H3K36me2/3 Binding and DNA Binding of the DNA Methyltransferase DNMT3A PWWP Domain Both Contribute to its Chromatin Interaction

Dukatz, Michael; Holzer, Katharina; Choudalakis, Michel; Emperle, Max; Lungu, Cristiana; Bashtrykov, Pavel; Jeltsch, Albert

doi:10.1016/j.jmb.2019.09.006

Cited by 59 publications

(64 citation statements)

References 28 publications

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“…We generated mutant mice carrying an aspartic acid (GAT) to alanine (GCT) substitution at codon 329 (D329A) of the DNMT3A PWWP domain ( Dnmt3a D329A mice) [ 31 , 37 , 41 ] using CRISPR/Cas9-mediated homology directed repair (see Materials and Methods ) ( Fig 1A ). Since the PWWP domain is present in common in both DNMT3A1 and DNMT3A2, this substitution affects both isoforms.…”

Section: Resultsmentioning

confidence: 99%

“…The PWWP domain of DNMT3A recognizes histone H3K36me2/3 [ 31 – 37 ] and may be particularly important for de novo DNA methylation in oocytes, which primarily occurs at H3K36me3-marked regions [ 24 ]. It was previously reported that substitutions of an aspartic acid in the DNMT3A PWWP domain (D329A in mouse and D333N in human) results in postnatal growth retardation [ 40 , 41 ].…”

Section: Discussionmentioning

confidence: 99%

“…Since we were not able to obtain oocytes from homozygous females due to the early lethality phenotype, we generated [ Dnmt3a 2lox/D329A , Zp3 -Cre] females, the oocytes of which only express DNMT3A D329A . Despite the fact that de novo CG methylation predominantly occurs in H3K36me3-marked regions [ 23 , 24 ] and that H3K36me2/3 recognition is severely affected by the D329A substitution [ 31 , 37 ], there was little, if any, loss of CG methylation in Dnmt3a 1lox/D329A oocytes. Notably, the maternally methylated imprinting control regions, which are transcribed and marked with H3K36me3 [ 21 – 24 ], remained highly methylated in Dnmt3a 1lox/D329A oocytes.…”

Section: Discussionmentioning

confidence: 99%

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The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes

et al. 2021

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DNA methylation at CG sites is important for gene regulation and embryonic development. In mouse oocytes, de novo CG methylation requires preceding transcription-coupled histone mark H3K36me3 and is mediated by a DNA methyltransferase DNMT3A. DNMT3A has a PWWP domain, which recognizes H3K36me2/3, and heterozygous mutations in this domain, including D329A substitution, cause aberrant CG hypermethylation of regions marked by H3K27me3 in somatic cells, leading to a dwarfism phenotype. We herein demonstrate that D329A homozygous mice show greater CG hypermethylation and severer dwarfism. In oocytes, D329A substitution did not affect CG methylation of H3K36me2/3-marked regions, including maternally methylated imprinting control regions; rather, it caused aberrant hypermethylation in regions lacking H3K36me2/3, including H3K27me3-marked regions. Thus, the role of the PWWP domain in CG methylation seems similar in somatic cells and oocytes; however, there were cell-type-specific differences in affected regions. The major satellite repeat was also hypermethylated in mutant oocytes. Contrary to the CA hypomethylation in somatic cells, the mutation caused hypermethylation at CH sites, including CA sites. Surprisingly, oocytes expressing only the mutated protein could support embryonic and postnatal development. Our study reveals that the DNMT3A PWWP domain is important for suppressing aberrant CG hypermethylation in both somatic cells and oocytes but that D329A mutation has little impact on the developmental potential of oocytes.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes

et al. 2021

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“…(4) There was no evidence that culture-associated DNAm is coherently modified at interacting chromatin domains. It is known that DNMTs accumulate in replication foci or punctate heterochromatic foci 38 , 39 and hence, it might be speculated that a targeted mechanism of an epigenetic writer would also involve the interaction of culture-associated chromatin domains. If culture-associated DNAm changes are not governed by targeting of epigenetic writers, there needs to be another—yet unknown— mechanism that disposes specific genomic regions to epigenetic drift.…”

Section: Discussionmentioning

confidence: 99%

DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift

et al. 2021

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Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift.

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“…This results in DNA hypermethylation and de-repression of developmental regulatory genes that manifests phenotypically as dominant postnatal growth retardation [24]. In the same way, the murine equivalent to the human Lys299Ile found in patients with PGL [15], disrupts both DNA and H3K36me2/3 binding by altering the aromatic cage conformation of the PWWP domain of DNMT3A, finally leading to disruption of the sub-nuclear localization of DNMT3A [25]. In PGL patients, we demonstrated that germline DNMT3A variants in residues within the PWWP domain caused significant hypermethylation of homeobox-containing genes involved in early embryonic development.…”

Section: Discussionmentioning

confidence: 99%

Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma

Mellid

Coloma

Calsina

et al. 2020

Cancers

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Over the past few years, next generation technologies have been applied to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. We recently found germline DNMT3A gain-of-function variants in two patients with head and neck paragangliomas causing a characteristic hypermethylated DNA profile. Here, whole-exome sequencing identifies a novel germline DNMT3A variant (p.Gly332Arg) in a patient with bilateral carotid paragangliomas, papillary thyroid carcinoma and idiopathic intellectual disability. The variant, located in the Pro-Trp-Trp-Pro (PWWP) domain of the protein involved in chromatin targeting, affects a residue mutated in papillary thyroid tumors and located between the two residues found mutated in microcephalic dwarfism patients. Structural modelling of the variant in the DNMT3A PWWP domain predicts that the interaction with H3K36me3 will be altered. An increased methylation of DNMT3A target genes, compatible with a gain-of-function effect of the alteration, was observed in saliva DNA from the proband and in one independent acute myeloid leukemia sample carrying the same p.Gly332Arg variant. Although further studies are needed to support a causal role of DNMT3A variants in paraganglioma, the description of a new DNMT3A alteration in a patient with multiple clinical features suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants.

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H3K36me2/3 Binding and DNA Binding of the DNA Methyltransferase DNMT3A PWWP Domain Both Contribute to its Chromatin Interaction

Cited by 59 publications

References 28 publications

The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes

The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes

DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift

Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma

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