DNMT3A (DNA (cytosine-5-)-methyltransferase 3 alpha)
2013-03-01 Yuan-Yeh Kuo  , Li-Yu Li  , Hwei-Fang Tien   AffiliationGraduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan (YYK, LYL); Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung-Shan S. Road, Taipei, Taiwan (HFT)
Identity
HGNC
LOCATION
2p23.3
IMAGE

LEGEND
Genomic localization of human DNMT3A gene. POMC, proopiomelanocortin; DTNB, dystrobrevin, beta.
LOCUSID
ALIAS
DNMT3A2,HESJAS,M.HsaIIIA,TBRS
FUSION GENES
DNA/RNA
Description
The DNMT3A gene structure is composed of 23 exons (Xie et al., 1999). A short isoform, named DNMT3A2, is produced from a downstream intronic promoter (Chen et al., 2002).
Transcription
Transcription of DNMT3A is initiated from the downstream intronic promoter and leads to expression of DNMT3A2, an isoform lacking the N-terminal region, in embryonic stem cells (ESCs). Expression of this shorter isoform gradually decreases upon ESC differentiation and switches to the full length DNMT3A which remains expressed at low level in most somatic tissues (Chedin, 2011; Chen et al., 2002).
Proteins

Structure of DNA methyltransferases. NLS, nuclear localization signal; CXXC, a cysteine rich region; BAH, a bromo-adjacent homology domain; PWWP, a proline-tryptophan-tryptophan-proline domain; ADD, an ATRX-DNMT3-DNMT3L-type zinc finger domain; Mtase, a methyltransferase domain.
Description
DNMT3A
AA: 912. EC number: 2.1.1.37. Estimated molecular weight: 101858 Dt.
DNMT3A2
AA: 689. Estimated molecular weight: 77817 Dt.
DNMT3A contains 3 main structure domains: a proline-tryptophan-tryptophan-proline (PWWP) domain, an ATRX, DNMT3, and DNMT3L-type zinc finger (ADD) domain, and the methyltransferase (Mtase) domain. The PWWP domain is responsible for targeting the enzyme to nucleic acid (Chen et al., 2004). In addition, the PWWP domain is also essential for targeting this enzyme to pericentric heterochromatin (Chen et al., 2004; Ge et al., 2004). The ADD domain mediates protein-protein interactions with transcription factors Myc, RP58, the heterochromatin protein HP1, histone deacetylases, and the histone methyltransferase Suv39h1 (Chen and Li, 2006). The Mtase domain contains six highly conserved cytosine C5-DNA methyltransferase motifs (Jurkowska et al., 2011).
AA: 912. EC number: 2.1.1.37. Estimated molecular weight: 101858 Dt.
DNMT3A2
AA: 689. Estimated molecular weight: 77817 Dt.
DNMT3A contains 3 main structure domains: a proline-tryptophan-tryptophan-proline (PWWP) domain, an ATRX, DNMT3, and DNMT3L-type zinc finger (ADD) domain, and the methyltransferase (Mtase) domain. The PWWP domain is responsible for targeting the enzyme to nucleic acid (Chen et al., 2004). In addition, the PWWP domain is also essential for targeting this enzyme to pericentric heterochromatin (Chen et al., 2004; Ge et al., 2004). The ADD domain mediates protein-protein interactions with transcription factors Myc, RP58, the heterochromatin protein HP1, histone deacetylases, and the histone methyltransferase Suv39h1 (Chen and Li, 2006). The Mtase domain contains six highly conserved cytosine C5-DNA methyltransferase motifs (Jurkowska et al., 2011).
Expression
In mouse, Dnmt3a was detected in all tissues except for small intestines, whereas Dnmt3a2 expression was more restricted in testis, spleen and thymus (Chen et al., 2002). In addition to normal tissues, overexpression of DNMT3A has been reported in various human cancers, such as prostate, pancreatic, gastric, liver cancers (Gravina et al., 2013; Oh et al., 2007; Yang et al., 2011; Zhang et al., 2012). Additionally, DNMT3A were detected substantially overexpressed in certain types of leukemia (Mizuno et al., 2001).
Localisation
Dnmt3a localizes in the nuclei and is concentrated in nuclear foci. In contrast, Dnmt3a2 showed a diffused pattern excluding nucleoli and heterochromatin. In general, Dnmt3a is thought to associate with heterochmatin, whereas Dnmt3a2 associates mainly with euchromatin (Chen et al., 2002).
Function
Similarly to Dnmt1, the Dnmt3a enzyme also uses S-adenosyl methionine (SAM) as the methyl group donor being transferred to the carbon 5 position of the cytosine ring in CpG dinucleotide in DNA. It is essential for the establishment of DNA methylation patterns during development (Jurkowska et al., 2011).In addition to the enzymatic function, Dnmt3a was also shown to suppress transcription, independent of its catalytic activity, that was mediated through the interaction with the histone deacetylase and other co-repressors, such as Mbd3 and Brg1 (Datta et al., 2005; Fuks et al., 2001). Sumoylation of DNMT3A has been reported in the N-terminal domain of the enzyme, which disrupts its interaction with histone deacetylases (HDACs) and thereby impairs the repressive capability of this protein (Ling et al., 2004).
Homology
Dnmt3 family proteins share some structural similarity with Dnmt1 at c-terminal Mtase domain. In addition, the DNMT3A and DNMT3B proteins also contain a conserved cystein-rich ATRX, DNMT3, and DNMT3L-type zinc finger (ADD) domain and the proline-tryptophan-tryptophan-proline (PWWP) domain. The N-terminal domains of Dnmt3a and Dnmt3b do not share any sequence homology (Chedin, 2011).
Mutations
Somatic
Recurrent DNMT3A gene mutations were recently reported in acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), myeloproliferative neoplasms (MPN), T-cell lymphoma, and T-cell acute lymphoblastic leukemia (ALL) (Couronne et al., 2012; Grossmann et al., 2013; Hou et al., 2012; Ley et al., 2010; Stegelmann et al., 2011; Walter et al., 2011). The most frequently mutated site is the Arg 882 (R882) residue located in the catalytic domain. These R882 mutants were reported to reduce DNA methylation activity of DNMT3A (Yan et al., 2011).
Implicated in
Entity name
Acute myeloid leukemia (AML)
Note
DNMT3A mutations frequently detected in 7-29% of AML patients. This mutation was associated with normal karyotype, older age, French-American-British (FAB) M4/M5 subtypes, and poor prognosis. Multivariate analysis demonstrated that the DNMT3A mutation was an independent poor prognostic factor for over-all survival and relapse-free survival (Hou et al., 2012; Ley et al., 2010; Thol et al., 2011a; Yan et al., 2011). This mutation was also reported in 35.1% of secondary AML and 16.4% of therapy-related AML in a study of a cohort of 98 patients and found that this mutation was associated with normal karyotype and IDH1/IDH2 mutations, but that it does not affect survival (Shih et al., 2013). Recent reports further demonstrated that the frequency of DNMT3A mutations is rare in childhood AML and MDS, suggesting that the frequency of DNMT3A gene mutation depends on age (Ho et al., 2011; Thol et al., 2011b). In addition, it was also reported that AML patients whose leukemic blasts have low DNMT3A activity, either due to loss-of-functions or low gene expression, may benefit from treatment with hypomethylating agents (Metzeler et al., 2012).
Entity name
Myelodysplastic syndrome (MDS)
Note
Mutations of the DNMT3A gene were detected in 6% of MDS patients and amino acid R882 was the most common mutation site. Patients with DNMT3A mutations had worse overall survival compared with patients without these mutations and more rapid progression to AML (Walter et al., 2011).
Entity name
Myeloproliferative neoplasms (MPN)
Note
In a study of a cohort of 155 patients with MPN, an overall frequency of 10% mutations were most frequently detected in secondary AML (sAML: 17%) and myelofibrosis (MF: 15%), followed by polycythemia vera (PV: 7%) and essential thrombocythemia (ET: 3%). These alterations occurred concurrently with JAK2, IDH1/2 and ASXL1 mutations. In addition, these mutations are associated with more advanced stages of MPNs and with an overall poor prognosis (Stegelmann et al., 2011).
Entity name
T-cell lymphoma
Note
DNMT3A mutations were reported in eleven of 98 patients with T-cell lymphoma and were associated with TET2 mutations (Couronne et al., 2012).
Entity name
Note
DNMT3A mutations were detected in 16 of 90 patients (17.8%) with T-ALL. These alterations were associated with normal karyotype, lower hemoglobin levels and mutually exclusive in cases with CDKN2A/CDKN2B deletions. Further, these mutations had a strong association with shorter overall survival (Grossmann et al., 2013).
Entity name
Lung cancer
Note
Deletion of Dnmt3a significantly promotes tumor growth and progression in lung cancer mouse model, suggesting that this gene may act like a tumor-suppressor gene and may be a crucial factor of lung cancer malignancy (Gao et al., 2011).
Article Bibliography
| Pubmed ID | Last Year | Title | Authors |
|---|---|---|---|
| 16570845 | 2006 | DNA methyltransferases: facts, clues, mysteries. | Brenner C et al |
| 21507354 | 2011 | The DNMT3 family of mammalian de novo DNA methyltransferases. | Chédin F et al |
| 16570848 | 2006 | Establishment and maintenance of DNA methylation patterns in mammals. | Chen T et al |
| 15456878 | 2004 | The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin. | Chen T et al |
| 12138111 | 2002 | A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. | Chen T et al |
| 22216861 | 2012 | TET2 and DNMT3A mutations in human T-cell lymphoma. | Couronné L et al |
| 16322236 | 2005 | Physical and functional interaction of DNA methyltransferase 3A with Mbd3 and Brg1 in mouse lymphosarcoma cells. | Datta J et al |
| 20060365 | 2010 | DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. | Figueroa ME et al |
| 11350943 | 2001 | Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription. | Fuks F et al |
| 22011581 | 2011 | Deletion of the de novo DNA methyltransferase Dnmt3a promotes lung tumor progression. | Gao Q et al |
| 14998998 | 2004 | Chromatin targeting of de novo DNA methyltransferases by the PWWP domain. | Ge YZ et al |
| 23254386 | 2013 | Increased levels of DNA methyltransferases are associated with the tumorigenic capacity of prostate cancer cells. | Gravina GL et al |
| 23341344 | 2013 | The molecular profile of adult T-cell acute lymphoblastic leukemia: mutations in RUNX1 and DNMT3A are associated with poor prognosis in T-ALL. | Grossmann V et al |
| 11934864 | 2002 | Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. | Hata K et al |
| 15526163 | 2004 | Biochemistry and biology of mammalian DNA methyltransferases. | Hermann A et al |
| 21504050 | 2011 | Leukemic mutations in the methylation-associated genes DNMT3A and IDH2 are rare events in pediatric AML: a report from the Children's Oncology Group. | Ho PA et al |
| 22077061 | 2012 | DNMT3A mutations in acute myeloid leukemia: stability during disease evolution and clinical implications. | Hou HA et al |
| 21243710 | 2011 | Structure and function of mammalian DNA methyltransferases. | Jurkowska RZ et al |
| 21067377 | 2010 | DNMT3A mutations in acute myeloid leukemia. | Ley TJ et al |
| 14752048 | 2004 | Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription. | Ling Y et al |
| 21130408 | 2010 | Epigenetics in AML. | Melnick AM et al |
| 22124213 | 2012 | DNMT3A mutations and response to the hypomethylating agent decitabine in acute myeloid leukemia. | Metzeler KH et al |
| 11222358 | 2001 | Expression of DNA methyltransferases DNMT1, 3A, and 3B in normal hematopoiesis and in acute and chronic myelogenous leukemia. | Mizuno S et al |
| 17549390 | 2007 | DNA methyltransferase expression and DNA methylation in human hepatocellular carcinoma and their clinicopathological correlation. | Oh BK et al |
| 17259967 | 2007 | Transcription factors in myeloid development: balancing differentiation with transformation. | Rosenbauer F et al |
| 23349305 | 2013 | Mutational analysis of therapy-related myelodysplastic syndromes and acute myelogenous leukemia. | Shih AH et al |
| 21537334 | 2011 | DNMT3A mutations in myeloproliferative neoplasms. | Stegelmann F et al |
| 15105426 | 2004 | DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. | Suetake I et al |
| 17420264 | 2007 | De novo DNA methyltransferase is essential for self-renewal, but not for differentiation, in hematopoietic stem cells. | Tadokoro Y et al |
| 21670448 | 2011 | Incidence and prognostic influence of DNMT3A mutations in acute myeloid leukemia. | Thol F et al |
| 21685466 | 2011 | DNMT3A mutations are rare in childhood acute myeloid leukemia. | Thol F et al |
| 19796624 | 2009 | DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. | Trowbridge JJ et al |
| 21415852 | 2011 | Recurrent DNMT3A mutations in patients with myelodysplastic syndromes. | Walter MJ et al |
| 10433969 | 1999 | Cloning, expression and chromosome locations of the human DNMT3 gene family. | Xie S et al |
| 21399634 | 2011 | Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. | Yan XJ et al |
| 21887466 | 2011 | Clinical significance of the expression of DNA methyltransferase proteins in gastric cancer. | Yang J et al |
| 22301400 | 2012 | Association of increased DNA methyltransferase expression with carcinogenesis and poor prognosis in pancreatic ductal adenocarcinoma. | Zhang JJ et al |
Other Information
Locus ID:
NCBI: 1788
MIM: 602769
HGNC: 2978
Ensembl: ENSG00000119772
Variants:
dbSNP: 1788
ClinVar: 1788
TCGA: ENSG00000119772
COSMIC: DNMT3A
RNA/Proteins
Expression (GTEx)
Pathways
Protein levels (Protein atlas)
PharmGKB
| Entity ID | Name | Type | Evidence | Association | PK | PD | PMIDs |
|---|---|---|---|---|---|---|---|
| PA166123431 | heart valve replacement | Disease | ClinicalAnnotation | associated | PD | 27740732 | |
| PA451906 | warfarin | Chemical | ClinicalAnnotation | associated | PD | 27740732 |
References
| Pubmed ID | Year | Title | Citations |
|---|---|---|---|
| 37743610 | 2024 | DNA methyltransferase 3A induces the occurrence of oral submucous fibrosis by promoting the methylation of the von Hippel-Lindau. | 1 |
| 37985411 | 2024 | Unveiling the impact of DNA methylation machinery: Dnmt1 and Dnmt3a in orchestrating oocyte development and cellular homeostasis. | 1 |
| 38183507 | 2024 | DNA methyltransferase 3a-induced hypermethylation of the fructose-1,6-bisphosphatase-2 promoter contributes to gastric carcinogenesis. | 0 |
| 38231881 | 2024 | Clonal haematopoiesis of indeterminate potential and atrial fibrillation: an east Asian cohort study. | 1 |
| 38242884 | 2024 | DNMT3A clonal hematopoiesis-driver mutations induce cardiac fibrosis by paracrine activation of fibroblasts. | 2 |
| 38380551 | 2024 | DNMT3A Cooperates with YAP/TAZ to Drive Gallbladder Cancer Metastasis. | 1 |
| 38438051 | 2024 | From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. | 2 |
| 38493481 | 2024 | Loss of Dnmt3a increases self-renewal and resistance to pegIFN-α in JAK2-V617F-positive myeloproliferative neoplasms. | 1 |
| 38600075 | 2024 | Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. | 0 |
| 38926973 | 2024 | [Relationship between DTA Mutations and Thromboembolism in Patients with Myeloproliferative Neoplasms]. | 0 |
| 37743610 | 2024 | DNA methyltransferase 3A induces the occurrence of oral submucous fibrosis by promoting the methylation of the von Hippel-Lindau. | 1 |
| 37985411 | 2024 | Unveiling the impact of DNA methylation machinery: Dnmt1 and Dnmt3a in orchestrating oocyte development and cellular homeostasis. | 1 |
| 38183507 | 2024 | DNA methyltransferase 3a-induced hypermethylation of the fructose-1,6-bisphosphatase-2 promoter contributes to gastric carcinogenesis. | 0 |
| 38231881 | 2024 | Clonal haematopoiesis of indeterminate potential and atrial fibrillation: an east Asian cohort study. | 1 |
| 38242884 | 2024 | DNMT3A clonal hematopoiesis-driver mutations induce cardiac fibrosis by paracrine activation of fibroblasts. | 2 |
Citation
Yuan-Yeh Kuo ; Li-Yu Li ; Hwei-Fang Tien
DNMT3A (DNA (cytosine-5-)-methyltransferase 3 alpha)
Atlas Genet Cytogenet Oncol Haematol. 2013-03-01
Online version: http://atlasgeneticsoncology.org/gene/40349/dnmt3a-(dna-(cytosine-5-)-methyltransferase-3-alpha)
