Functional Insights into Chromatin Remodelling from Studies on CHARGE Syndrome
Authors: M. Albert Basson, Conny van Ravenswaaij-Arts
Journal: Trends in Genetics (2015)

CHARGE syndrome is a rare genetic syndrome characterised by a unique combination of multiple organ anomalies. Dominant loss-of-function mutations in the gene encoding chromodomain helicase DNA binding protein 7 (CHD7), which is an ATP-dependent chromatin remodeller, have been identified as the cause of CHARGE syndrome. Here, we review recent work aimed at understanding the mechanism of CHD7 function in normal and pathological states, highlighting results from biochemical and in vivo studies. The emerging picture from this work suggests that the mechanisms by which CHD7 fine-tunes gene expression are context specific, consistent with the pleiotropic nature of CHARGE syndrome. CHARGE syndrome is a rare genetic syndrome characterised by a unique combination of multiple organ anomalies. Dominant loss-of-function mutations in the gene encoding chromodomain helicase DNA binding protein 7 (CHD7), which is an ATP-dependent chromatin remodeller, have been identified as the cause of CHARGE syndrome. Here, we review recent work aimed at understanding the mechanism of CHD7 function in normal and pathological states, highlighting results from biochemical and in vivo studies. The emerging picture from this work suggests that the mechanisms by which CHD7 fine-tunes gene expression are context specific, consistent with the pleiotropic nature of CHARGE syndrome. The expressivity and penetrance of CHARGE phenotypes show little correlation with the CHD7 genotype.The hypothesis that mutations or polymorphisms in other genes modify disease phenotypes in humans remains unproven.CHARGE-associated CHD7 mutations can affect its nucleosome remodelling activity in vitro.The role of CHD7 in regulating nucleosome positioning in vivo and the effects of this activity on gene expression require further study.CHD7 pleiotropy may result from its interactions with cell type-specific transcription factors.CHD7 recruitment to cell type-specific enhancers may underlie context-specific roles. The expressivity and penetrance of CHARGE phenotypes show little correlation with the CHD7 genotype. The hypothesis that mutations or polymorphisms in other genes modify disease phenotypes in humans remains unproven. CHARGE-associated CHD7 mutations can affect its nucleosome remodelling activity in vitro. The role of CHD7 in regulating nucleosome positioning in vivo and the effects of this activity on gene expression require further study. CHD7 pleiotropy may result from its interactions with cell type-specific transcription factors. CHD7 recruitment to cell type-specific enhancers may underlie context-specific roles. Advances in genomics over the past few years have led to impressive achievements in the identification of mutations responsible for rare genetic diseases, especially those with simple, monogenetic aetiologies [1Boycott K.M. et al.Rare-disease genetics in the era of next-generation sequencing: discovery to translation.Nat. Rev. Genet. 2013; 14: 681-691Crossref PubMed Scopus (505) Google Scholar]. The identification of the genetic cause of a disease represents a major milestone because biochemical and gene targeting approaches can then be used to explore the biological functions of the gene in question and investigate the molecular mechanisms that underlie the disease. Typically, the insights gained from these studies have wide-reaching implications by revealing fundamental biological principles that control development and homeostasis. CHARGE syndrome (MIM 214800) is a good example of such a case. This syndrome is diagnosed in 1/10 000 live births and is characterised by dysmorphic features and congenital anomalies in multiple organs. The development of the nervous system (especially cranial nerves), ears and vestibular organs, eyes, heart, urogenital, and endocrine systems can be affected and growth retardation is often observed. The presence and severity of these anomalies show remarkable variation between patients. In 2004, shortly before the next-generation sequencing era, mutations in the CHD7 gene (MIM 608892) were identified in patients with CHARGE syndrome [2Vissers L.E. et al.Mutations in a new member of the chromodomain gene family cause CHARGE syndrome.Nat. Genet. 2004; 36: 955-957Crossref PubMed Scopus (949) Google Scholar]. CHD7 encodes a chromatin-remodelling factor (CRF), which implied an epigenetic aetiology for CHARGE syndrome. CRFs have evolved to deal with the additional complexity and hindrance that the tight association of eukaryotic DNA with histone proteins imposes on replication and transcription (Box 1). CRFs perform several essential functions. For instance, the clearance of nucleosomes from promoters and other regulatory elements is necessary for the recruitment of some transcription factors (TFs) and the core transcriptional machinery, and nucleosome eviction is essential for efficient transcriptional elongation. Conversely, the maintenance of heterochromatin is an important mechanism for stable gene repression. Thus, different classes of CRF can have opposing activities and functions, and local chromatin context can determine the effects of a CRF at a specific locus [3Klement K. et al.Opposing ISWI- and CHD-class chromatin remodeling activities orchestrate heterochromatic DNA repair.J. Cell Biol. 2014; 207: 717-733Crossref PubMed Scopus (56) Google Scholar].Box 1The Concept of Chromatin RemodellingChromatin remodelling refers to the active process of changing the structure and organisation of chromatin. Histone subunits, termed H2A, H2B, H3, and H4, that comprise the core nucleosomal particles around which DNA is wound, are globular proteins with exposed N-terminal 'tails' that contain several amino acid residues that are accessible to modifying enzymes that catalyse the covalent addition of chemical moieties. These modifications include acetylation, methylation, phosphorylation, ubiquitination, and ADP ribosylation, among others [66Tessarz P. Kouzarides T. Histone core modifications regulating nucleosome structure and dynamics.Nat. Rev. Mol. Cell Biol. 2014; 15: 703-708Crossref PubMed Scopus (606) Google Scholar]. The linker histone H1 is also subject to covalent modification. Histone modifications can alter the chemical properties of the nucleosome and its interaction with DNA [67Hong L. et al.Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 'tail' to DNA.J. Biol. Chem. 1993; 268: 305-314Abstract Full Text PDF PubMed Google Scholar]. The combination of histone modifications carried by a nucleosomal array on chromatin creates unique binding sites, which can affect CRF recruitment to this region. The most direct and dramatic changes in chromatin structure are catalysed by chromatin-remodelling enzymes. These CRFs are ATP-dependent molecular machines that can alter the position of nucleosomes on chromatin. Repositioning nucleosomes, or even evicting them completely from chromatin at a given locus, changes the accessibility of specific DNA sequences. As a consequence, TF binding sites may either become available for, or be obscured from, binding by their cognate TF (Figure 2, main text). These changes may affect chromatin architecture on a larger scale if the DNA–protein interactions that are altered upon the action of CRFs are involved in maintaining higher order chromatin organisation, such as those mediated by insulating factors, including CTCF.ATP-dependent CRFs are classified in three different groups: SWI/SNF, ISWI, and CHD. CRFs typically function in large, multi-subunit protein complexes. The composition of these complexes may differ between different cell types, thereby altering the nature of the complex, as exemplified by the BAF complex [68Son E.Y. Crabtree G.R. The role of BAF (mSWI/SNF) complexes in mammalian neural development.Am. J. Med. Genet. 2014; 166C: 333-349Crossref PubMed Scopus (93) Google Scholar]. The observation that active gene promoters and enhancer elements can be identified empirically by nuclease-sensitivity assays as a proxy for DNA accessibility implicates CRFs in the establishment and maintenance of chromatin structure at regulatory elements. Chromatin remodelling refers to the active process of changing the structure and organisation of chromatin. Histone subunits, termed H2A, H2B, H3, and H4, that comprise the core nucleosomal particles around which DNA is wound, are globular proteins with exposed N-terminal 'tails' that contain several amino acid residues that are accessible to modifying enzymes that catalyse the covalent addition of chemical moieties. These modifications include acetylation, methylation, phosphorylation, ubiquitination, and ADP ribosylation, among others [66Tessarz P. Kouzarides T. Histone core modifications regulating nucleosome structure and dynamics.Nat. Rev. Mol. Cell Biol. 2014; 15: 703-708Crossref PubMed Scopus (606) Google Scholar]. The linker histone H1 is also subject to covalent modification. Histone modifications can alter the chemical properties of the nucleosome and its interaction with DNA [67Hong L. et al.Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 'tail' to DNA.J. Biol. Chem. 1993; 268: 305-314Abstract Full Text PDF PubMed Google Scholar]. The combination of histone modifications carried by a nucleosomal array on chromatin creates unique binding sites, which can affect CRF recruitment to this region. The most direct and dramatic changes in chromatin structure are catalysed by chromatin-remodelling enzymes. These CRFs are ATP-dependent molecular machines that can alter the position of nucleosomes on chromatin. Repositioning nucleosomes, or even evicting them completely from chromatin at a given locus, changes the accessibility of specific DNA sequences. As a consequence, TF binding sites may either become available for, or be obscured from, binding by their cognate TF (Figure 2, main text). These changes may affect chromatin architecture on a larger scale if the DNA–protein interactions that are altered upon the action of CRFs are involved in maintaining higher order chromatin organisation, such as those mediated by insulating factors, including CTCF. ATP-dependent CRFs are classified in three different groups: SWI/SNF, ISWI, and CHD. CRFs typically function in large, multi-subunit protein complexes. The composition of these complexes may differ between different cell types, thereby altering the nature of the complex, as exemplified by the BAF complex [68Son E.Y. Crabtree G.R. The role of BAF (mSWI/SNF) complexes in mammalian neural development.Am. J. Med. Genet. 2014; 166C: 333-349Crossref PubMed Scopus (93) Google Scholar]. The observation that active gene promoters and enhancer elements can be identified empirically by nuclease-sensitivity assays as a proxy for DNA accessibility implicates CRFs in the establishment and maintenance of chromatin structure at regulatory elements. In this review, we summarise some of the most recent studies that link CHD7 to specific developmental genes and pathways. We discuss in vitro experiments that provide insights into CHD7 mechanism and highlight the significant gaps in our understanding of how CHD7 acts in vivo to fine-tune gene expression and control development. However, we begin with the clinical data obtained from patients and summarise our current knowledge of CHD7 mutations that cause CHARGE syndrome. CHARGE syndrome is characterised by a multitude of congenital aberrations that can vary in both severity and presence. The most frequent features seen in patients with a CHD7 mutation are: external ear malformations (97%); cranial nerve dysfunction (99%, causing facial palsy in 66%); semicircular canal anomalies (94%); coloboma (81%; see Glossary); choanal atresia (55%); cleft lip and/or palate (48%); anosmia (80%); genital hypoplasia (81%); congenital heart defects (76%); and tracheoesophageal anomalies (29%). In addition, severe feeding problems (82%), delayed motor development milestones (99%), intellectual disability (74%), and growth retardation (37%) are observed [4Lalani S.R. et al.CHARGE syndrome.in: Pagon R.A. GeneReviews. University of Washington, 2012Google Scholar, 5Jongmans M.C. et al.CHARGE syndrome: the phenotypic spectrum of mutations in the CHD7 gene.J. Med. Genet. 2006; 43: 306-314Crossref PubMed Scopus (331) Google Scholar, 6Lalani S.R. et al.Spectrum of CHD7 mutations in 110 individuals with CHARGE syndrome and genotype-phenotype correlation.Am. J. Hum. Genet. 2006; 78: 303-314Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar, 7Zentner G.E. et al.Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome.Am. J. Med. Genet. 2010; 152A: 674-686Crossref PubMed Scopus (231) Google Scholar, 8Bergman J.E. et al.CHD7 mutations and CHARGE syndrome: the clinical implications of an expanding phenotype.J. Med. Genet. 2011; 48: 334-342Crossref PubMed Scopus (210) Google Scholar] (percentages according to [8Bergman J.E. et al.CHD7 mutations and CHARGE syndrome: the clinical implications of an expanding phenotype.J. Med. Genet. 2011; 48: 334-342Crossref PubMed Scopus (210) Google Scholar]). The clinical diagnosis of CHARGE syndrome is based on major and minor diagnostic criteria formulated by Blake [9Blake K.D. et al.CHARGE association: an update and review for the primary pediatrician.Clin. Pediatr. 1998; 37: 159-173Crossref PubMed Scopus (361) Google Scholar], which were later refined by Verloes [10Verloes A. Updated diagnostic criteria for CHARGE syndrome: a proposal.Am. J. Med. Genet. 2005; 133A: 306-308Crossref PubMed Scopus (296) Google Scholar]. Major criteria are the presence of coloboma, choanal atresia, characteristic ear malformations, and cranial nerve dysfunction for Blake, and the presence of coloboma, choanal atresia, and hypoplastic semicircular canals for Verloes. To reach a clinical diagnosis of typical CHARGE syndrome, at least three out of four major criteria should be met according to Blake and two out of three for Verloes. Given that up to 17% of patients with a CHD7 mutation do not fulfil these strict diagnostic criteria [5Jongmans M.C. et al.CHARGE syndrome: the phenotypic spectrum of mutations in the CHD7 gene.J. Med. Genet. 2006; 43: 306-314Crossref PubMed Scopus (331) Google Scholar, 8Bergman J.E. et al.CHD7 mutations and CHARGE syndrome: the clinical implications of an expanding phenotype.J. Med. Genet. 2011; 48: 334-342Crossref PubMed Scopus (210) Google Scholar], molecular genetic testing of CHD7 is important to confirm a diagnosis of CHARGE syndrome and enable appropriate health guidance and genetic counselling. CHARGE syndrome is typically a sporadic condition and almost all CHD7 mutations occur de novo. However, familial CHARGE syndrome has been reported [11Jongmans M.C. et al.Familial CHARGE syndrome and the CHD7 gene: a recurrent missense mutation, intrafamilial recurrence and variability.Am. J. Med. Genet. 2008; 146A: 43-50Crossref PubMed Scopus (72) Google Scholar]. Due to germline mosaicism, the recurrence risk is only 2–3% for parents of children with a de novo mutation [11Jongmans M.C. et al.Familial CHARGE syndrome and the CHD7 gene: a recurrent missense mutation, intrafamilial recurrence and variability.Am. J. Med. Genet. 2008; 146A: 43-50Crossref PubMed Scopus (72) Google Scholar, 12Pauli S. et al.Proven germline mosaicism in a father of two children with CHARGE syndrome.Clin. Genet. 2009; 75: 473-479Crossref PubMed Scopus (25) Google Scholar]. However, patients with CHD7 mutations have a 50% chance of transmitting the dominant CHD7 mutation to their offspring [12Pauli S. et al.Proven germline mosaicism in a father of two children with CHARGE syndrome.Clin. Genet. 2009; 75: 473-479Crossref PubMed Scopus (25) Google Scholar]. Over 500 different pathogenic CHD7 alterations have been identified [13Janssen N. et al.Mutation update on the CHD7 gene involved in CHARGE syndrome.Hum. Mutat. 2012; 33: 1149-1160Crossref PubMed Scopus (166) Google Scholar, 14Zentner G.E. et al.CHD7 functions in the nucleolus as a positive regulator of ribosomal RNA biogenesis.Hum. Mol. Genet. 2010; 19: 3491-3501Crossref PubMed Scopus (77) Google Scholar]. A schematic representation of CHD7 and the positions of mutations within the gene are shown in Figure 1. The distribution of types of mutation is summarised in Table 1. Nonsense mutations (44%) and frame shift deletions or insertions (34%) are the most prevalent. These mutations are distributed throughout the entire coding region, suggesting that premature termination of the protein, even at the C terminus, is detrimental to protein function. Splice site (11%) and missense mutations (8%) are predominantly located in the middle of the protein, in or near coding regions for the known functional domains of CHD7, where they are predicted to be pathogenic (Figure 1). Overall, approximately 30% of mutations are located within regions coding for a functional domain. Whole-exon deletions rarely occur (<1%) and deletions encompassing the complete CHD7 gene have been described in only ten cases in the literature. Translocations at chromosome 8q12 that disrupt CHD7 have been identified in three cases, with one resulting in an additional deletion of a portion of CHD7 (reviewed in [13Janssen N. et al.Mutation update on the CHD7 gene involved in CHARGE syndrome.Hum. Mutat. 2012; 33: 1149-1160Crossref PubMed Scopus (166) Google Scholar]).Table 1Types of Pathogenic Variant in CHD7, Based on CHD7 dataiMutation typeNumber of patientsPercentageNonsense35243.9Frame shift indels27334.0Splice site9011.2Missense668.2In-frame deletions20.2Whole-exon deletions and duplications70.9Whole-gene deletions101.2Translocations20.2Total802 Open table in a new tab Carriers of a CHD7 mutation display a striking phenotypic variability, even within the rare familial cases, where family members carry an identical mutation [8Bergman J.E. et al.CHD7 mutations and CHARGE syndrome: the clinical implications of an expanding phenotype.J. Med. Genet. 2011; 48: 334-342Crossref PubMed Scopus (210) Google Scholar, 11Jongmans M.C. et al.Familial CHARGE syndrome and the CHD7 gene: a recurrent missense mutation, intrafamilial recurrence and variability.Am. J. Med. Genet. 2008; 146A: 43-50Crossref PubMed Scopus (72) Google Scholar]. In general, missense mutations are associated with a milder phenotype and a lower prevalence of choanal atresia, cleft lip and/or palate, and congenital heart defects [5Jongmans M.C. et al.CHARGE syndrome: the phenotypic spectrum of mutations in the CHD7 gene.J. Med. Genet. 2006; 43: 306-314Crossref PubMed Scopus (331) Google Scholar, 15Bergman J.E. et al.A novel classification system to predict the pathogenic effects of CHD7 missense variants in CHARGE syndrome.Hum. Mutat. 2012; 33: 1251-1260Crossref PubMed Scopus (53) Google Scholar]. In families with parent-to-child transmission, the CHARGE phenotype is usually atypical. In four out of seven (57%) two-generation families, a missense mutation in CHD7 was found, contrasting with the 8% missense mutations in the general CHARGE population [8Bergman J.E. et al.CHD7 mutations and CHARGE syndrome: the clinical implications of an expanding phenotype.J. Med. Genet. 2011; 48: 334-342Crossref PubMed Scopus (210) Google Scholar]. With the exception of this association of a milder phenotype with missense mutations, there is no clear genotype–phenotype correlation. In patients with clinically typical CHARGE syndrome, the detection rate of CHD7 mutations is over 90%. In research studies, detection rates range from 33% to 100%, depending on the inclusion criteria (reviewed in [13Janssen N. et al.Mutation update on the CHD7 gene involved in CHARGE syndrome.Hum. Mutat. 2012; 33: 1149-1160Crossref PubMed Scopus (166) Google Scholar]). In a routine clinical setting, sequencing of CHD7 reveals a mutation in 32–41% of the patients suspected of having CHARGE syndrome [13Janssen N. et al.Mutation update on the CHD7 gene involved in CHARGE syndrome.Hum. Mutat. 2012; 33: 1149-1160Crossref PubMed Scopus (166) Google Scholar, 16Bartels C.F. et al.Mutations in the CHD7 gene: the experience of a commercial laboratory.Genet. Test. Mol. Biomarkers. 2010; 14: 881-891Crossref PubMed Scopus (37) Google Scholar]. Thus, the chance of finding a mutation is critically dependent on the accuracy of the initial clinical diagnosis. In the remaining 5–10% of patients with clinically typical CHARGE syndrome, the apparent lack of CHD7 mutations may be explained by alterations in CHD7 that are not detected with routine genotyping strategies. These may include intragenic rearrangements or mutations in intronic or promoter regions, and whole-gene or whole-exon deletions on one allele, which are not always screened for. The application of next-generation sequencing techniques, especially whole-genome sequencing in combination with analysis for deletions and rearrangements, is expected to solve a major proportion of the 5–10% of patients with unexplained typical CHARGE syndrome. It should also be kept in mind that mutations within sequenced regions can be missed by conventional techniques. For example, whole-exome sequencing of all coding exons including at least 20-base pair (bp) intronic DNA to capture intron–exon boundaries, of seven patients with clinically typical CHARGE syndrome, for whom standard Sanger sequencing failed to identify a CHD7 mutation, identified two intronic (c.5051-15T>A and c.5405-17G>A) mutations in the CHD7 gene in two patients (N. Corsten-Janssen, unpublished). Despite most patients carrying mutations in CHD7, it is still possible that other genes are involved in CHARGE syndrome. In 2004, the gene encoding sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E (SEMA3E) was shown to be interrupted by a de novo balanced translocation [t(2;7)(p14;q21.11)] in a patient with CHARGE syndrome [17Lalani S.R. et al.SEMA3E mutation in a patient with CHARGE syndrome.J. Med. Genet. 2004; 41: e94Crossref PubMed Scopus (117) Google Scholar]. However, there is little additional evidence that SEMA3E has a major role: only one de novo missense mutation in SEMA3E was found in a cohort of 24 patients with CHARGE syndrome, and Sema3e mutant mice do not phenocopy any of the cardinal features of CHARGE syndrome [18Gu C. et al.Semaphorin 3E and plexin-D1 control vascular pattern independently of neuropilins.Science. 2005; 307: 265-268Crossref PubMed Scopus (431) Google Scholar]. Other genetic alterations that can phenocopy CHARGE syndrome, resulting in a clinical diagnosis of CHARGE syndrome, include chromosomal aberrations [e.g., 22q11.2 deletion syndrome, involving the gene encoding T-box 1 (TBX1) [19Corsten-Janssen N. et al.More clinical overlap between 22q11.2 deletion syndrome and CHARGE syndrome than often anticipated.Mol. Syndromol. 2013; 4: 235-245PubMed Google Scholar], 3p13-p21 deletions [20Moustafa-Hawash N. et al.CHARGE syndrome with del(3)(p13p21): expanding the genotype.Isr. Med. Assoc. J. 2012; 14: 133-134PubMed Google Scholar], and 5q11.2 deletion syndrome [21Snijders Blok C. et al.Definition of 5q11.2 microdeletion syndrome reveals overlap with CHARGE syndrome and 22q11 deletion syndrome phenotypes.Am. J. Med. Genet. 2014; 164A: 2843-2848Crossref PubMed Scopus (7) Google Scholar]], teratogen exposure (e.g., retinoic acid or antithyroid drugs [22Komoike Y. et al.Potential teratogenicity of methimazole: exposure of zebrafish embryos to methimazole causes similar developmental anomalies to human methimazole embryopathy.Birth Defects Res. B. 2013; 98: 222-229Crossref PubMed Scopus (14) Google Scholar]), or maternal diabetes. CHD7 is a member of the chromodomain helicase DNA-binding family of ATP-dependent chromatin remodelling enzymes. These proteins share a conserved Snf2 helicase-like ATPase domain that catalyses the translocation of nucleosomes along DNA in chromatin [23Petty E. Pillus L. Balancing chromatin remodeling and histone modifications in transcription.Trends Genet. 2013; 29: 621-629Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar]. Mechanisms that maintain specific nucleosome positioning at regulatory regions are critical for normal gene regulation, because tight nucleosome–DNA interactions can preclude the productive association of DNA with TFs and core transcription machinery (Figure 2). Furthermore, nucleosome eviction downstream of gene promoters might be required for efficient transcriptional elongation. For example, CHD1-mediated nucleosome depletion downstream of active gene promoters was recently shown to be important to overcome a nucleosomal barrier to transcriptional elongation [24Skene P.J. et al.The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1.Elife. 2014; 3: e02042Crossref Scopus (88) Google Scholar]. In a recent study, it was shown that CHD7 has ATP-dependent nucleosome remodelling activity in in vitro assays [25Bouazoune K. Kingston R.E. Chromatin remodeling by the CHD7 protein is impaired by mutations that cause human developmental disorders.Proc. Natl. Acad. Sci. U.S.A. 2012; 109: 19238-19243Crossref PubMed Scopus (83) Google Scholar]. The authors confirmed that CHD7 remodelling activity was dependent upon the presence of extranucleosomal, free DNA, a feature shared by remodellers belonging to the imitation switch (ISWI) and CHD classes [26Brehm A. et al.dMi-2 and ISWI chromatin remodelling factors have distinct nucleosome binding and mobilization properties.EMBO J. 2000; 19: 4332-4341Crossref PubMed Scopus (156) Google Scholar, 27Whitehouse I. et al.Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme.Mol. Cell. Biol. 2003; 23: 1935-1945Crossref PubMed Scopus (122) Google Scholar, 28McKnight J.N. et al.Extranucleosomal DNA binding directs nucleosome sliding by Chd1.Mol. Cell. Biol. 2011; 31: 4746-4759Crossref PubMed Scopus (85) Google Scholar]. In an in vitro 'sliding' assay, CHD7 primarily translocated nucleosomes from one end of a DNA fragment to the centre, an activity shared with SNF2H [25Bouazoune K. Kingston R.E. Chromatin remodeling by the CHD7 protein is impaired by mutations that cause human developmental disorders.Proc. Natl. Acad. Sci. U.S.A. 2012; 109: 19238-19243Crossref PubMed Scopus (83) Google Scholar]. This observation is consistent with the notion that these remodellers require contact with both DNA and nucleosomes to catalyse nucleosomal repositioning for maintaining regularly spaced nucleosomal arrays on DNA. By contrast, Switch/Sucrose NonFermentable (SWI/SNF) and chromatin structure remodelling complex (RSC) remodellers can also destabilise nucleosome–DNA interactions leading to nucleosome eviction from chromatin [29Yang J.G. et al.The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing.Nat. Struct. Mol. Biol. 2006; 13: 1078-1083Crossref PubMed Scopus (155) Google Scholar]. These observations predict that CHD7 might preferentially remodel poised enhancer and/or promoter regions with already exposed DNA [30Schnetz M.P. et al.Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns.Genome Res. 2009; 19: 590-601Crossref PubMed Scopus (189) Google Scholar, 31Schnetz M.P. et al.CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.PLoS Genet. 2010; 6: e1001023Crossref PubMed Scopus (186) Google Scholar] (Figure 2). However, CHD7 can also associate with the polybromo-associated BAF (PBAF) chromatin remodelling complex in neural crest cells [32Bajpai R. et al.CHD7 cooperates with PBAF to control multipotent neural crest formation.Nature. 2010; 463: 958-962Crossref PubMed Scopus (426) Google Scholar]. This mega-complex containing both CHD and SWI/SNF components might be capable of both nucleosome sliding and eviction, which could account for the synergistic action of these factors on neural crest gene expression [32Bajpai R. et al.CHD7 cooperates with PBAF to control multipotent neural crest formation.Nature. 2010; 463: 958-962Crossref PubMed Scopus (426) Google Scholar]. A recent study showed that CHD7 is required for the maintenance of an open, accessible chromatin state at the promoters of CHD7 target genes in neural stem cells [33Feng W. et al.The chromatin remodeler CHD7 regulates adult neurogenesis via activation of SoxC transcription factors.Cell Stem Cell. 2013; 13: 62-72Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar]. Further experiments will be necessary to define whether these effects are due to nucleosome translocation or eviction and whether a more open chromatin state at enhancers is always associated with enhanced gene expression. The CHD7 domains necessary for ATP-dependent remodelling have been defined. In addition to the critical function of the DExD helicase domains, the C-terminal SANT-like ISWI domain/switching-defective protein 3 (Swi3), adaptor 2 (Ada2), nuclear receptor co-repressor (N-CoR), TFIIIB (SLIDE/SANT) and N-terminal chromodomains were shown to have important roles in nucleosome remodelling activity [25Bouazoune K. Kingston R.E. Chromatin remodeling by the CHD7 protein is impaired by mutations that cause human developmental disorders.Proc. Natl. Acad. Sci. U.S.A. 2012; 109: 19238-19243Crossref PubMed Scopus (83) Google Scholar]. A CHARGE syndrome-associated mutation in the first chromodomain (S834F) completely abolished CHD7 activity and mutations in the second chromodomain (K907T and T917M) significantly affected remodelling activity, with K907T being the most severe. The tandem chromodomains in CHD7 are thought to mediate the recruitment of CHD7 to enhancer regions through interactions with sp