Alternative titles; symbols
HGNC Approved Gene Symbol: DNMT3L
Cytogenetic location: 21q22.3 Genomic coordinates (GRCh38) : 21:44,246,339-44,261,897 (from NCBI)
DNMT3L is an enzymatically inactive regulatory factor that shares sequence homology with the DNA methyltransferases DNMT3A (602769) and DNMT3B (602900). DNMT3L is involved in the establishment of DNA methylation patterns during gametogenesis. In mammals, DNA methylation is used for heritable silencing of retrotransposons and imprinted genes and for inactivation of the X chromosome in females (summary by Ooi et al., 2007).
By database analysis, PCR with specific primers based on predicted and trapped exon sequences, and screening of testis, fetal liver, placenta, and thymus mRNA and cDNA libraries, Aapola et al. (2000) isolated a cDNA encoding DNMT3L. Sequence analysis predicted that the 387-amino acid protein contains a cysteine-rich region with a novel ADD (for ATRX (300032), DNMT3, and DNMT3L) C2-C2 zinc finger motif near an imperfect PHD zinc finger with C4-C4. RT-PCR analysis detected highest expression of DNMT3L in testis, followed by ovary, thymus, and fetal thymus. Northern blot analysis failed to detected expression of DNMT3L.
By genomic sequence analysis, Aapola et al. (2000) determined that the DNMT3L gene contains 12 exons and spans 16 kb. The translation initiation codon is in exon 2. The authors detected a splice variant lacking exon 8.
By genomic DNA sequence analysis, Aapola et al. (2000) localized the DNMT3L gene to chromosome 21q22.3, 24 kb centromeric to the AIRE gene (240300) and 5.4 kb telomeric to the KIAA0653 gene (B7H2; 605717).
Using mass spectrometry, Ooi et al. (2007) identified the main proteins that interacted in vivo with the product of an epitope-tagged allele of the endogenous DNMT3L gene as DNMT3A2 (602769), DNMT3B (602900), and the 4 core histones. Peptide interaction assays showed that DNMT3L specifically interacts with the extreme amino terminus of histone H3 (see 602810); this interaction was strongly inhibited by methylation at lysine-4 of histone H3 but was insensitive to modifications at other positions. Crystallographic studies of human DNMT3L showed that the protein has a carboxy-terminal methyltransferase-like domain and an N-terminal cysteine-rich domain. Cocrystallization of DNMT3L with the tail of histone H3 revealed that the tail bound to the cysteine-rich domain of DNMT3L, and substitution of key residues in the binding site eliminated the H3 tail-DNMT3L interaction. Ooi et al. (2007) concluded that DNMT3L recognizes histone H3 tails that are unmethylated at lysine-4 and induces de novo DNA methylation by recruitment or activation of DNMT3A2.
Hu et al. (2008) showed that expression of the mouse Dnmt3l gene was regulated by Dnmt3a and Dnmt3b and by autoregulation. Disruption of both Dnmt3a and Dnmt3b genes in mouse rendered the Dnmt3l promoter devoid of methylation, causing incomplete repression of Dnmt3l transcription in embryonic stem cells and embryos. In addition, methylation of Dnmt3l was significantly reduced in mouse models of ICF syndrome (242860) caused by point mutations in Dnmt3b.
Smallwood et al. (2011) identified over a thousand methylated CpG islands in mature mouse oocytes. Both Dnmt3a -/- and Dnmt3l -/- oocytes showed a gross, genomewide reduction in CpG methylation, including at repetitive elements and CpG islands independent of their genic location. Smallwood et al. (2011) concluded that DNMT3A and DNMT3L have a genomewide role in CpG island methylation beyond genomic imprinting.
Crystal Structure
Jia et al. (2007) used crystallography to show that the C-terminal domain of human DNMT3L interacts with the catalytic domain of DNMT3A, demonstrating that DNMT3L has dual functions of binding the unmethylated histone tail and activating DNA methyltransferase. The complex C-terminal domains of DNMT3A and DNMT3L showed further dimerization through DNMT3A-DNMT3A interaction, forming a tetrameric complex with 2 active sites. Substitution of key noncatalytic residues at the DNMT3A-DNMT3L interface or the DNMT3A-DNMT3A interface eliminated enzymatic activity. Molecular modeling of a DNA-DNMT3A dimer indicated that the 2 active sites are separated by about 1 DNA helical turn. The C-terminal domain of DNMT3A oligomerizes on DNA to form a nucleoprotein filament. A periodicity in the activity of DNMT3A on long DNA revealed a correlation of methylated CpG sites at distances of 8 to 10 basepairs, indicating that oligomerization leads DNMT3A to methylate DNA in a periodic pattern. A similar periodicity is observed for the frequency of CpG sites in the differentially methylated regions of 12 maternally imprinted mouse genes. Jia et al. (2007) concluded that their results suggested a basis for the recognition and methylation of differentially methylated regions in imprinted genes, involving the detection of both nucleosome modification and CpG spacing.
El-Maarri et al. (2009) detected 111 polymorphisms among the 5 DNMT family genes, including DNMT3L, in 192 healthy males and females. Polymorphisms leading to an amino acid change were investigated for changes in global DNA methylation by differential methylation hybridization. A rare C-T transition in exon 10 of the DNMT3L gene, resulting in an arg271-to-gln (R271Q) substitution, was associated with significant DNA hypomethylation. Biochemical characterization confirmed that DNMT3L-R271Q was impaired in its ability to stimulate de novo DNA methylation by DNMT3A. Methylated DNA immunoprecipitation-based analysis using CpG island microarrays revealed that the hypomethylation in this sample preferentially clustered to subtelomeric genomic regions with affected loci corresponding to a subset of repetitive CpG islands with low predicted promoter potential located outside of genes.
By disrupting homologous recombination in mouse embryonic stem cells, Bourc'his et al. (2001) generated viable but sterile mice with mutated Dnmt3l (termed Dnmt3lG) in which male testes had severe hypogonadism and a Sertoli cell-only phenotype. The heterozygous offspring of females with Dnmt3lG failed to develop past 9.5 days postcoitum due to embryonic rather than uterine defects. Bisulfite genomic sequence analysis of the differentially methylated region (DMR) of imprinted and maternally repressed genes such as Snrpn (182279) detected undermethylation of oocytes from Dnmt3lG homozygous females, showing that Dnmt3l is required for the establishment of maternal methylation imprints. Heterozygous embryos from Dnmt3lG homozygotes displayed biallelic expression of genes that are normally expressed only from the allele of paternal origin. Bourc'his et al. (2001) concluded that DNMT3L is required specifically for the establishment of genomic imprints but is dispensable for their propagation, and it is essential for the de novo methylation of single-copy DNA sequences. The authors proposed that DNMT3L is likely to function as a regulator of methylation at imprinted loci rather than a DNA cytosine methyltransferase because of a lack of catalytic motifs in its sequence.
Bourc'his and Bestor (2004) demonstrated that in mice, Dnmt3l is expressed in testes during a brief perinatal period in the nondividing precursors of spermatogonial stem cells at a stage where retrotransposons undergo de novo methylation. Deletion of the Dnmt3l gene prevented the de novo methylation of both long terminal repeat (LTR) and non-LTR retrotransposons, which were transcribed at high levels in spermatogonia and spermatocytes. Loss of Dnmt3l from early germ cells also caused meiotic failure in spermatocytes, which do not express Dnmt3l. Whereas dispersed repeated sequences were demethylated in mutant germ cells, tandem repeats in pericentric regions were methylated normally. Bourc'his and Bestor (2004) concluded that the DNMT3L protein might have a function in the de novo methylation of dispersed repeated sequences in a premeiotic genome scanning process that occurs in male germ cells at about the time of birth.
Webster et al. (2005) found that, in addition to hypomethylation in early stages of spermatogenesis, Dnmt3l -/- spermatocytes showed abnormalities during later stages of development. Chromatin compaction was impaired in meiotic cells, as evidenced by differences in the accessibility of histone epitopes. Homologous chromosomes failed to align and form synaptonemal complexes, leading to spermatogenetic arrest and loss of spermatocytes through apoptosis and sloughing. Webster et al. (2005) concluded that many of the specialized changes in chromatin morphology during meiosis require DNMT3L, either directly or indirectly.
Henckel et al. (2009) analyzed histone modifications at imprinting control regions (ICRs) in midgestation mouse embryos that were obtained from Dnmt3L-null females, in which DNA methylation imprints at ICRs are not established during oogenesis. The absence of maternal DNA methylation imprints in these conceptuses led to a marked decrease and loss of allele specificity of the repressive H3K9me3, H4K20me3, and H2A/H4R3me2 histone modifications, providing evidence of a mechanistic link between DNA and histone methylation at ICRs. When DNA methylation was still present at the Snrpn (182279) and Peg3 (601483) ICRs in some of the progeny of Dnmt3L-null females, these ICRs were associated with the usual patterns of histone methylation. The authors concluded that DNA methylation is involved in the acquisition and/or maintenance of histone methylation at ICRs.
Aapola, U., Shibuya, K., Scott, H. S., Ollila, J., Vihinen, M., Heino, M., Shintani, A., Kawasaki, K., Minoshima, S., Krohn, K., Antonarakis, S. E., Shimizu, N., Kudoh, J., Peterson, P. Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cysteine-5-methyltransferase 3 gene family. Genomics 65: 293-298, 2000. [PubMed: 10857753] [Full Text: https://doi.org/10.1006/geno.2000.6168]
Bourc'his, D., Bestor, T. H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96-98, 2004. [PubMed: 15318244] [Full Text: https://doi.org/10.1038/nature02886]
Bourc'his, D., Xu, G.-L., Lin, C.-S., Bollman, B., Bestor, T. H. Dnmt3L and the establishment of maternal genomic imprints. Science 294: 2536-2539, 2001. [PubMed: 11719692] [Full Text: https://doi.org/10.1126/science.1065848]
El-Maarri, O., Kareta, M. S., Mikeska, T., Becker, T., Diaz-Lacava, A., Junen, J., Nusgen, N., Behne, F., Wienker, T., Waha, A., Olderburg, J., Chedin, F. A systemic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. Hum. Molec. Genet. 18: 1755-1768, 2009. [PubMed: 19246518] [Full Text: https://doi.org/10.1093/hmg/ddp088]
Henckel, A., Nakabayashi, K., Sanz, L. A., Feil, R., Hata, K., Arnaud, P. Histone methylation is mechanistically linked to DNA methylation at imprinting control regions in mammals. Hum. Molec. Genet. 18: 3375-3383, 2009. [PubMed: 19515852] [Full Text: https://doi.org/10.1093/hmg/ddp277]
Hu, Y.-G., Hirasawa, R., Hu, J.-L., Hata, K., Li, C.-L., Jin, Y., Chen, T., Li, E., Rigolet, M., Viegas-Pequignot, E., Sasaki, H., Xu, G.-L. Regulation of DNA methylation activity through Dnmt3L promoter methylation by Dnmt3 enzymes in embryonic development. Hum. Molec. Genet. 17: 2654-2664, 2008. [PubMed: 18544626] [Full Text: https://doi.org/10.1093/hmg/ddn165]
Jia, D., Jurkowska, R. Z., Zhang, X., Jeltsch, A., Cheng, X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449: 248-251, 2007. [PubMed: 17713477] [Full Text: https://doi.org/10.1038/nature06146]
Ooi, S. K. T., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument-Bromage, H., Tempst, P., Lin, S.-P., Allis, C. D., Cheng, X., Bestor, T. H. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448: 714-717, 2007. [PubMed: 17687327] [Full Text: https://doi.org/10.1038/nature05987]
Smallwood, S. A., Tomizawa, S., Krueger, F., Ruf, N., Carli, N., Segonds-Pichon, A., Sato, S., Hata, K., Andrews, S. R., Kelsey, G. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nature Genet. 43: 811-814, 2011. [PubMed: 21706000] [Full Text: https://doi.org/10.1038/ng.864]
Webster, K. E., O'Bryan, M. K., Fletcher, S., Crewther, P. E., Aapola, U., Craig, J., Harrison, D. K., Aung, H., Phutikanit, N., Lyle, R., Meachem, S. J., Antonarakis, S. E., de Kretser, D. M., Hedger, M. P., Peterson, P., Carroll, B. J., Scott, H. S. Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc. Nat. Acad. Sci. 102: 4068-4073, 2005. [PubMed: 15753313] [Full Text: https://doi.org/10.1073/pnas.0500702102]