Chromatin remodeling is of crucial importance during brain development. Pathogenic alterations of several chromatin remodeling ATPases have been implicated in neurodevelopmental disorders. We describe an index case with a de novo missense mutation in CHD3, identified during whole genome sequencing of a cohort of children with rare speech disorders. To gain a comprehensive view of features associated with disruption of this gene, we use a genotype-driven approach, collecting and characterizing 35 individuals with de novo CHD3 mutations and overlapping phenotypes. Most mutations cluster within the ATPase/helicase domain of the encoded protein. Modeling their impact on the three-dimensional structure demonstrates disturbance of critical binding and interaction motifs. Experimental assays with six of the identified mutations show that a subset directly affects ATPase activity, and all but one yield alterations in chromatin remodeling. We implicate de novo CHD3 mutations in a syndrome characterized by intellectual disability, macrocephaly, and impaired speech and language.
The Chromodomain Helicase DNA-binding (CHD) protein family is a key class of ATP-dependent chromatin remodeling proteins, which utilize energy derived from ATP hydrolysis to regulate chromatin structure, thereby modulating gene expression1,2. CHD proteins are crucial for developmental processes1,3, with various members implicated in major neurodevelopmental disorders including CHD2 in epileptic encephalopathy4, CHD7 in CHARGE syndrome5, CHD8 in autism6,7, and more recently CHD4 and CHD1 in neurodevelopmental syndromes8,9. Three CHD proteins (CHD3, CHD4, and CHD5) can exert their chromatin remodeling activity by forming the core ATPase subunit of the NuRD complex1,10,11,12. The NuRD complex is associated with various fundamental cellular mechanisms, including genomic integrity and cell cycle progression13, and plays important roles in embryonic stem cell differentiation14. A recent study reports that the different CHD factors within the NuRD complex (CHD3, CHD4, and CHD5) are developmentally regulated in the mouse brain, each having distinct and mostly non-redundant functions during cortical development15. In particular, the CHD3 protein has been implicated in late neural radial migration and cortical layer specification.
In contrast to most other members of the CHD protein family, a specific syndrome associated with mutations in CHD3 (MIM 602120) has not yet been characterized. In this study, based on an index case from whole genome sequencing of children with rare speech disorders, we assemble a set of 35 probands carrying de novo mutations that disrupt CHD3. We characterize the overlapping phenotypic features of probands with CHD3 mutations, including intellectual disability (with a wide range of severity), developmental delays, macrocephaly, impaired speech and language skills, and characteristic facial features. We identify mainly missense mutations that cluster in and around the ATPase/helicase domain of the CHD3 protein, and are predicted to disturb function, based on three-dimensional modeling. We use functional assays to describe the effects of multiple different CHD3 mutations on ATPase activity and chromatin remodeling capacities. Taken together, our data demonstrate that de novo missense mutations in CHD3 disturb chromatin remodeling activities of the encoded protein, thereby causing a neurodevelopmental disorder.
De novo CHD3 mutations cause a neurodevelopmental phenotype
During whole genome sequencing of a cohort of 19 unrelated children with a primary diagnosis of Childhood Apraxia of Speech (CAS)16, we discovered a de novo missense mutation in CHD3, predicted to disrupt the helicase domain of the encoded protein. CAS is a rare neurodevelopmental disorder characterized by impairments in learning to produce the coordinated sequences of mouth and face movements underlying fluent speech. Remarkably, the CHD3 protein is one of the few documented interaction partners of FOXP2 (see Supplementary Table S1 in ref. 17), a transcription factor that has been implicated in monogenic forms of CAS, accompanied by wide-ranging language problems, in multiple families and unrelated cases18,19,20.
Discovery of the CHD3 mutation (NM_001005273.2, p.Arg1169Trp) in our index case motivated a search for other de novo mutations in this gene. Studies of large numbers of simplex families with an autistic proband have documented just two single non-synonymous de novo variants in CHD3 in probands21,22, while eight additional non-synonymous variants were recently recorded in a study of thousands of children with unexplained developmental disorders from the UK23, with limited information on phenotypic profiles of carriers of CHD3 variants. Via GeneMatcher24 we assemble a cohort of 35 independently diagnosed probands with de novo mutations disrupting CHD3, to systematically assess the phenotypic consequences of damage to this gene.
The 35 probands with de novo mutations in CHD3 show overlapping phenotypes, summarized in Table 1 and in more detail in Supplementary Data 1. All individuals have global developmental delays and/or intellectual disability, with a total IQ varying from 70–85 (borderline intellectual functioning) to below 35 (severe intellectual disability). Nine individuals (29%) show autism or autism-like features, including stereotypic and hand-flapping behavior. Interestingly, the majority of individuals (19 individuals; 58%) have macrocephaly, and in cases where neuroimaging has been performed, widening of cerebrospinal fluid spaces is noted in 10 out of 30 MRI reports (33%). One individual (individual 5) has microcephaly. Hypotonia is reported in 21 individuals (75%). The facial phenotype consists of widely spaced eyes, a broad and bossing forehead, periorbital fullness and narrow palpebral fissures, laterally sparse eyebrows, low-set and often simple ears with thick helices, and a pointed chin (Fig. 1). Joint dislocations and/or hyperlaxity are reported in 12 cases, and five individuals have inguinal or umbilical hernias. Five of the 21 male individuals have undescended testes. Vision problems are quite common and include hypermetropia (11 individuals), strabismus (10 individuals), and cerebral visual impairment (three individuals). One individual (individual 34) developed epilepsy, two additional individuals had neonatal convulsions. In many individuals an abnormal and often unsteady gait is reported, and one individual (individual 13) developed symptoms of Parkinsonism at a later age.
Given that our index case was ascertained on the basis of a formal diagnosis of CAS, we pay special attention to the association of CHD3 mutations with speech and language deficits. The index case was diagnosed with severe speech apraxia at the age of 3 years, and then used sign language to communicate effectively. He has severe problems with expressive speech, against relatively normal scores on language comprehension tests and a composite IQ (KBIT) of 72. In all 33 subjects that were at least 2 years old at the last evaluation, CHD3 disruptions are associated with delayed milestones in the speech and language domain. The average age for first spoken words in this cohort is 2 years and 10 months (range: 1.5–5.5 years, after excluding six individuals that were non-verbal at the last evaluation). Our data suggest that expressive language is more affected than receptive language, and intelligibility is often impaired. Speech-related problems identified in our cohort include dysarthria, speech apraxia, oromotor problems, and stuttering.
De novo CHD3 mutations cluster in the helicase domain
The 35 unrelated probands have 23 different de novo mutations in CHD3 (Fig. 2a, b). None of these mutations are present in the GnomAD database (http://gnomad.broadinstitute.com). Except for four individuals, all individuals have missense mutations. Interestingly, within our cohort there are multiple cases of recurrent identical de novo mutations, revealing mutational hotspots. The most striking is p.Arg985Trp, found in six children from five different families, while two additional individuals have a different substitution affecting the same residue (p.Arg985Gln).
The CHD3 protein is characterized by a SNF2-like ATPase/helicase domain, together with two plant homeodomain (PHD) fingers and two chromodomains (Fig. 2b, c)1,11, which mediate chromatin interactions and nucleosome remodeling1. The overwhelming majority of missense mutations (17/19) cluster within and around the ATPase/helicase motif, a functional domain that consists of two subdomains: a Helicase ATP-binding lobe and a Helicase C-terminal lobe. This domain provides energy for nucleosome remodeling through its ATPase activity. All missense mutations affect amino acids that are highly conserved, both in different species and also in the other CHD proteins that can be part of the NuRD complex (Supplementary Fig. 1), and clearly cluster in and around highly conserved SF2-family helicase motifs (Supplementary Fig. 1). All are predicted to be pathogenic by Polyphen-2 and/or SIFT, and have CADD scores above 24 (Supplementary Data 1).
The identified de novo mutations also include one in-frame deletion of one amino acid (p.Gly1109del) and two truncating mutations (p.Glu457* and p.Phe1935Glufs*108), although the latter causes a frameshift at the very end of the protein, leading to a stop codon after 108 amino acids. RNA sequencing of transcripts with and without cycloheximide showed that this mutation escapes nonsense-mediated decay (Supplementary Fig. 2). Finally, one case has a splice-site mutation (c.4073-2A>G) which is predicted to yield skipping of exon 27, while preserving the reading frame (Fig. 2a). Data from the ExAC database (http://exac.broadinstitute.com) indicate that CHD3 is extremely intolerant for loss-of-function mutations (loss-of-function intolerance score of 1.0) and highly intolerant for missense mutations (Z-score of +7.15)25, supporting the pathogenicity of the mutations that we found.
All CHD3 mutations were determined to be the most likely causal variant contributing to the disorder of the proband. In proband 15 who has a de novo CHD3 p.Asp1120His mutation, a de novo truncating mutation in CIC was also identified (NM_015125.3:c.1444G>T; p.Glu482*). Since truncating mutations in CIC were recently suggested as a potential cause of intellectual disability (ID)26, both mutations might be involved in the phenotype of this proband.
A subset of CHD3 mutations directly affects ATP hydrolysis
The striking clustering of almost all missense mutations in the ATPase/helicase domain of the CHD3 protein led us to hypothesize that disturbance of ATPase and/or chromatin remodeling activities of CHD3 could be potential pathogenic mechanisms. Three-dimensional modeling and mutation analysis of all missense mutations, including analysis of the conserved SF2-characteristic helicase motifs, demonstrates clear clustering of mutations and disturbance of important binding and interaction domains (Fig. 2d and Supplementary Note 1). Direct fluorescence imaging of mCherry-tagged CHD3 mutations in cellular models revealed no differences in subcellular localization for the mutated proteins as compared to wild-type CHD3 (Supplementary Fig. 3).
We experimentally assessed ATPase activity of six representative mutations, selected to include one mutation in the Helicase ATP-binding lobe and several mutations in the Helicase C-terminal lobe. FLAG-tagged full-length wild-type CHD3 protein and each of the six mutant proteins were transiently expressed in mammalian HEK293 cells and purified (Supplementary Fig. 4). Radiometric ATPase assays were performed to assess the activity of these mutant proteins relative to wild-type, in the presence of dsDNA (Fig. 3), recombinant nucleosomes (Fig. 3), or in the absence of DNA substrates as a control (Supplementary Fig. 5). ATPase activities of p.Arg1121Pro and p.Arg1172Gln were significantly lower than wild-type for both substrate conditions. These findings are consistent with the modeling data, since p.Arg1121Pro is predicted to disrupt a helix integral to motif V, while p.Arg1172Gln is located in helicase motif VI, and both motifs are known to be critical in ATP hydrolysis. The activity of p.Asn1159Lys was significantly lower only in the presence of dsDNA, although the reason for the different activity depending on the substrate is currently unknown. The protein with the p.Leu915Phe mutation, located in conserved SNF2-motif III, is significantly hyperactive under both conditions. The p.Arg1187Pro and p.Trp1158Arg mutations do not show statistically significant differences from the wild-type protein in these ATPase assays. According to the three-dimensional structure, the location of p.Arg1187Pro is not close to the ATP-binding or interaction surface. To assess whether mutant protein could impact activity of wild-type enzyme, we mixed wild-type protein with equimolar amounts of several mutant proteins, finding no biochemical evidence in this assay for interference (Supplementary Fig. 6).
CHD3 mutations disturb chromatin remodeling capacities
We measured the effects of six mutations on the chromatin remodeling activity of CHD3, by assessing restriction enzyme accessibility to nucleosomal DNA27. Consistent with its reduced activity in the ATPase assays, the p.Arg1172Gln mutant was partially, but not fully, active at chromatin remodeling (Fig. 4). p.Arg1121Pro, which showed severely reduced ATPase activity, was highly compromised in the chromatin remodeling assay. Moreover, p.Leu915Phe demonstrated hyperactivity in this assay, mirroring its elevated ATPase activity. Crucially, chromatin remodeling assays can also detect functional defects beyond ATP hydrolysis27. Two of the mutant proteins, p.Trp1158Arg and p.Asn1159Lys, exhibited severely compromised ability to remodel chromatin (Fig. 4) against a background of some preserved ATPase activity (c.f. Fig. 3). In sum, with the sole exception of p.Arg1187Pro, all the mutant versions of CHD3 that we tested differ from wild-type protein in their ability to remodel chromatin, with some mutants exhibiting decreased activity while one shows increased activity.
In this study, we show that de novo CHD3 mutations cause a neurodevelopmental disorder. We demonstrate defining clinical features of this syndrome. The characteristic phenotype of individuals with CHD3 mutations overlaps with that reported for de novo mutations in CHD4, in which intellectual disability, macrocephaly, ventriculomegaly, undescended testes, and similar facial features have been reported. However, comparisons to the CHD4-related syndrome are currently limited because so far only five individuals with CHD4 mutations have been clinically characterized. Also interesting in this context is the fact that four of the six recently described patients with missense mutations in CHD1 have a diagnosis of speech apraxia9, a relatively rare condition. Although CHD1 does not function in the same protein complex as CHD3 and has different expression patterns9, there might be shared pathogenic mechanisms leading to speech problems in patients with mutations in these chromatin remodelers.
Based on the molecular and phenotypic data of individuals in our cohort, there is no obvious correlation between the precise type or location of the mutation, and the severity of the variable features of the resulting syndrome. However, the only individual in our cohort with epilepsy is also the only case with a missense mutation in the C-terminal domain of the protein. Future identification of more individuals with missense mutations in this region of the protein will help resolve whether this reflects a phenotype–genotype correlation.
In addition to defining the phenotype associated with CHD3 mutations, we aimed to characterize the effects of CHD3 mutations at a molecular and functional level. ATPase assays with six different mutant CHD3 constructs showed a clearly decreased ATPase activity for two mutations (p.Arg1121Pro and p.Arg1172Gln) and increased ATPase activity for one mutation (p.Leu915Phe). The disturbed ATPase activities are associated with corresponding effects on chromatin remodeling capacities for these three mutants, as shown by the restriction enzyme accessibility assays. It is currently unclear how deactivating and activating mutations can both yield similarly disruptive effects on neurodevelopmental outcomes. However, a recent study of cancer-specific mutations in the chromatin remodeling ATPase SMARCA4 concluded that mutations in the ATPase core of this enzyme had dominant-negative impacts on the global chromatin landscape regardless of whether they displayed increased or decreased dynamic recovery in fluorescence after photobleaching28. By analogy, it seems plausible that perturbed chromatin remodeling activity of CHD3, whether by gain or loss of activity relative to wild-type or by affecting its interactions, might likewise alter chromatin landscapes, to contribute to a neurodevelopmental phenotype.
Two mutations (p.Trp1158Arg and p.Asn1159Lys) show severely decreased chromatin remodeling capacities, despite unaffected ATPase activity in the presence of recombinant nucleosomes. In line with these findings, the highly conserved tryptophan residue at a position analogous to CHD3 residue 1158 has recently been shown to be critical for chromatin remodeling, but not for ATP hydrolysis, in the context of yeast SNF227. Interestingly, the mutation in our cohort affecting this amino acid (p.Trp1158Arg) directly matches the position of a previously published mutation in CHD48 (Supplementary Fig. 1), while the other previously published de novo missense mutations in CHD4-related syndrome are also mainly affecting the orthologous Helicase domain of CHD4 (Supplementary Fig. 1)8,29.
To systematically assess whether the distribution of the missense mutations in CHD3 reflects mutational hotspots in the gene, we performed a formal clustering analysis based on mutual distances, as previously described30. This analysis revealed significant clustering within the transcript (P = 0.0017), a finding that argues against simple haploinsufficiency as an underlying molecular mechanism. The paucity of patients with truncating mutations compared to the 31 patients with missense mutations in our cohort also supports this view, although the precise mechanistic effects of CHD3 mutations during neurodevelopment are a topic for future study.
Taken together, with our research we identify a recognizable neurodevelopmental disorder. We define the phenotypic spectrum associated with mutations in CHD3, and show the effects of several different mutations on ATPase activity and chromatin remodeling capacities. Our findings highlight the importance of chromatin remodeling factors, and specifically the CHD3 protein, in human brain development.
Individuals and consents
The authors affirm that (the legal representatives of) all human research participants provided informed consent for publication of the images in Fig. 1. Informed consent was also derived for the use of biological materials from all individuals or their legal representative. Genetic testing and research were performed in accordance with protocols approved by the local Institutional Review Boards where the patients were followed. Specifically, research exomes were performed after informed consent on protocols approved by the Institutional Review Boards of the following institutions: University of British Columbia, Augustana College, CHU Dijon, Mass General Hospital for Children, University of Erlangen-Nuremberg, Hamburg Chamber of Physicians, Cambridge South—UK Research Ethics Committee, University of Wisconsin-Madison Social & Behavioral Sciences.
Annotation of mutations
All mutations in this report are annotated in GRCh37 (hg19) and CHD3 transcript variant 1 (NM_001005273.2).
For the index case (individual 22), whole genome sequencing was performed using Illumina’s HiSeq X Ten technology, the Burrows–Wheeler Aligner (BWA) software version 0.7.8-r45531 and GATK v.3.432. In other individuals, exome or genome sequencing and data analysis were performed as previously described33,34,35,36,37,38,39,40,41,42,43,44.
Expression and purification of FLAG-CHD3
CHD3 proteins were prepared as previously described45, with the following modifications. FLAG-CHD3 constructs were cloned into expression vectors (kindly provided by Guang Hu) using Gateway Cloning technology. Primer sequences are provided in Supplementary Table 1. HEK293-f (ThermoFisher, FreeStyle™ 293-F Cells) were grown in suspension culture using FreeStyle™ 293 Expression Medium (ThermoFisher) in optimum growth flasks (Thomson) using a shaking incubator set at 8% CO2, 80% humidity, and 150 rpm shaker rate. The cell count was 106 cells/ml on the day of transfection. Cells were transfected with 1 mg of expression vector using PEI max (Polysciences). Cells were harvested 48 h after transfection by centrifugation at 400 × g for 6 min. Cells were washed once with phosphate buffer saline solution prior to storage at −80 °C or protein purification.
The cell pellet was resuspended in lysis buffer (20 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 1 mM DTT, 1 mM PMSF, and 1× cOmplete® protease-inhibitor EDTA-free (Roche), pH 7.6). Cells were incubated on ice for 30 min, vortexed briefly, and nuclei were collected by centrifugation (5 min, 3300 × g, 4 °C). The supernatant was discarded and the nuclear pellet was resuspended in nuclear extraction buffer (20 mM HEPES, 0.5 M KCl, 1.5 mM MgCl2, 0.2 mM EDTA, 20% glycerol, 0.2% NP-40, 1 mM DTT, 1 mM PMSF, and 1× cOmplete® protease-inhibitor EDTA-free (Roche), pH 7.6). The nuclear pellet was homogenized using a Dounce homogenizer, incubated on ice for 30 min, and insoluble material was removed by centrifugation (20 min, 110,000 × g, 4 °C). The supernatant (nuclear extract) was incubated with α-FLAG M2 affinity gel (Sigma-Aldrich) and rotated overnight at 4 °C. The α-FLAG beads were then washed twice with nuclear extraction buffer, followed by 2 additional washes with wash buffer (20 mM HEPES, 0.1 M KCl, 0.2% NP-40, 20% glycerol, and 1 mM DTT, pH 7.6). The FLAG-CHD3 protein was eluted with 0.3 mg/ml 3XFLAG peptide (in 20 mM HEPES, 0.1 M KCl, 0.05% NP-40, 20% glycerol, and 1 mM DTT, pH 7.6). Wild-type and mutant protein samples were analyzed by SDS-PAGE and stained with Coomassie Brilliant Blue (Supplementary Fig. 4). The concentration of the CHD3 proteins was estimated from BSA standards in SDS-PAGE gels stained with Coomassie Brilliant Blue.
Radiometric ATPase assay
Each ATPase reaction (10 μL) contained 20 mM Tris–HCl, pH 7.5, 1 mM MgCl2, 0.1 mg/ml BSA, 1 mM DTT, 100 μM ATP, 1 μCi of [γ-32P]ATP as a tracer. 25 nM of each CHD3 purified protein was incubated with 70 nM of recombinant nucleosomes or naked dsDNA. Nucleosome was reconstituted by the salt gradient dialysis method using recombinant histone octamer and 201 bp 601 DNA fragment46. The reactions were initiated by the addition of nucleosome or DNA substrate and incubated at 37 °C for 40 min. The reaction was quenched by the addition of EDTA to a final concentration of 100 mM. Aliquots (2.5 μL) were removed and spotted on PEI-cellulose thin-layer chromatography plates and developed in 1 M formic acid and 0.5 M LiCl. ATP hydrolysis was quantified using a Phosphorimager with Image Quant Software. For the mixing experiment, all reaction components except for CHD3 protein were incubated for 10 min at 37 °C, and the CHD3 protein mixture was added last to start the reaction. This experiment was performed 3 times per condition (N = 3) for all conditions, except for the conditions “no CHD3”, “WT 12.5 nM” and “WT 25 nM” (N = 2).
For the quantification analysis, we performed 3 individual experiments for each of the two biological replicates (total N = 6), except for the p.Trp1158Arg mutant (one biological replicate, total N = 3). An unpaired t-test was used to determine whether the activity of the mutant proteins differed significantly from wild-type protein activity.
Restriction enzyme accessibility assay
Remodeling activities were measured with a restriction enzyme accessibility assay as previously described27. 12.5 nM nucleosomes (347 bp) were incubated with the indicated amounts of CHD3 proteins at 37 °C for 60 min in the remodeling buffer (20 mM Tris–HCl pH 7.5, 1 mM DTT, 1 mM MgCl2, 1 mM ATP, 0.1 mg/ml BSA, and 5 U HhaI). The reactions were stopped by adding 2 µL of proteinase K buffer containing 6.7 mg/ml proteinase K, 167 mM EDTA, and 1.7% SDS. After incubation at 50 °C for 10 min, the DNAs were analyzed by 6% native polyacrylamide gel electrophoresis. The separated DNA fragments were visualized with UV light on the ChemiDox XRS system (BIO-RAD). The band intensities were quantified by ImageJ.
Cloning constructs for immunofluorescence
Wild-type CHD3 (NM_001005273.2) was amplified by PCR and cloned into pCR2.1-TOPO (Invitrogen) as described47. CHD3 mutation constructs were generated using the QuikChange II Site-Directed Mutagenesis Kit (Agilent), primer sequences are provided in Supplementary Table 1. CHD3 cDNAs were subcloned using BamHI/NheI restriction sites into a modified pmCherry-C1 vector (Clontech). All constructs were verified by Sanger sequencing.
HEK293 cells were obtained from ECACC (Catalogue number 85120602) and grown in Dulbecco’s modified Eagle’s medium (Invitrogen), supplemented with 10% fetal bovine serum (Invitrogen). Transfection was performed using GeneJuice (Merck-Millipore). The cells were seeded onto coverslips coated with poly-L-lysine (Sigma). At 36 h post-transfection, cells were fixed using 4% paraformaldehyde solution (Electron Microscopy Sciences) for 10 min at room temperature. The mCherry fusion proteins were visualized by direct fluorescence, nuclei were visualized with Hoechst 33342 (Invitrogen). Fluorescence images were obtained using an Axiovert A-1 fluorescent microscope with ZEN Image Software (Zeiss).
As no experimentally solved 3D-structure of CHD3 exists, we performed homology modeling using the modeling option with standard parameters in the YASARA48 & WHAT IF49 twinset. Several models of the ATPase/helicase domain were created. The best scoring model was based on template PDB-file 5JXR (sequence identity 41% over the aligned residues). We also studied the model based on PDB-file 3MWY (sequence identity 45%), which shows a more open conformation and contains an ATP substitute. These two models provided information about the relative position of the mutated residues in the different conformation of the protein complex.
Clustering analysis of missense mutations
The locations of observed de novo missense mutations were permutated 1,000,000 times over the cDNA of the CHD3 gene (RefSeq transcript: NM_001005273.2). The distances between missense mutations were adjusted to take into account the total size of the coding region of CHD3 (6003 bp). Then, the geometric mean (the nth root of the product of n of all distances separating the mutations) was calculated, giving an index of clustering, as previously described30. To circumvent a mean distance of 0 as the result of recurrent mutations, pseudocount (adding 1 to all distances and 1 to the gene size) was used. To avoid artificial deflation of the clustering P-value, only one of the recurrent mutations present in the sibling-pair (individuals 7 and 8) and twin-pair (individuals 20 and 21) were included for the analysis.
All genotypic and phenotypic data supporting the findings of this study are available within the paper and supplementary files. Data are also freely available in the ClinVar database, under accession numbers SCV000787629–SCV000787651. Raw data of functional experiments are available from the corresponding authors (P.M.C. and S.E.F.) upon request.
Marfella, C. G. & Imbalzano, A. N. The Chd family of chromatin remodelers. Mutat. Res. 618, 30–40 (2007).
Hargreaves, D. C. & Crabtree, G. R. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 21, 396–420 (2011).
Ho, L. & Crabtree, G. R. Chromatin remodelling during development. Nature 463, 474–484 (2010).
Carvill, G. L. et al. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. Nat. Genet. 45, 825–830 (2013).
Vissers, L. E. et al. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat. Genet. 36, 955–957 (2004).
O'Roak, B. J. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246–250 (2012).
Bernier, R. et al. Disruptive CHD8 mutations define a subtype of autism early in development. Cell 158, 263–276 (2014).
Weiss, K. et al. De novo mutations in CHD4, an ATP-dependent chromatin remodeler gene, cause an intellectual disability syndrome with distinctive dysmorphisms. Am. J. Hum. Genet. 99, 934–941 (2016).
Pilarowski, G. O. et al. Missense variants in the chromatin remodeler CHD1 are associated with neurodevelopmental disability. J. Med. Genet. 55, 561–566 (2017).
Zhang, Y., LeRoy, G., Seelig, H. P., Lane, W. S. & Reinberg, D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 95, 279–289 (1998).
Woodage, T., Basrai, M. A., Baxevanis, A. D., Hieter, P. & Collins, F. S. Characterization of the CHD family of proteins. Proc. Natl Acad. Sci. USA 94, 11472–11477 (1997).
Kolla, V. et al. The tumour suppressor CHD5 forms a NuRD-type chromatin remodelling complex. Biochem. J. 468, 345–352 (2015).
Lai, A. Y. & Wade, P. A. Cancer biology and NuRD: a multifaceted chromatin remodelling complex. Nat. Rev. Cancer 11, 588–596 (2011).
Basta, J. & Rauchman, M. The nucleosome remodeling and deacetylase complex in development and disease. Transl. Res. 165, 36–47 (2015).
Nitarska, J. et al. A functional switch of NuRD chromatin remodeling complex subunits regulates mouse cortical development. Cell Rep. 17, 1683–1698 (2016).
Eising, E. et al. A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development. Mol. Psychiatry. https://doi.org/10.1038/s41380-018-0020-x (2018).
Estruch, S. B., Graham, S. A., Deriziotis, P. & Fisher, S. E. The language-related transcription factor FOXP2 is post-translationally modified with small ubiquitin-like modifiers. Sci. Rep. 6, 20911 (2016).
Lai, C. S., Fisher, S. E., Hurst, J. A., Vargha-Khadem, F. & Monaco, A. P. A forkhead-domain gene is mutated in a severe speech and language disorder. Nature 413, 519–523 (2001).
Graham, S. A. & Fisher, S. E. Understanding language from a genomic perspective. Annu. Rev. Genet. 49, 131–160 (2015).
Morgan, A., Fisher, S.E., Scheffer, I. & Hildebrand, M. FOXP2-related Speech and Language Disorders. in GeneReviews(R) (eds Pagon, R.A. et al.) (Seattle, WA, 2017).
Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014).
Yuen, R. K. et al. Genome-wide characteristics of de novo mutations in autism. Genom. Med. 1, 16027 (2016).
Deciphering Developmental Disorders Study. Prevalence and architecture of de novo mutations in developmental disorders. Nature 542, 433–438 (2017).
Sobreira, N., Schiettecatte, F., Valle, D. & Hamosh, A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum. Mutat. 36, 928–930 (2015).
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
Lu, H. C. et al. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat. Genet. 49, 527–536 (2017).
Liu, X., Li, M., Xia, X., Li, X. & Chen, Z. Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. Nature 544, 440–445 (2017).
Hodges, H. C. et al. Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. Nat. Struct. Mol. Biol. 25, 61–72 (2018).
Sifrim, A. et al. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing. Nat. Genet. 48, 1060–1065 (2016).
Lelieveld, S. H. et al. Spatial clustering of de novo missense mutations identifies candidate neurodevelopmental disorder-associated genes. Am. J. Hum. Genet. 101, 478–484 (2017).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Neveling, K. et al. A post-hoc comparison of the utility of Sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases. Hum. Mutat. 34, 1721–1726 (2013).
Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature 519, 223–228 (2015).
Hollink, I. et al. Acute myeloid leukaemia in a case with Tatton–Brown–Rahman syndrome: the peculiar DNMT3A R882 mutation. J. Med. Genet. 54, 805–808 (2017).
Gibson, W. T. et al. Mutations in EZH2 cause Weaver syndrome. Am. J. Hum. Genet. 90, 110–118 (2012).
Cohen, A. S. et al. A novel mutation in EED associated with overgrowth. J. Hum. Genet. 60, 339–342 (2015).
Lelieveld, S. H. et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat. Neurosci. 19, 1194–1196 (2016).
Thevenon, J. et al. Diagnostic odyssey in severe neurodevelopmental disorders: toward clinical whole-exome sequencing as a first-line diagnostic test. Clin. Genet. 89, 700–707 (2016).
Louie, R. J. et al. Novel pathogenic variants in FOXP3 in fetuses with echogenic bowel and skin desquamation identified by ultrasound. Am. J. Med. Genet. A 173, 1219–1225 (2017).
Hempel, M. et al. De novo mutations in CHAMP1 cause intellectual disability with severe speech impairment. Am. J. Hum. Genet. 97, 493–500 (2015).
Popp, B. et al. Do the exome: a case of Williams–Beuren syndrome with severe epilepsy due to a truncating de novo variant in GABRA1. Eur. J. Med. Genet. 59, 549–553 (2016).
Tanaka, A. J. et al. Mutations in SPATA5 are associated with microcephaly, intellectual disability, seizures, and hearing loss. Am. J. Hum. Genet. 97, 457–464 (2015).
Kremer, L. S. et al. Genetic diagnosis of Mendelian disorders via RNA sequencing. Nat. Commun. 8, 15824 (2017).
Low, J. K. et al. CHD4 is a peripheral component of the nucleosome remodeling and deacetylase complex. J. Biol. Chem. 291, 15853–15866 (2016).
Taguchi, H., Horikoshi, N., Arimura, Y. & Kurumizaka, H. A method for evaluating nucleosome stability with a protein-binding fluorescent dye. Methods 70, 119–126 (2014).
Deriziotis, P. et al. De novo TBR1 mutations in sporadic autism disrupt protein functions. Nat. Commun. 5, 4954 (2014).
Krieger, E., Koraimann, G. & Vriend, G. Increasing the precision of comparative models with YASARA NOVA—a self-parameterizing force field. Proteins 47, 393–402 (2002).
Vriend, G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8, 29 (1990).
We thank all individuals and families for their contribution. We thank Amaia Carrión Castillo and Else Eising for assistance with the WGS analysis of the index individual, and Sarah Graham and Elliot Sollis for cloning the wild-type CHD3 construct for immunofluorescence. This work was supported by the Netherlands Organization for Scientific Research (NWO) Gravitation Grant 24.001.006 to the Language in Interaction Consortium (L.S.B., S.E.F., and H.G.B.), the Max Planck Society (S.E.F.), the National Institute on Deafness and Other Communication Disorders Grant DC000496 (L.Sh.) and a core grant to the Waisman Center from the National Institute of Child Health and Human Development (Grant U54 HD090256) to L.Sh., the Canadian Institutes of Health Research Grants MOP-119595 and PJT-148830 to W.T.G. Individuals 11, 16, 24, and 28 were part of The DDD Study cohort. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund [Grant number HICF-1009-003], a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute [Grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of the Wellcome Trust or the Department of Health. The DDD study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12, granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network.
The authors declare no competing interests.
Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Snijders Blok, L., Rousseau, J., Twist, J. et al. CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language. Nat Commun 9, 4619 (2018). https://doi.org/10.1038/s41467-018-06014-6
This article is cited by
Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration
Cell & Bioscience (2023)
The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective
Cellular and Molecular Life Sciences (2021)
Multidisziplinäre Diagnostik von Entwicklungsstörungen: Grundlage der „personalized precision medicine“
Monatsschrift Kinderheilkunde (2021)
Missense and truncating variants in CHD5 in a dominant neurodevelopmental disorder with intellectual disability, behavioral disturbances, and epilepsy
Human Genetics (2021)
The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain
Nature Communications (2020)
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.