Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions
DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A , which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global gr...
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| Published in | Nature genetics Vol. 51; no. 1; pp. 96 - 105 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.01.2019
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in
DNMT3A
, which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of
Dnmt3a
W326R
pluripotent cells in vitro, and is also evident in
Dnmt3a
W326R/+
dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2 and H3K36me3 normally limits DNA methylation of Polycomb-marked regions. Our findings implicate the interplay between DNA methylation and Polycomb at key developmental regulators as a determinant of organism size in mammals.
Gain-of-function mutations altering the PWWP domain of DNMT3A are identified as a new cause of microcephalic dwarfism. These mutations abrogate DNMT3A binding to H3K36me2 and H3K36me3 and lead to aberrant DNA methylation of Polycomb-marked regions. |
|---|---|
| AbstractList | DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A, which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of Dnmt3a.sup.W326R pluripotent cells in vitro, and is also evident in Dnmt3a.sup.W326R/+ dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2 and H3K36me3 normally limits DNA methylation of Polycomb-marked regions. Our findings implicate the interplay between DNA methylation and Polycomb at key developmental regulators as a determinant of organism size in mammals. DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A, which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of Dnmt3aW326R pluripotent cells in vitro, and is also evident in Dnmt3aW326R/+ dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2 and H3K36me3 normally limits DNA methylation of Polycomb-marked regions. Our findings implicate the interplay between DNA methylation and Polycomb at key developmental regulators as a determinant of organism size in mammals. DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A, which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of Dnmt3a pluripotent cells in vitro, and is also evident in Dnmt3a dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2 and H3K36me3 normally limits DNA methylation of Polycomb-marked regions. Our findings implicate the interplay between DNA methylation and Polycomb at key developmental regulators as a determinant of organism size in mammals. DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A, encoding the DNA methyltransferase DNMT3A, that cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2/3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation canyons/valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of Dnmt3a W326R pluripotent cells in vitro, and is also evident in Dnmt3a W326R/+ dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2/3 normally limits DNA methylation of polycomb-marked regions. Our findings implicate the interplay between DNA methylation and polycomb at key developmental regulators as a determinant of organism size in mammals. DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A , which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of Dnmt3a W326R pluripotent cells in vitro, and is also evident in Dnmt3a W326R/+ dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2 and H3K36me3 normally limits DNA methylation of Polycomb-marked regions. Our findings implicate the interplay between DNA methylation and Polycomb at key developmental regulators as a determinant of organism size in mammals. Gain-of-function mutations altering the PWWP domain of DNMT3A are identified as a new cause of microcephalic dwarfism. These mutations abrogate DNMT3A binding to H3K36me2 and H3K36me3 and lead to aberrant DNA methylation of Polycomb-marked regions. DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in DNMT3A, which encodes the DNA methyltransferase DNMT3A. These mutations cause microcephalic dwarfism, a hypocellular disorder of extreme global growth failure. Substitutions in the PWWP domain abrogate binding to the histone modifications H3K36me2 and H3K36me3, and alter DNA methylation in patient cells. Polycomb-associated DNA methylation valleys, hypomethylated domains encompassing developmental genes, become methylated with concomitant depletion of H3K27me3 and H3K4me3 bivalent marks. Such de novo DNA methylation occurs during differentiation of Dnmt3a.sup.W326R pluripotent cells in vitro, and is also evident in Dnmt3a.sup.W326R/+ dwarf mice. We therefore propose that the interaction of the DNMT3A PWWP domain with H3K36me2 and H3K36me3 normally limits DNA methylation of Polycomb-marked regions. Our findings implicate the interplay between DNA methylation and Polycomb at key developmental regulators as a determinant of organism size in mammals. Gain-of-function mutations altering the PWWP domain of DNMT3A are identified as a new cause of microcephalic dwarfism. These mutations abrogate DNMT3A binding to H3K36me2 and H3K36me3 and lead to aberrant DNA methylation of Polycomb-marked regions. |
| Audience | Academic |
| Author | Logan, Clare V. Cormier-Daire, Valerie Fong, Chin-To Sproul, Duncan Marsh, Joseph A. Jackson, Andrew P. Rappsilber, Juri Parry, David A. Hwa, Vivian Challis, Rachel C. Martin, Carol-Anne Allshire, Robin C. Ibáñez, Lourdes Fluteau, Adeline Reijns, Martin A. M. Robertson, Stephen P. Gibson, Kate Heyn, Patricia Sebastiani, Giorgia Dauber, Andrew Auchynnikava, Tatsiana Taglini, Francesca Kilanowski, Fiona |
| AuthorAffiliation | 12. Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany 1. MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK 13. Division of Endocrinology, Children’s National Medical Center, Washington, D.C., USA 6. Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand 3. Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK 11. Neonatology Unit, Hospital Clinic-Maternitat, ICGON, BCNatal, University of Barcelona, Spain 7. Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA 10. Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand 2. Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK 4. Department of Medical Genetics, INSERM UMR 1163, Université Paris-Descart |
| AuthorAffiliation_xml | – name: 1. MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK – name: 7. Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA – name: 10. Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand – name: 8. Department of Endocrinology, Pediatric Research Institute Sant Joan de Déu, University of Barcelona, Barcelona, Spain – name: 11. Neonatology Unit, Hospital Clinic-Maternitat, ICGON, BCNatal, University of Barcelona, Spain – name: 12. Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany – name: 13. Division of Endocrinology, Children’s National Medical Center, Washington, D.C., USA – name: 4. Department of Medical Genetics, INSERM UMR 1163, Université Paris-Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker-Enfants Malades, Paris, France – name: 2. Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK – name: 5. Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA – name: 3. Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK – name: 6. Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand – name: 9. Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain |
| Author_xml | – sequence: 1 givenname: Patricia surname: Heyn fullname: Heyn, Patricia organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 2 givenname: Clare V. surname: Logan fullname: Logan, Clare V. organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 3 givenname: Adeline surname: Fluteau fullname: Fluteau, Adeline organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 4 givenname: Rachel C. orcidid: 0000-0001-9723-5743 surname: Challis fullname: Challis, Rachel C. organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 5 givenname: Tatsiana surname: Auchynnikava fullname: Auchynnikava, Tatsiana organization: Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh – sequence: 6 givenname: Carol-Anne surname: Martin fullname: Martin, Carol-Anne organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 7 givenname: Joseph A. orcidid: 0000-0003-4132-0628 surname: Marsh fullname: Marsh, Joseph A. organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 8 givenname: Francesca surname: Taglini fullname: Taglini, Francesca organization: MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh Cancer Research Centre, IGMM, University of Edinburgh – sequence: 9 givenname: Fiona surname: Kilanowski fullname: Kilanowski, Fiona organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 10 givenname: David A. orcidid: 0000-0003-0376-7736 surname: Parry fullname: Parry, David A. organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 11 givenname: Valerie surname: Cormier-Daire fullname: Cormier-Daire, Valerie organization: Department of Medical Genetics, INSERM UMR 1163, Université Paris-Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker–Enfants Malades – sequence: 12 givenname: Chin-To surname: Fong fullname: Fong, Chin-To organization: Department of Pediatrics, University of Rochester School of Medicine and Dentistry – sequence: 13 givenname: Kate surname: Gibson fullname: Gibson, Kate organization: Genetic Health Service New Zealand, Christchurch Hospital – sequence: 14 givenname: Vivian orcidid: 0000-0003-0517-9049 surname: Hwa fullname: Hwa, Vivian organization: Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine – sequence: 15 givenname: Lourdes surname: Ibáñez fullname: Ibáñez, Lourdes organization: Department of Endocrinology, Pediatric Research Institute Sant Joan de Déu, University of Barcelona, Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII – sequence: 16 givenname: Stephen P. orcidid: 0000-0002-5181-7809 surname: Robertson fullname: Robertson, Stephen P. organization: Department of Women’s and Children’s Health, Dunedin School of Medicine, University of Otago – sequence: 17 givenname: Giorgia surname: Sebastiani fullname: Sebastiani, Giorgia organization: Neonatology Unit, Hospital Clinic-Maternitat, ICGON, BCNatal, University of Barcelona – sequence: 18 givenname: Juri surname: Rappsilber fullname: Rappsilber, Juri organization: Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Bioanalytics, Institute of Biotechnology, Technische Universität Berlin – sequence: 19 givenname: Robin C. orcidid: 0000-0002-8005-3625 surname: Allshire fullname: Allshire, Robin C. organization: Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh – sequence: 20 givenname: Martin A. M. orcidid: 0000-0002-5048-2752 surname: Reijns fullname: Reijns, Martin A. M. organization: MRC Human Genetics Unit, IGMM, University of Edinburgh – sequence: 21 givenname: Andrew orcidid: 0000-0003-4890-0262 surname: Dauber fullname: Dauber, Andrew organization: Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Division of Endocrinology, Children’s National Medical Center – sequence: 22 givenname: Duncan orcidid: 0000-0001-6168-4563 surname: Sproul fullname: Sproul, Duncan email: duncan.sproul@igmm.ed.ac.uk organization: MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh Cancer Research Centre, IGMM, University of Edinburgh – sequence: 23 givenname: Andrew P. orcidid: 0000-0002-8739-2646 surname: Jackson fullname: Jackson, Andrew P. email: andrew.jackson@igmm.ed.ac.uk organization: MRC Human Genetics Unit, IGMM, University of Edinburgh |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30478443$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | The Author(s), under exclusive licence to Springer Nature America, Inc. 2018 COPYRIGHT 2019 Nature Publishing Group Copyright Nature Publishing Group Jan 2019 |
| Copyright_xml | – notice: The Author(s), under exclusive licence to Springer Nature America, Inc. 2018 – notice: COPYRIGHT 2019 Nature Publishing Group – notice: Copyright Nature Publishing Group Jan 2019 |
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| DOI | 10.1038/s41588-018-0274-x |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 CVL, RCC, DAP, AD performed molecular genetic studies to identify patient mutations. PH designed the cell biology experiments, and performed these with CVL, AF, FT, FK and MAMR. PH, AF and CAM characterized the mouse model. JAM performed structural modelling. TA performed mass spectrometry with support from RCA and JR. VCD, CTF, KG, VH, LI, SPR, GS, and AD ascertained subjects, obtained samples and/or assisted with clinical studies. DS performed computational analyses of DNA methylation, ChIPseq and RNAseq datasets. PH, DS and APJ wrote the manuscript with input from MAMR, and all authors reviewed it. DS and APJ planned and supervised the study. Author Contributions |
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| PublicationTitle | Nature genetics |
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| Snippet | DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in
DNMT3A... DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in... DNA methylation and Polycomb are key factors in the establishment of vertebrate cellular identity and fate. Here we report de novo missense mutations in... |
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| SubjectTerms | 13 13/1 13/106 38 38/23 38/91 631/208 631/208/176 64 64/60 82 82/58 82/79 Agriculture Amino acids Animal Genetics and Genomics Animals Bioinformatics Biomedical and Life Sciences Biomedicine Cancer Research Cell cycle Cell Line, Tumor Cells, Cultured Deoxyribonucleic acid Depletion DNA DNA (Cytosine-5-)-Methyltransferases - genetics DNA methylation DNA Methylation - genetics DNA methyltransferase DNA Methyltransferase 3A DNA Modification Methylases - genetics Domains Dwarfism Dwarfism - genetics Female Fibroblasts Gain of Function Mutation - genetics Gene expression Gene Function Gene mutation Genomes HeLa Cells Histones - genetics Human Genetics Humans Male Methylation Methyltransferases Mice Mice, Transgenic - genetics Microcephaly Microcephaly - genetics Missense mutation Mutation Patients Peptides Pluripotency Polycomb group proteins Polycomb-Group Proteins - genetics Protein Binding - genetics Proteins Regulators Regulatory Sequences, Nucleic Acid - genetics Stem cells Transferases |
| Title | Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions |
| URI | https://link.springer.com/article/10.1038/s41588-018-0274-x https://www.ncbi.nlm.nih.gov/pubmed/30478443 https://www.proquest.com/docview/2161264000 https://search.proquest.com/docview/2138649128 https://pubmed.ncbi.nlm.nih.gov/PMC6520989 |
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