomain and a C-terminal SET domain. The encoded protein is a histone methyltransferase that trimethylates lysine 9 of histone H3, which results in transcriptional gene silencing. Loss of function of this gene disrupts heterochromatin formation and may cause chromosome instability. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 6839 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 30 total
• Druggable target: yes
• MANE Select transcript: NM_003173

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11479
Approved symbol	SUV39H1
Name	SUV39H1 histone lysine methyltransferase
Location	Xp11.23
Locus type	gene with protein product
Status	Approved
Aliases	KMT1A
Ensembl gene	ENSG00000101945
Ensembl biotype	protein_coding
OMIM	300254
Entrez	6839

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000337852, ENST00000376687, ENST00000462786, ENST00000482260, ENST00000936593, ENST00000956168

RefSeq mRNA: 2 — MANE Select: NM_003173 NM_001282166, NM_003173

CCDS: CCDS14304, CCDS65252

Canonical transcript exons

ENST00000376687 — 6 exons

Exon	Start	End
ENSE00001045610	48696734	48696803
ENSE00001318410	48700091	48700753
ENSE00001846136	48707437	48709016
ENSE00003480420	48706498	48706627
ENSE00003529239	48698902	48699047
ENSE00003637168	48706265	48706411

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 81.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.8549 / max 71.8621, expressed in 1564 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196282	6.8549	1564

Top tissues by expression

264 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.22	gold quality
granulocyte	CL:0000094	79.15	gold quality
ventricular zone	UBERON:0003053	78.51	gold quality
apex of heart	UBERON:0002098	77.76	gold quality
mucosa of transverse colon	UBERON:0004991	77.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.32	gold quality
epithelium of esophagus	UBERON:0001976	76.95	silver quality
esophagus squamous epithelium	UBERON:0006920	76.79	silver quality
tibialis anterior	UBERON:0001385	76.64	silver quality
ganglionic eminence	UBERON:0004023	76.39	gold quality
embryo	UBERON:0000922	76.22	gold quality
ileal mucosa	UBERON:0000331	76.11	silver quality
gastrocnemius	UBERON:0001388	75.91	gold quality
gingival epithelium	UBERON:0001949	75.74	silver quality
muscle of leg	UBERON:0001383	75.64	gold quality
stromal cell of endometrium	CL:0002255	75.54	gold quality
right lobe of liver	UBERON:0001114	75.44	gold quality
squamous epithelium	UBERON:0006914	75.42	silver quality
pancreatic ductal cell	CL:0002079	75.34	silver quality
lower esophagus mucosa	UBERON:0035834	75.02	gold quality
lymph node	UBERON:0000029	74.86	gold quality
hindlimb stylopod muscle	UBERON:0004252	74.65	gold quality
esophagus mucosa	UBERON:0002469	74.39	gold quality
spleen	UBERON:0002106	74.18	gold quality
bone marrow cell	CL:0002092	73.99	silver quality
tibial artery	UBERON:0007610	73.82	gold quality
popliteal artery	UBERON:0002250	73.81	gold quality
blood	UBERON:0000178	73.69	gold quality
right frontal lobe	UBERON:0002810	73.34	gold quality
vermiform appendix	UBERON:0001154	73.23	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.30

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
FOXP3
MYOD1	Repression
MYOG	Repression

Upstream regulators (CollecTRI, top): DNMT1, DNMT3B, E2F4, EZH2, MBD2

miRNA regulators (miRDB)

97 targeting SUV39H1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687

Literature-anchored findings (GeneRIF, showing 40)

• The human SUV39H1 gene is able to partially rescue Su(var)3-9 silencing defects in Drosophila. (PMID:11867540)
• Suv39h1 enhanced MBD1-mediated transcriptional repression via MBD, not the C-terminal transcriptional repression domain of MBD1. MBD1 links to histone deacetylases through Suv39h1, causing methylation and deacetylation of histones for gene inactivation (PMID:12711603)
• We investigated occupancy of ER-alpha promoter by pRb2/p130-E2F4/5-HDAC1-SUV39 H1-p300 and pRb2/p130-E2F4/5-HDAC1-SUV39H1-DNMT1 complexes, and provided a link between pRb2/p130 and chromatin-modifying enzymes in the regulation of ER-alpha transcription (PMID:12789259)
• SUV39H interacts with Smads and cooperates in BMP-induced repression. (PMID:15107829)
• Kaposi’s Sarcoma-Associated Herpesvirus (KSHV)LANA (Latency-associated nuclear antigen)interacts with SUV39H1 histone methyltransferase, a key component of heterochromatin formation, in KSHV-infected cells (PMID:15220403)
• The recruitment of SUV39H1 to heterochromatin is at least partly independent from that of HP1 and that HP1 transiently interacts with SUV39H1 at heterochromatin. (PMID:16103223)
• Interaction between HTLV-1Tax and human SUV39H1 and tethering of SUV39H1 by Tax to the HTLV-1 long terminal repeat (PMID:16409643)
• permanent transcriptional silencing is mediated by the association of PML-RAR with chromatin-modifying enzymes and by recruitment of the histone methyltransferase SUV39H1, responsible for trimethylation of lysine 9 of histone H3 (PMID:16449642)
• The association between RUNX1, histone deacetylases and SUV39H1 provides a molecular mechanism for repression and possibly gene silencing mediated by RUNX1. (PMID:16652147)
• Cabin1 recruits chromatin-modifying enzymes, both histone deacetylases and a histone methyltransferase, to repress myocyte enhancer factor 2 transcriptional activity (PMID:17172641)
• Suv39H1, HP1gamma and histone H3Lys9 trimethylation play a major role in chromatin-mediated repression of integrated HIV-1 gene expression. (PMID:17245432)
• SUV39H1 is significantly associated with DNMT1, but not with euchromatic promoter methylation in colorectal cancer (PMID:17657744)
• Presence of SUV39H1 enhances Evi1 transcriptional repression in a dose dependent manner. (PMID:18619962)
• Results identify DBC1 as a novel cellular inhibitor of SUV39H1 activity, and suggest that DBC1 may be an important regulator of heterochromatin formation and genomic stability by disrupting the SUV39H1-SirT1 complex and inactivating both enzymes. (PMID:19218236)
• CTIP2 is a constitutive p21 gene suppressor that cooperates with SUV39H1 and histone methylation to silence the p21 gene transcription. (PMID:19581932)
• MDM2 mediates formation of p53-SUV39H1/EHMT1 complex capable of methylating H3-K9 in vitro and on p53 target promoters in vivo. (PMID:20588255)
• RFX1 recruits SUV39H1 to the promoter regions of the CD11a and CD70 genes in CD4(+) T cells, thereby regulating local H3K9 tri-methylation levels. (PMID:21192791)
• findings suggest that Suv39H1 and Suv39H2 are key hypoxia-induced methyltransferases; their decline in fetal lung during late gestation is critical for epigenetic changes resulting in the developmental induction of SP-A (PMID:21402781)
• SirT1 preserves heterochromatin structure: it modulates Suv39h1 protein levels in stress conditions by preventing MDM2-mediated polyubiquitination at K87. (PMID:21504832)
• genetic association studies in a Finnish population with type I diabetes: No associations were found between SNPs in SUV39H1 and the diabetic complications studied. (PMID:21896933)
• The methylation of Sp1 increased the recruitment of Su(var) 3-9 homologue 1(Suv39H1)to the cyclin B1 promoter, resulting in deacetylation and methylation of histone H3 and subsequent downregulation of cyclin B1. (PMID:22036763)
• Snail interacted with Suv39H1 and recruited it to the E-cadherin promoter for transcriptional repression. (PMID:22562246)
• SUV39H1 generates a gradient of methylation marks at the kinetochore that provides spatiotemporal information essential for accurate chromosome segregation in mitosis. (PMID:22831836)
• Our study demonstrated that SUV39H1 up-regulation contributed to hepatocellular carcinoma development and metastasis. The tumor-suppressive miR-125b served as a negative regulator of SUV39H1. (PMID:22991213)
• The SUV39H1 chromodomain was shown to recognize histone H3K9me2/3 specifically. (PMID:23285239)
• Results suggest that by regulating JMJD2b and SUV39H1 expression, p53 not only controls transcription but also promotes HC relaxation to accelerate a rate-limiting step in the repair of complex genomes. (PMID:23376847)
• Methylation of SUV39H1 by SET7/9 results in heterochromatin relaxation and genome instability. (PMID:23509280)
• SUV39H1 expression was upregulated in glioma cell lines and in glioma tissues compared to normal brain, being positively correlated with grade and histological malignancy. (PMID:23943221)
• CRL4B promotes tumorigenesis by coordinating with SUV39H1/HP1/DNMT3A in DNA methylation-based epigenetic silencing (PMID:24292684)
• Short-chain fatty acids from periodontal pathogens suppress EZH2, and SUV39H1 to promote Kaposi’s sarcoma-associated herpesvirus replication. (PMID:24501407)
• results suggest that Suv39 h1-H3K9me3 epigenetic repression is involved in BZLF1 transcriptional silencing, providing a molecular basis for understanding the mechanism by which EBV latency is maintained (PMID:24588869)
• Suv39H1 induced apoptosis and inhibited cell proliferation in the gastric cancer MGC803 cell line, while decreasing BCL-2, pro-caspase-9, pro-caspase-3 and C-myc. Suv39H1 may be a potential gene target for anti-gastric carcinoma therapy. (PMID:24737085)
• High SUV39H1 expression is associated with hepatocellular carcinoma. (PMID:24844570)
• These results suggest a model in which SUV39H1 downregulation promotes the establishment of cellular senescence. (PMID:25063769)
• PHF2 is likely to repress rDNA transcription by competing with PHF8 for binding of ribosomal DNA promoter and by recruiting H3K9me2/3 methyltransferase SUV39H1. (PMID:25204660)
• we describe the synthesis of multidomain ‘designer chromatin’ templates and their application to dissecting the regulation of human Suv39h1 (PMID:26807716)
• KAT7-containing acetyltransferases associating with the Mis18 complex provides competence for histone turnover/exchange activity on alphoid DNA and prevents Suv39h1-mediated heterochromatin invasion into centromeres. (PMID:27270040)
• Overexpression of miR-125b and inhibition of its target, SUV39H1, in aging individuals reduces hematopoietic stem cells capacity of B cells generation. (PMID:27304919)
• Suv39h1 deficiency abrogates stress-dependent upregulation of HP1alpha and gamma, and enhances HP1beta levels. (PMID:28059589)
• Lysine methyltransferases (KMTs) that mediate methylation marks on histone and non-histone proteins are now recognized as important regulators of gene expression in cycling and non-cycling cells. Among these, the SUV39 sub-family of KMTs. (PMID:28106510)

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
danio_rerio	suv39h1a	ENSDARG00000026799
danio_rerio	suv39h1b	ENSDARG00000055753
mus_musculus	Suv39h1	ENSMUSG00000039231
rattus_norvegicus	Suv39h1	ENSRNOG00000039576
rattus_norvegicus		ENSRNOG00000063631
drosophila_melanogaster	Su(var)3-9	FBGN0263755
caenorhabditis_elegans	set-32	WBGENE00008062
caenorhabditis_elegans		WBGENE00008206
caenorhabditis_elegans		WBGENE00008527
caenorhabditis_elegans	met-1	WBGENE00016603
caenorhabditis_elegans		WBGENE00018023
caenorhabditis_elegans		WBGENE00019690
caenorhabditis_elegans		WBGENE00020006
caenorhabditis_elegans		WBGENE00020919
caenorhabditis_elegans		WBGENE00021282

Paralogs (19): KMT2C (ENSG00000055609), SETD1A (ENSG00000099381), EZH2 (ENSG00000106462), EZH1 (ENSG00000108799), NSD2 (ENSG00000109685), ASH1L (ENSG00000116539), KMT2A (ENSG00000118058), SETDB2 (ENSG00000136169), SETD1B (ENSG00000139718), SETDB1 (ENSG00000143379), NSD3 (ENSG00000147548), SETBP1 (ENSG00000152217), SUV39H2 (ENSG00000152455), NSD1 (ENSG00000165671), KMT2D (ENSG00000167548), EHMT1 (ENSG00000181090), SETD2 (ENSG00000181555), EHMT2 (ENSG00000204371), KMT2B (ENSG00000272333)

Protein

Protein identifiers

Histone-lysine N-methyltransferase SUV39H1 — O43463 (reviewed: O43463)

Alternative names: Histone H3-K9 methyltransferase 1, Lysine N-methyltransferase 1A, Position-effect variegation 3-9 homolog, Suppressor of variegation 3-9 homolog 1

All UniProt accessions (1): O43463

UniProt curated annotations — full annotation on UniProt →

Function. Histone methyltransferase that specifically mediates trimethylation of ‘Lys-9’ of histone H3 (H3K9me3) using monomethylated H3 ‘Lys-9’ (H3K9me1) as substrate. Also weakly methylates histone H1 (in vitro). H3 ‘Lys-9’ trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. H3 ‘Lys-9’ trimethylation is also required to direct DNA methylation at pericentric repeats. SUV39H1 is targeted to histone H3 via its interaction with RB1 and is involved in many processes, such as repression of MYOD1-stimulated differentiation, regulation of the control switch for exiting the cell cycle and entering differentiation, repression by the PML-RARA fusion protein, BMP-induced repression, repression of switch recombination to IgA and regulation of telomere length. Involved in the maintenance of H3K9me3 mark following DNA replication, when histone marks are diluted: HP1 recognizes the preexisting H3K9me3 mark and serves as a platform to recruit SUV39H1 to modify the adjacent newly incorporated histones. Component of the eNoSC (energy-dependent nucleolar silencing) complex, a complex that mediates silencing of rDNA in response to intracellular energy status and acts by recruiting histone-modifying enzymes. The eNoSC complex is able to sense the energy status of cell: upon glucose starvation, elevation of NAD(+)/NADP(+) ratio activates SIRT1, leading to histone H3 deacetylation followed by dimethylation of H3 at ‘Lys-9’ (H3K9me2) by SUV39H1 and the formation of silent chromatin in the rDNA locus. Recruited by the large PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1, contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 ‘Lys-9’ trimethylation. (Microbial infection) Plays a role in defense against mycobacterial infections. Methylates M.tuberculosis HupB on ‘Lys-140’, probably methylates HupB of M.bovis also. Methylation has an inhibitory effect on mycobacterial growth in the host. Macrophages expressing about 60% SUV39H1 are slightly more susceptible to M.bovis or M.tuberculosis infection. Chaetocin (an inhibitor of this enzyme) increases macrophage survival of M.tuberculosis. This protein inhibits biofilm formation by M.tuberculosis via ‘Lys-140’ trimethylation.

Subunit / interactions. Interacts with H3 and H4 histones. Interacts with GFI1B, DNMT3B, CBX1, CBX4, CCAR2, MBD1, RUNX1, RUNX3, MYOD1, SMAD5 and RB1. Interacts with SBF1 through the SET domain. Interacts with HDAC1 and HDAC2 through the N-terminus and associates with the core histone deacetylase complex composed of HDAC1, HDAC2, RBBP4 and RBBP7. Component of the eNoSC complex, composed of SIRT1, SUV39H1 and RRP8. Interacts (via SET domain) with MECOM; enhances MECOM transcriptional repression activity. Interacts with LMNA; the interaction increases stability of SUV39H1. The large PER complex involved in the histone methylation is composed of at least PER2, CBX3, TRIM28, SUV39H1 and/or SUV39H2; CBX3 mediates the formation of the complex. Interacts with ZNF152; this interaction initiates heterochromatin formation. (Microbial infection) Interacts with HTLV-1 Tax protein, leading to abrogate Tax transactivation of HTLV-1 LTR.

Subcellular location. Nucleus. Chromosome. Nucleus lamina. Nucleoplasm. Centromere Cytoplasmic vesicle. Phagosome lumen. Cell membrane.

Post-translational modifications. Phosphorylated on serine residues, and to a lesser degree, on threonine residues. The phosphorylated form is stabilized by SBF1 and is less active in its transcriptional repressor function. Phosphorylated at Ser-391 by CDK2 during S-M phases, impairing localization to heterochromatin. Ubiquitinated by the DCX(DCAF13) E3 ubiquitin ligase complex, leading to its degradation. Ubiquitinated at Lys-138 by the ECS(ASB7) complex, leading to its degradation. Acetylated at Lys-266, leading to inhibition of enzyme activity. SIRT1-mediated deacetylation relieves this inhibition. (Microbial infection) A higher molecular weight form is also seen in M.bovis infected cells.

Activity regulation. Inhibited by S-adenosyl-L-homocysteine. Negatively regulated by CCAR2.

Domain organisation. Although the SET domain contains the active site of enzymatic activity, both pre-SET and post-SET domains are required for methyltransferase activity. The SET domain also participates in stable binding to heterochromatin. In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.

Induction. (Microbial infection) Rapidly induced in macrophages upon infection by Mycobacterium bovis, M.smegmatis and M.tuberculosis but not E.coli or Candida glabrata (at protein level).

Similarity. Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
O43463-1	1	yes
O43463-2	2

RefSeq proteins (2): NP_001269095, NP_003164* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000953	Chromo/chromo_shadow_dom	Domain
IPR001214	SET_dom	Domain
IPR003616	Post-SET_dom	Domain
IPR007728	Pre-SET_dom	Domain
IPR011381	H3-K9_MeTrfase_SUV39H1/2-like	Family
IPR016197	Chromo-like_dom_sf	Homologous_superfamily
IPR023779	Chromodomain_CS	Conserved_site
IPR023780	Chromo_domain	Domain
IPR046341	SET_dom_sf	Homologous_superfamily
IPR050973	H3K9_Histone-Lys_N-MTase	Family

Pfam: PF00385, PF00856, PF05033

Enzyme classification (BRENDA):

• EC 2.1.1.355 — [histone H3]-lysine9 N-trimethyltransferase (BRENDA: 12 organisms, 83 substrates, 52 inhibitors, 11 Km, 11 kcat entries)

Substrate kinetics (BRENDA)

10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
HISTONE H3	0.0003–0.0009	2
BIOTINYL-MARTKQTARKSTGGKAPRKQ	0.0074	1
HISTONE H3 (1-13)	0.0011	1
HISTONE H3 (T11PHOS)	0.0006	1
HISTONE H3(K27A)	0.0002	1
HISTONE H3(K4A)	0.0002	1
HISTONE K4-ACETYLK9	0.0022	1
HISTONE K4-TRIMETHYLK9	0.0006	1
HISTONE K4AK9	0.0015	1
HISTONE H3 (S10PHOS)	—	0

Catalyzed reactions (Rhea), 2 shown:

• N(6)-methyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine + H(+) (RHEA:60284)
• N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine + H(+) (RHEA:60288)

UniProt features (49 total): binding site 20, mutagenesis site 11, domain 4, strand 3, helix 3, modified residue 2, region of interest 2, chain 1, cross-link 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
3MTS	X-RAY DIFFRACTION	2.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43463-F1	89.06	0.73

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (20): 186; 186; 194; 195; 195; 222; 222; 226; 228; 232; 254–256; 297 …

Post-translational modifications (3): 266, 391, 138

Mutagenesis-validated functional residues (11):

Position	Phenotype
64	abolishes methyltransferase activity.
67	abolishes methyltransferase activity.
138	abolished ubiquitination by the ecs(asb7) complex.
224	does not affect phosphorylation by cdk2.
266	loss of sirt1-mediated up-regulation of enzymatic activity.
266	significant loss of enzymatic activity.
320	strongly increases methylation of histone h3.
324	abolishes methylation of histone h3.
326	abolishes methylation of histone h3.
391	abolished phosphorylation by cdk2, promoting localization to heterochromatin. does not affect its interaction with asb7.
391	mimics phosphorylation; impaired localization to heterochromatin. does not affect its interaction with asb7.

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-3214841	PKMTs methylate histone lysines
R-HSA-427359	SIRT1 negatively regulates rRNA expression
R-HSA-212165	Epigenetic regulation of gene expression
R-HSA-3247509	Chromatin modifying enzymes
R-HSA-4839726	Chromatin organization
R-HSA-5250941	Negative epigenetic regulation of rRNA expression
R-HSA-74160	Gene expression (Transcription)

MSigDB gene sets: 285 (showing top): GOBP_CIRCADIAN_RHYTHM, E2F_Q4_01, GOBP_RIBOSOME_BIOGENESIS, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, E2F4DP1_01, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_GROWTH, GOBP_CELLULAR_SENESCENCE, GOBP_REGULATION_OF_DNA_REPAIR, AGGCACT_MIR5153P, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, CEBP_Q2

GO Biological Process (25): negative regulation of transcription by RNA polymerase II (GO:0000122), rDNA heterochromatin formation (GO:0000183), blastocyst hatching (GO:0001835), regulation of DNA repair (GO:0006282), chromatin organization (GO:0006325), rRNA processing (GO:0006364), DNA damage response (GO:0006974), circadian rhythm (GO:0007623), determination of adult lifespan (GO:0008340), cell differentiation (GO:0030154), regulation of bone mineralization (GO:0030500), heterochromatin formation (GO:0031507), methylation (GO:0032259), regulation of multicellular organism growth (GO:0040014), cellular response to glucose starvation (GO:0042149), epigenetic programming in the zygotic pronuclei (GO:0044725), negative regulation of cell cycle (GO:0045786), negative regulation of DNA-templated transcription (GO:0045892), regulation of transcription by glucose (GO:0046015), heterochromatin organization (GO:0070828), cellular response to hypoxia (GO:0071456), energy homeostasis (GO:0097009), regulation of cellular senescence (GO:2000772), negative regulation of gene expression, epigenetic (GO:0045814), rhythmic process (GO:0048511)

GO Molecular Function (14): transcription cis-regulatory region binding (GO:0000976), RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), chromatin binding (GO:0003682), zinc ion binding (GO:0008270), S-adenosylmethionine-dependent methyltransferase activity (GO:0008757), histone methyltransferase activity (GO:0042054), histone H3K9 methyltransferase activity (GO:0046974), histone H3 methyltransferase activity (GO:0140938), histone H3K9me2 methyltransferase activity (GO:0140947), histone H3K9 trimethyltransferase activity (GO:0140949), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (15): chromosome, centromeric region (GO:0000775), chromatin (GO:0000785), heterochromatin (GO:0000792), condensed nuclear chromosome (GO:0000794), nucleus (GO:0005634), nuclear lamina (GO:0005652), nucleoplasm (GO:0005654), chromatin silencing complex (GO:0005677), nucleolus (GO:0005730), plasma membrane (GO:0005886), cytoplasmic vesicle (GO:0031410), rDNA heterochromatin (GO:0033553), eNoSc complex (GO:0061773), chromosome (GO:0005694), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Chromatin modifying enzymes	1
Negative epigenetic regulation of rRNA expression	1
Gene expression (Transcription)	1
Chromatin organization	1
Epigenetic regulation of gene expression	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
regulation of DNA-templated transcription	2
binding	2
histone H3K9 methyltransferase activity	2
nuclear lumen	2
intracellular membraneless organelle	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
facultative heterochromatin formation	1
nucleolar chromatin organization	1
blastocyst development	1
hatching	1
DNA repair	1
regulation of DNA metabolic process	1
regulation of cellular response to stress	1
cellular component organization	1
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
cellular response to stress	1
rhythmic process	1
multicellular organismal process	1
cellular developmental process	1
regulation of ossification	1
bone mineralization	1
regulation of biomineral tissue development	1
cellular component assembly	1
heterochromatin boundary formation	1
negative regulation of gene expression, epigenetic	1
heterochromatin organization	1
metabolic process	1
multicellular organism growth	1
regulation of developmental growth	1
regulation of multicellular organismal process	1
cellular response to starvation	1
epigenetic programming of gene expression	1
cell cycle	1
negative regulation of cellular process	1
regulation of cell cycle	1

Protein interactions and networks

STRING

3595 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SUV39H1	DNMT1	P26358	997
SUV39H1	DNMT3A	Q9Y6K1	995
SUV39H1	CBX5	P45973	994
SUV39H1	MECP2	P51608	991
SUV39H1	SIRT1	Q96EB6	990
SUV39H1	CBX3	Q13185	990
SUV39H1	HDAC1	Q13547	989
SUV39H1	DNMT3B	Q9UBC3	986
SUV39H1	SETDB1	Q15047	975
SUV39H1	EHMT2	Q96KQ7	964
SUV39H1	CBX1	P23197	959
SUV39H1	RRP8	O43159	945
SUV39H1	E2F4	Q16254	936
SUV39H1	BCL11B	Q9C0K0	924
SUV39H1	EZH2	Q15910	910

IntAct

263 interactions, top by confidence:

A	B	Type	Score
SUV39H1	CBX5	psi-mi:“MI:0914”(association)	0.950
SUV39H1	CBX5	psi-mi:“MI:0915”(physical association)	0.950
CBX5	SUV39H1	psi-mi:“MI:0915”(physical association)	0.950
SUV39H1	CBX3	psi-mi:“MI:0915”(physical association)	0.800
SUV39H1	CBX1	psi-mi:“MI:0915”(physical association)	0.740
SUV39H1	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.720
SUV39H1	LZTS2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-7	SUV39H1	psi-mi:“MI:0915”(physical association)	0.720
LZTS2	SUV39H1	psi-mi:“MI:0915”(physical association)	0.720
HOOK2	SUV39H1	psi-mi:“MI:0915”(physical association)	0.670
SUV39H1	CEP70	psi-mi:“MI:0915”(physical association)	0.560
HEL25	SUV39H1	psi-mi:“MI:0915”(physical association)	0.560
CEP70	SUV39H1	psi-mi:“MI:0915”(physical association)	0.560
SUV39H1	HEL25	psi-mi:“MI:0915”(physical association)	0.560
SUV39H1	DVL3	psi-mi:“MI:0915”(physical association)	0.560
SUV39H1	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.560
SUV39H1	ZRANB1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (362): CBX5 (Two-hybrid), HOOK2 (Two-hybrid), CEP70 (Two-hybrid), LZTS2 (Two-hybrid), KRTAP10-7 (Two-hybrid), ESR1 (Biochemical Activity), SUV39H1 (Biochemical Activity), H3F3A (Biochemical Activity), HIST1H3A (Biochemical Activity), SUV39H1 (Affinity Capture-Western), SUV39H1 (Affinity Capture-Western), SUV39H1 (Reconstituted Complex), CBX5 (Two-hybrid), SUV39H1 (Synthetic Growth Defect), SUV39H1 (Two-hybrid)

ESM2 similar proteins: A0A1L7TZE5, A0A559KX76, A1C7E4, A1CS00, A1DHW6, A2QCU8, A6SDQ3, A7F045, B0XTS1, B2WKR4, B6Q4Z5, B8M7Q5, B8NGT5, O22781, O43463, O54864, P0CY36, P93025, P97443, Q00659, Q0CY32, Q0E908, Q0VD24, Q28CQ7, Q2NL30, Q2UES9, Q2UFN8, Q32PH7, Q4IJ84, Q4R3E0, Q4WVM1, Q4X0A9, Q5BHD6, Q5E9N5, Q5F3W5, Q5I0M0, Q5PP37, Q5RB81, Q60649, Q6DGD3

Diamond homologs: A0A1L7TZE5, A4IGY9, A7E2Z2, A8XI75, J9VWH9, O43463, O54864, O60016, O65312, O82175, O88491, O88974, O96028, P20659, P42124, P45975, P46995, P55200, P70351, P93831, Q03164, Q06ZW3, Q08BR4, Q08BS4, Q0VD24, Q15047, Q15910, Q24742, Q28CQ7, Q28D84, Q294B9, Q2NL30, Q32PH7, Q4PB36, Q4R381, Q4R3E0, Q4V863, Q53H47, Q5DW34, Q5F3W5

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
PAX7-FOXO1	“up-regulates quantity by expression”	SUV39H1	“transcriptional regulation”
SUV39H1	“down-regulates quantity by repression”	MYOD1	“transcriptional regulation”
SUV39H1	“down-regulates quantity by repression”	MYOG	“transcriptional regulation”
MDM2	“down-regulates quantity by destabilization”	SUV39H1	ubiquitination
CCAR2	“down-regulates activity”	SUV39H1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 123 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Transcriptional Regulation by E2F6	5	20.6×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
DNA methylation-dependent constitutive heterochromatin formation	5	26.4×	3e-04
epigenetic regulation of gene expression	6	22.3×	8e-05
heterochromatin formation	7	17.4×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

30 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	13
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1024 predictions. Top by Δscore:

Variant	Effect	Δscore
X:48698890:C:A	acceptor_gain	1.0000
X:48698894:T:A	acceptor_gain	1.0000
X:48698899:CA:C	acceptor_loss	1.0000
X:48698900:A:AG	acceptor_gain	1.0000
X:48698900:AG:A	acceptor_gain	1.0000
X:48698901:G:GA	acceptor_gain	1.0000
X:48698901:GG:G	acceptor_gain	1.0000
X:48698901:GGC:G	acceptor_gain	1.0000
X:48698901:GGCT:G	acceptor_gain	1.0000
X:48699043:TCCGC:T	donor_gain	1.0000
X:48699045:CGCG:C	donor_loss	1.0000
X:48699046:GC:G	donor_gain	1.0000
X:48699047:CG:C	donor_loss	1.0000
X:48699048:G:GG	donor_gain	1.0000
X:48700738:GGA:G	donor_gain	1.0000
X:48700739:GAG:G	donor_gain	1.0000
X:48700741:G:GG	donor_gain	1.0000
X:48706263:A:AG	acceptor_gain	1.0000
X:48706264:G:GG	acceptor_gain	1.0000
X:48706264:GATC:G	acceptor_gain	1.0000
X:48706410:GT:G	donor_gain	1.0000
X:48706491:C:A	acceptor_gain	1.0000
X:48706496:A:AG	acceptor_gain	1.0000
X:48706496:A:T	acceptor_loss	1.0000
X:48706496:AGT:A	acceptor_gain	1.0000
X:48706496:AGTGT:A	acceptor_gain	1.0000
X:48706497:G:GT	acceptor_gain	1.0000
X:48706497:GT:G	acceptor_gain	1.0000
X:48706497:GTG:G	acceptor_gain	1.0000
X:48706497:GTGT:G	acceptor_gain	1.0000

AlphaMissense

2696 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:48700589:T:A	C222S	1.000
X:48700589:T:C	C222R	1.000
X:48700590:G:C	C222S	1.000
X:48700691:T:A	W256R	1.000
X:48700691:T:C	W256R	1.000
X:48700693:G:C	W256C	1.000
X:48700693:G:T	W256C	1.000
X:48700698:T:A	V258D	1.000
X:48700734:T:A	V270D	1.000
X:48700742:T:C	Y273H	1.000
X:48700748:G:A	G275R	1.000
X:48700748:G:C	G275R	1.000
X:48700749:G:A	G275E	1.000
X:48700749:G:T	G275V	1.000
X:48706293:G:C	R286P	1.000
X:48706329:T:C	L298P	1.000
X:48706331:T:A	F299I	1.000
X:48706331:T:C	F299L	1.000
X:48706331:T:G	F299V	1.000
X:48706332:T:C	F299S	1.000
X:48706333:T:A	F299L	1.000
X:48706333:T:G	F299L	1.000
X:48706338:T:C	L301P	1.000
X:48706383:G:A	G316D	1.000
X:48706387:C:A	N317K	1.000
X:48706387:C:G	N317K	1.000
X:48706394:C:G	H320D	1.000
X:48706397:T:C	F321L	1.000
X:48706399:T:A	F321L	1.000
X:48706399:T:G	F321L	1.000

dbSNP variants (sampled 300 via entrez): RS1000273076 (X:48708384 G>A), RS1003157103 (X:48695484 G>A,T), RS1003347483 (X:48705468 C>T), RS1003935273 (X:48707369 C>A,T), RS1004041039 (X:48697183 G>A), RS1004153912 (X:48697548 G>A), RS1004866175 (X:48708875 A>G), RS1005048329 (X:48699602 A>G), RS1006052630 (X:48702126 G>C), RS1006167181 (X:48702871 T>C), RS1006667313 (X:48694830 A>G), RS1007047807 (X:48704658 A>C), RS1007124452 (X:48705064 C>T), RS1007558497 (X:48696439 G>T), RS1008085836 (X:48696652 C>A,G,T)

Disease associations

OMIM: gene MIM:300254 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): ependymoma (MONDO:0016698)

Orphanet (1): Ependymoma (Orphanet:251636)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D004806	Ependymoma	C04.557.465.625.600.380.290; C04.557.470.670.380.290; C04.557.580.625.600.380.290

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL1795118 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — 2.1.1.43 Histone methyltransferases (HMTs)

Most potent curated ligand interactions (1 total), top 1:

Ligand	Action	Affinity	Parameter
chaetocin	Inhibition	6.96	pIC50

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL2172426	IC50	530 nM

ChEMBL bioactivities

13 potent at pChembl≥5 of 20 total, top 10 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.18	IC50	66	nM	CHETOMIN
6.58	IC50	260	nM	GLIOTOXIN
6.28	IC50	530	nM	CHEMBL2172426
6.10	IC50	800	nM	CHAETOCIN
5.96	IC50	1100	nM	CHEMBL1797937
5.92	IC50	1200	nM	S-ADENOSYLHOMOCYSTEINE
5.40	IC50	4000	nM	CHEMBL5402316
5.31	Ki	4900	nM	S-ADENOSYLHOMOCYSTEINE
5.16	IC50	7000	nM	CHEMBL5633108
5.02	IC50	9500	nM	CHEMBL3397332

PubChem BioAssay actives

11 with measured affinity, of 154 total; 8 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
(1S,3S,11R,14S)-14-(hydroxymethyl)-3-[3-[[(1S,4S)-4-(hydroxymethyl)-5,7-dimethyl-6,8-dioxo-2,3-dithia-5,7-diazabicyclo[2.2.2]octan-1-yl]methyl]indol-1-yl]-18-methyl-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.01,12.03,11.04,9]octadeca-4,6,8-triene-13,17-dione	700488: Inhibition of SUV39H1	ic50	0.0660	uM
(1R,7S,8S,11R)-7-hydroxy-11-(hydroxymethyl)-15-methyl-12,13-dithia-9,15-diazatetracyclo[9.2.2.01,9.03,8]pentadeca-3,5-diene-10,14-dione	700488: Inhibition of SUV39H1	ic50	0.2600	uM
(1S,3R,11R,14S)-3-[(1S,3R,11R,14S)-14,18-dimethyl-13,17-dioxo-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.01,12.03,11.04,9]octadeca-4,6,8-trien-3-yl]-14,18-dimethyl-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.01,12.03,11.04,9]octadeca-4,6,8-triene-13,17-dione	700488: Inhibition of SUV39H1	ic50	0.5300	uM
(1S,3R,11R,14S)-14-(hydroxymethyl)-3-[(1S,3R,11R,14S)-14-(hydroxymethyl)-18-methyl-13,17-dioxo-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.01,12.03,11.04,9]octadeca-4,6,8-trien-3-yl]-18-methyl-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.01,12.03,11.04,9]octadeca-4,6,8-triene-13,17-dione	1072844: Inhibition of human Histone-lysine N-methyltransferase SUV39H1	ic50	0.8000	uM
(2S)-2-amino-4-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methylsulfanyl]butanoic acid	1192333: Inhibition of SUV39H1 (unknown origin) by HMT assay	ic50	1.2000	uM
[2-(4-bromoanilino)-2-oxoethyl] 3-(furan-3-yl)-1H-pyrazole-5-carboxylate	1991321: Inhibition of human SUV39H1 using Biotin-tagged histone H3 and 3H-SAM as substrate incubated for 1 hrs by TopCount scintillation proximity assay	ic50	4.0000	uM
N-[4-(aminomethyl)phenyl]-4-(4-aminopiperidin-1-yl)quinazoline-7-carboxamide	2138378: Displacement of 3H-SAM from SUV39H1 (unknown origin) using biotinylated-histone H3 peptide as substrate incubated for 45 mins by SPA assay	ic50	7.0000	uM
(2S)-2-amino-4-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methylsulfanyl]-N-[(3-phenyl-1H-pyrazol-5-yl)methyl]butanamide	1192333: Inhibition of SUV39H1 (unknown origin) by HMT assay	ic50	9.5000	uM

CTD chemical–gene interactions

73 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects reaction, increases abundance, increases expression, increases reaction, decreases expression (+2 more)	6
bisphenol A	decreases expression, increases expression	3
Acetaminophen	decreases expression, increases expression	2
Benzo(a)pyrene	affects binding, decreases expression, affects cotreatment, affects reaction, increases abundance (+3 more)	2
Carbamazepine	affects expression	2
Cisplatin	decreases expression, increases expression	2
Cadmium Chloride	decreases expression	2
FR900359	decreases phosphorylation	1
bisphenol F	increases methylation, affects cotreatment	1
dicrotophos	increases expression	1
triptolide	decreases expression	1
propionaldehyde	decreases expression	1
trichostatin A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
coumarin	increases phosphorylation	1
beta-glycerophosphoric acid	affects cotreatment, decreases expression	1
hydroquinone	increases expression, decreases reaction	1
1-aminomethylphosphonic acid	decreases expression	1
diallyl trisulfide	decreases expression	1
3-deazaneplanocin	increases expression	1
phenethyl isothiocyanate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
benzyloxycarbonylleucyl-leucyl-leucine aldehyde	affects reaction, decreases expression, affects cotreatment, decreases reaction, increases ubiquitination	1
chromium hexavalent ion	decreases expression, increases abundance	1
perfluorooctane sulfonic acid	decreases expression	1
azoxystrobin	decreases expression	1
CGP 52608	affects binding, increases reaction	1

ChEMBL screening assays

81 unique, capped per target: 81 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1804756	Binding	Inhibition of Suv39H1-mediated methylation of nucleosome at 100 uM after 90 mins by scintillation counting in presence of S-adenosyl-l-[methyl-3H]methionine	Novel 3,5-bis(bromohydroxybenzylidene)piperidin-4-ones as coactivator-associated arginine methyltransferase 1 inhibitors: enzyme selectivity and cellular activity. — J Med Chem

Cellosaurus cell lines

6 cell lines: 5 cancer cell line, 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B0JM	EHTJUi005-A-1	Induced pluripotent stem cell	Female
CVCL_B7ZQ	Abcam Raji SUV39H1 KO	Cancer cell line	Male
CVCL_C0AI	Abcam THP-1 SUV39H1 KO	Cancer cell line	Male
CVCL_C7C6	Abcam PC-3 SUV39H1 KO	Cancer cell line	Male
CVCL_TR28	HAP1 SUV39H1 (-) 1	Cancer cell line	Male
CVCL_TR29	HAP1 SUV39H1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

95 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00517959	PHASE3	UNKNOWN	SCRT Versus Conventional RT in Children and Young Adults With Low Grade and Benign Brain Tumors
NCT01096368	PHASE3	COMPLETED	Maintenance Chemotherapy or Observation Following Induction Chemotherapy and Radiation Therapy in Treating Patients With Newly Diagnosed Ependymoma
NCT00003479	PHASE2	TERMINATED	Antineoplaston Therapy in Treating Patients With Ependymoma
NCT00520936	PHASE2	COMPLETED	A Study of Pemetrexed in Children With Recurrent Cancer
NCT00840047	PHASE2	ACTIVE_NOT_RECRUITING	Methionine PET/CT Studies In Patients With Cancer
NCT01088035	PHASE2	TERMINATED	Carboplatin as a Radiosensitizer in Treating Childhood Ependymoma
NCT01247922	PHASE2	TERMINATED	Single-agent Erlotinib in Patients Previously Treated With Oral Etoposide in Protocol OSI-774-205
NCT01288235	PHASE2	COMPLETED	Proton Radiotherapy for Pediatric Brain Tumors Requiring Partial Brain Irradiation
NCT01295944	PHASE2	COMPLETED	Carboplatin and Bevacizumab for Recurrent Ependymoma
NCT01356290	PHASE2	RECRUITING	Antiangiogenic Therapy for Children With Recurrent Medulloblastoma, Ependymoma, ATRT and Rare CNS Tumors
NCT01836549	PHASE2	TERMINATED	Imetelstat Sodium in Treating Younger Patients With Recurrent or Refractory Brain Tumors
NCT02125786	PHASE2	ACTIVE_NOT_RECRUITING	A Trial of Surgery and Fractionated Re-Irradiation for Recurrent Ependymoma
NCT02689336	PHASE2	WITHDRAWN	Erlotinib in Combination With Temozolomide in Treating Relapsed/Recurrent/Refractory Pediatric Solid Tumors
NCT03095248	PHASE2	TERMINATED	Trial of Selumetinib in Patients With Neurofibromatosis Type II Related Tumors
NCT03155620	PHASE2	ACTIVE_NOT_RECRUITING	Targeted Therapy Directed by Genetic Testing in Treating Pediatric Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphomas, or Histiocytic Disorders (The Pediatric MATCH Screening Trial)
NCT03173950	PHASE2	COMPLETED	Immune Checkpoint Inhibitor Nivolumab in People With Recurrent Select Rare CNS Cancers
NCT03194906	PHASE2	COMPLETED	Memantine for Prevention of Cognitive Late Effects in Pediatric Patients Receiving Cranial Radiation Therapy for Localized Brain Tumors
NCT03210714	PHASE2	ACTIVE_NOT_RECRUITING	Erdafitinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With FGFR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213652	PHASE2	ACTIVE_NOT_RECRUITING	Ensartinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With ALK or ROS1 Genomic Alterations (A Pediatric MATCH Treatment Trial)
NCT03213665	PHASE2	COMPLETED	Tazemetostat in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With EZH2, SMARCB1, or SMARCA4 Gene Mutations (A Pediatric MATCH Treatment Trial)
NCT03213678	PHASE2	COMPLETED	Samotolisib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With TSC or PI3K/MTOR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213704	PHASE2	ACTIVE_NOT_RECRUITING	Larotrectinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With NTRK Fusions (A Pediatric MATCH Treatment Trial)
NCT03220035	PHASE2	COMPLETED	Vemurafenib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With BRAF V600 Mutations (A Pediatric MATCH Treatment Trial)
NCT03233204	PHASE2	COMPLETED	Olaparib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Defects in DNA Damage Repair Genes (A Pediatric MATCH Treatment Trial)
NCT03526250	PHASE2	COMPLETED	Palbociclib in Treating Patients With Relapsed or Refractory Rb Positive Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Activating Alterations in Cell Cycle Genes (A Pediatric MATCH Treatment Trial)
NCT03698994	PHASE2	ACTIVE_NOT_RECRUITING	Ulixertinib in Treating Patients With Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With MAPK Pathway Mutations (A Pediatric MATCH Treatment Trial)
NCT03727841	PHASE2	TERMINATED	Marizomib for Recurrent Low-Grade and Anaplastic Supratentorial, Infratentorial, and Spinal Cord Ependymoma
NCT04049669	PHASE2	ACTIVE_NOT_RECRUITING	Pediatric Trial of Indoximod With Chemotherapy and Radiation for Relapsed Brain Tumors or Newly Diagnosed DIPG
NCT04195555	PHASE2	ACTIVE_NOT_RECRUITING	Ivosidenib in Treating Patients With Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With IDH1 Mutations (A Pediatric MATCH Treatment Trial)
NCT04284774	PHASE2	ACTIVE_NOT_RECRUITING	Tipifarnib for the Treatment of Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With HRAS Gene Alterations, a Pediatric MATCH Treatment Trial
NCT04320888	PHASE2	ACTIVE_NOT_RECRUITING	Selpercatinib for the Treatment of Advanced Solid Tumors, Lymphomas, or Histiocytic Disorders With Activating RET Gene Alterations, a Pediatric MATCH Treatment Trial
NCT04374305	PHASE2	RECRUITING	Innovative Trial for Understanding the Impact of Targeted Therapies in NF2-Related Schwannomatosis (INTUITT-NF2)
NCT04743661	PHASE2	ACTIVE_NOT_RECRUITING	131I-Omburtamab, in Recurrent Medulloblastoma and Ependymoma
NCT06804655	PHASE2	NOT_YET_RECRUITING	Pharmacoscopy for Patients With Refractory Primary Brain Tumors
NCT07424092	PHASE2	RECRUITING	Intratumoral DNX-2401 for High Grade Pediatric Brain Tumors
NCT00634231	PHASE1	COMPLETED	A Phase I Study of AdV-tk + Prodrug Therapy in Combination With Radiation Therapy for Pediatric Brain Tumors
NCT00994071	PHASE1	COMPLETED	A Phase I Study of ABT-888, an Oral Inhibitor of Poly(ADP-ribose) Polymerase and Temozolomide in Children With Recurrent/Refractory CNS Tumors
NCT01171469	PHASE1	COMPLETED	Vaccination With Dendritic Cells Loaded With Brain Tumor Stem Cells for Progressive Malignant Brain Tumor
NCT01331135	PHASE1	COMPLETED	Aflac ST0901 CHOANOME - Sirolimus in Solid Tumors
NCT01498783	PHASE1	COMPLETED	Phase I Study of 5-Fluorouracil in Children and Young Adults With Recurrent Ependymoma