Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder
Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo var...
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| Published in | PLoS genetics Vol. 13; no. 10; p. e1006864 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Public Library of Science
25.10.2017
Public Library of Science (PLoS) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1553-7404 1553-7390 1553-7404 |
| DOI | 10.1371/journal.pgen.1006864 |
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| Abstract | Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome. Here, we present a novel cohort of five patients with de novo loss of function mutations affecting the histone methyltransferase KMT2C. Our clinical data delineates the KMT2C phenotypic spectrum and reinforces the phenotypic overlap with Kleefstra syndrome and other related ID disorders. To elucidate the common molecular basis of the neuropathology associated with mutations in KMT2C and EHMT1, we characterized the role of the Drosophila KMT2C ortholog, trithorax related (trr), in the nervous system. Similar to the Drosophila EHMT1 ortholog, G9a, trr is required in the mushroom body for short term memory. Trr ChIP-seq identified 3371 binding sites, mainly in the promoter of genes involved in neuronal processes. Transcriptional profiling of pan-neuronal trr knockdown and G9a null mutant fly heads identified 613 and 1123 misregulated genes, respectively. These gene sets show a significant overlap and are associated with nearly identical gene ontology enrichments. The majority of the observed biological convergence is derived from predicted indirect target genes. However, trr and G9a also have common direct targets, including the Drosophila ortholog of Arc (Arc1), a key regulator of synaptic plasticity. Our data highlight the clinical and molecular convergence between the KMT2 and EHMT protein families, which may contribute to a molecular network underlying a larger group of ID/ASD-related disorders. |
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| AbstractList | Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome. Here, we present a novel cohort of five patients with de novo loss of function mutations affecting the histone methyltransferase KMT2C. Our clinical data delineates the KMT2C phenotypic spectrum and reinforces the phenotypic overlap with Kleefstra syndrome and other related ID disorders. To elucidate the common molecular basis of the neuropathology associated with mutations in KMT2C and EHMT1, we characterized the role of the Drosophila KMT2C ortholog, trithorax related (trr), in the nervous system. Similar to the Drosophila EHMT1 ortholog, G9a, trr is required in the mushroom body for short term memory. Trr ChIP-seq identified 3371 binding sites, mainly in the promoter of genes involved in neuronal processes. Transcriptional profiling of pan-neuronal trr knockdown and G9a null mutant fly heads identified 613 and 1123 misregulated genes, respectively. These gene sets show a significant overlap and are associated with nearly identical gene ontology enrichments. The majority of the observed biological convergence is derived from predicted indirect target genes. However, trr and G9a also have common direct targets, including the Drosophila ortholog of Arc (Arc1), a key regulator of synaptic plasticity. Our data highlight the clinical and molecular convergence between the KMT2 and EHMT protein families, which may contribute to a molecular network underlying a larger group of ID/ASD-related disorders. Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome. Here, we present a novel cohort of five patients with de novo loss of function mutations affecting the histone methyltransferase KMT2C. Our clinical data delineates the KMT2C phenotypic spectrum and reinforces the phenotypic overlap with Kleefstra syndrome and other related ID disorders. To elucidate the common molecular basis of the neuropathology associated with mutations in KMT2C and EHMT1, we characterized the role of the Drosophila KMT2C ortholog, trithorax related (trr), in the nervous system. Similar to the Drosophila EHMT1 ortholog, G9a, trr is required in the mushroom body for short term memory. Trr ChIP-seq identified 3371 binding sites, mainly in the promoter of genes involved in neuronal processes. Transcriptional profiling of pan-neuronal trr knockdown and G9a null mutant fly heads identified 613 and 1123 misregulated genes, respectively. These gene sets show a significant overlap and are associated with nearly identical gene ontology enrichments. The majority of the observed biological convergence is derived from predicted indirect target genes. However, trr and G9a also have common direct targets, including the Drosophila ortholog of Arc (Arc1), a key regulator of synaptic plasticity. Our data highlight the clinical and molecular convergence between the KMT2 and EHMT protein families, which may contribute to a molecular network underlying a larger group of ID/ASD-related disorders.Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome. Here, we present a novel cohort of five patients with de novo loss of function mutations affecting the histone methyltransferase KMT2C. Our clinical data delineates the KMT2C phenotypic spectrum and reinforces the phenotypic overlap with Kleefstra syndrome and other related ID disorders. To elucidate the common molecular basis of the neuropathology associated with mutations in KMT2C and EHMT1, we characterized the role of the Drosophila KMT2C ortholog, trithorax related (trr), in the nervous system. Similar to the Drosophila EHMT1 ortholog, G9a, trr is required in the mushroom body for short term memory. Trr ChIP-seq identified 3371 binding sites, mainly in the promoter of genes involved in neuronal processes. Transcriptional profiling of pan-neuronal trr knockdown and G9a null mutant fly heads identified 613 and 1123 misregulated genes, respectively. These gene sets show a significant overlap and are associated with nearly identical gene ontology enrichments. The majority of the observed biological convergence is derived from predicted indirect target genes. However, trr and G9a also have common direct targets, including the Drosophila ortholog of Arc (Arc1), a key regulator of synaptic plasticity. Our data highlight the clinical and molecular convergence between the KMT2 and EHMT protein families, which may contribute to a molecular network underlying a larger group of ID/ASD-related disorders. Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome. Here, we present a novel cohort of five patients with de novo loss of function mutations affecting the histone methyltransferase KMT2C. Our clinical data delineates the KMT2C phenotypic spectrum and reinforces the phenotypic overlap with Kleefstra syndrome and other related ID disorders. To elucidate the common molecular basis of the neuropathology associated with mutations in KMT2C and EHMT1, we characterized the role of the Drosophila KMT2C ortholog, trithorax related (trr), in the nervous system. Similar to the Drosophila EHMT1 ortholog, G9a, trr is required in the mushroom body for short term memory. Trr ChIP-seq identified 3371 binding sites, mainly in the promoter of genes involved in neuronal processes. Transcriptional profiling of pan-neuronal trr knockdown and G9a null mutant fly heads identified 613 and 1123 misregulated genes, respectively. These gene sets show a significant overlap and are associated with nearly identical gene ontology enrichments. The majority of the observed biological convergence is derived from predicted indirect target genes. However, trr and G9a also have common direct targets, including the Drosophila ortholog of Arc (Arc1), a key regulator of synaptic plasticity. Our data highlight the clinical and molecular convergence between the KMT2 and EHMT protein families, which may contribute to a molecular network underlying a larger group of ID/ASD-related disorders. Neurodevelopmental disorders (NDDs) like intellectual disability (ID) and autism spectrum disorder (ASD) present an enormous challenge to affected individuals, their families, and society. Understanding the mechanisms underlying NDDs may lead to the development of targeted therapeutics, but this is complicated by the great clinical and genetic heterogeneity seen in patients. Mutations in hundreds of genes have been implicated in NDDs, giving rise to diverse clinical presentations. However, evidence suggests that many of these genes lie in common biological pathways, and mutations in genes that are involved in similar biological functions give rise to more similar clinical phenotypes. Here, we define a novel ID disorder with comorbid ASD (ID/ASD) caused by mutations in KMT2C. This disorder is defined by clinical features that overlap with a group of other disorders, including Kleefstra syndrome, which is caused by EHMT1 mutations. In the fruit fly, we show that the KMT2 and EHMT protein families regulate a highly converging set of biological processes. Both EHMT1 and KMT2C encode histone methyltransferases, which regulate gene transcription by modifying chromatin structure. Further understanding of the common gene regulatory networks associated with this group of ID- and ASD-related disorders may lead to the identification of novel therapeutic targets. |
| Audience | Academic |
| Author | Bok, Levinus A. Pfundt, Rolph Zhou, Huiqing Chubak, Melissa C. Willemsen, Marjolein H. Kramer, Jamie M. Koemans, Tom S. Sifuentes Saenz, Margarita Stegmann, Alexander P. A. Byerly, Kyna A. Baughn, Linda B. Reijnders, Margot R. F. van Bokhoven, Hans de Munnik, Sonja Fenckova, Michaela Stumpel, Connie T. R. M. Stone, Max H. Schenck, Annette Kleefstra, Tjitske |
| AuthorAffiliation | 3 Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands 1 Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands 8 Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, Colorado 5 Division of Genetics and Development, Children’s Health Research Institute, London, Ontario, Canada 9 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 2 Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands 6 Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, the Netherlands 7 Department of Pediatrics, Máxima Medical Centre, Veldhoven, The Netherlands 11 Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada 4 Department of Biology, Faculty of Science, Western University, London, Ontario, Canada 10 Department of Molecular Devel |
| AuthorAffiliation_xml | – name: 11 Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada – name: 4 Department of Biology, Faculty of Science, Western University, London, Ontario, Canada – name: 9 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota – name: 3 Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands – name: 8 Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, Colorado – name: MRC Human Genetics Unit, UNITED KINGDOM – name: 5 Division of Genetics and Development, Children’s Health Research Institute, London, Ontario, Canada – name: 1 Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands – name: 2 Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands – name: 7 Department of Pediatrics, Máxima Medical Centre, Veldhoven, The Netherlands – name: 6 Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, the Netherlands – name: 10 Department of Molecular Developmental Biology, Radboud University, Nijmegen, The Netherlands |
| Author_xml | – sequence: 1 givenname: Tom S. surname: Koemans fullname: Koemans, Tom S. – sequence: 2 givenname: Tjitske surname: Kleefstra fullname: Kleefstra, Tjitske – sequence: 3 givenname: Melissa C. surname: Chubak fullname: Chubak, Melissa C. – sequence: 4 givenname: Max H. orcidid: 0000-0003-3938-0621 surname: Stone fullname: Stone, Max H. – sequence: 5 givenname: Margot R. F. orcidid: 0000-0002-6379-7147 surname: Reijnders fullname: Reijnders, Margot R. F. – sequence: 6 givenname: Sonja surname: de Munnik fullname: de Munnik, Sonja – sequence: 7 givenname: Marjolein H. surname: Willemsen fullname: Willemsen, Marjolein H. – sequence: 8 givenname: Michaela surname: Fenckova fullname: Fenckova, Michaela – sequence: 9 givenname: Connie T. R. M. surname: Stumpel fullname: Stumpel, Connie T. R. M. – sequence: 10 givenname: Levinus A. orcidid: 0000-0002-8125-3389 surname: Bok fullname: Bok, Levinus A. – sequence: 11 givenname: Margarita surname: Sifuentes Saenz fullname: Sifuentes Saenz, Margarita – sequence: 12 givenname: Kyna A. surname: Byerly fullname: Byerly, Kyna A. – sequence: 13 givenname: Linda B. orcidid: 0000-0001-5229-4897 surname: Baughn fullname: Baughn, Linda B. – sequence: 14 givenname: Alexander P. A. surname: Stegmann fullname: Stegmann, Alexander P. A. – sequence: 15 givenname: Rolph orcidid: 0000-0002-0584-4398 surname: Pfundt fullname: Pfundt, Rolph – sequence: 16 givenname: Huiqing surname: Zhou fullname: Zhou, Huiqing – sequence: 17 givenname: Hans surname: van Bokhoven fullname: van Bokhoven, Hans – sequence: 18 givenname: Annette surname: Schenck fullname: Schenck, Annette – sequence: 19 givenname: Jamie M. orcidid: 0000-0002-0924-1279 surname: Kramer fullname: Kramer, Jamie M. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29069077$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | COPYRIGHT 2017 Public Library of Science 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Koemans TS, Kleefstra T, Chubak MC, Stone MH, Reijnders MRF, de Munnik S, et al. (2017) Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder. PLoS Genet13(10): e1006864. https://doi.org/10.1371/journal.pgen.1006864 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Koemans TS, Kleefstra T, Chubak MC, Stone MH, Reijnders MRF, de Munnik S, et al. (2017) Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder. PLoS Genet13(10): e1006864. https://doi.org/10.1371/journal.pgen.1006864 |
| Copyright_xml | – notice: COPYRIGHT 2017 Public Library of Science – notice: 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Koemans TS, Kleefstra T, Chubak MC, Stone MH, Reijnders MRF, de Munnik S, et al. (2017) Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder. PLoS Genet13(10): e1006864. https://doi.org/10.1371/journal.pgen.1006864 – notice: 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Koemans TS, Kleefstra T, Chubak MC, Stone MH, Reijnders MRF, de Munnik S, et al. (2017) Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder. PLoS Genet13(10): e1006864. https://doi.org/10.1371/journal.pgen.1006864 |
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| SubjectTerms | Adolescent Adult Animals Autism Autism Spectrum Disorder - genetics Autism Spectrum Disorder - physiopathology Binding Sites - genetics Bioinformatics Biology and Life Sciences Brain research Child Chromosome Deletion Chromosomes, Human, Pair 9 - genetics Cognition & reasoning Convergence Craniofacial Abnormalities - genetics Craniofacial Abnormalities - physiopathology Cytoskeletal Proteins - genetics Developmental biology DNA-Binding Proteins - genetics Drosophila Drosophila melanogaster - genetics Drosophila Proteins - genetics Euchromatin Female Funding Gene Expression Regulation Genes Genetics Genomics Haploinsufficiency Head Heart Defects, Congenital - genetics Heart Defects, Congenital - physiopathology Histone methyltransferase Histone-Lysine N-Methyltransferase - genetics Histones Histones - genetics Humans Insects Intellectual disabilities Intellectual Disability - genetics Intellectual Disability - physiopathology Laboratories Life sciences Male Medical research Memory Mental retardation Methyltransferases Mutation Nerve Tissue Proteins - genetics Nervous system Neuronal Plasticity - genetics Neurosciences Pervasive developmental disorders Physiological aspects Promoter Regions, Genetic Protein families Research and Analysis Methods Short term memory Supervision Synaptic plasticity Transcription |
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| Title | Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder |
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