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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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2
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Chen CA, Yin J, Lewis RA, Schaaf CP. Genetic causes of optic nerve hypoplasia. J Med Genet 2017; 54:441-449. [PMID: 28501829 DOI: 10.1136/jmedgenet-2017-104626] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/05/2017] [Indexed: 01/25/2023]
Abstract
Optic nerve hypoplasia (ONH) is the most common congenital optic nerve anomaly and a leading cause of blindness in the USA. Although most cases of ONH occur as isolated cases within their respective families, the advancement in molecular diagnostic technology has made us realise that a substantial fraction of cases has identifiable genetic causes, typically de novo mutations. An increasing number of genes has been reported, mutations of which can cause ONH. Many of the genes involved serve as transcription factors, participating in an intricate multistep process critical to eye development and neurogenesis in the neural retina. This review will discuss the respective genes and mutations, human phenotypes, and animal models that have been created to gain a deeper understanding of the disorders. The identification of the underlying gene and mutation provides an important step in diagnosis, medical care and counselling for the affected individuals and their families. We envision that future research will lead to further disease gene identification, but will also teach us about gene-gene and gene-environment interactions relevant to optic nerve development. How much of the functional impairment of the various forms of ONH is a reflection of altered morphogenesis versus neuronal homeostasis will determine the prospect of therapeutic intervention, with the ultimate goal of improving the quality of life of the individuals affected with ONH.
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Affiliation(s)
- Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Jiani Yin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
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3
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Vial ML, Zencak D, Grkovic T, Gorse AD, Mackay-Sim A, Mellick GD, Wood SA, Quinn RJ. A Grand Challenge. 2. Phenotypic Profiling of a Natural Product Library on Parkinson's Patient-Derived Cells. JOURNAL OF NATURAL PRODUCTS 2016; 79:1982-1989. [PMID: 27447544 DOI: 10.1021/acs.jnatprod.6b00258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Harnessing the inherent biological relevance of natural products requires a method for the recognition of biological effects that may subsequently lead to the discovery of particular targets. An unbiased multidimensional profiling method was used to examine the activities of natural products on primary cells derived from a Parkinson's disease patient. The biological signature of 482 natural products was examined using multiparametric analysis to investigate known cellular pathways and organelles implicated in Parkinson's disease such as mitochondria, lysosomes, endosomes, apoptosis, and autophagy. By targeting several cell components simultaneously the chance of finding a phenotype was increased. The phenotypes were then clustered using an uncentered correlation. The multidimensional phenotypic screening showed that all natural products, in our screening set, were biologically relevant compounds as determined by an observed phenotypic effect. Multidimensional phenotypic screening can predict the cellular function and subcellular site of activity of new compounds, while the cluster analysis provides correlation with compounds with known mechanisms of action. This study reinforces the value of natural products as biologically relevant compounds.
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Affiliation(s)
- Marie-Laure Vial
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111, Australia
| | - Dusan Zencak
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111, Australia
| | - Tanja Grkovic
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111, Australia
| | - Alain-Dominique Gorse
- QFAB Bioinformatics, Institute for Molecular Bioscience, The University of Queensland , St Lucia, QLD 4072, Australia
| | - Alan Mackay-Sim
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111, Australia
| | - George D Mellick
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111, Australia
| | - Stephen A Wood
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111, Australia
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111, Australia
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4
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Li Q, Wang Z, Lian J, Schiøtt M, Jin L, Zhang P, Zhang Y, Nygaard S, Peng Z, Zhou Y, Deng Y, Zhang W, Boomsma JJ, Zhang G. Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior. Nat Commun 2014; 5:4943. [PMID: 25266559 PMCID: PMC4200514 DOI: 10.1038/ncomms5943] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 08/08/2014] [Indexed: 01/16/2023] Open
Abstract
Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome. Recent studies suggest that RNA editing might enhance the diversity of gene products at the post-transcriptional level, particularly to induce functional changes in the nervous system. Using head samples from the leaf-cutting ant Acromyrmex echinatior, we compare RNA editomes across eusocial castes, identifying ca. 11,000 RNA editing sites in gynes, large workers and small workers. Those editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis. Most A. echinatior editing sites are species specific, but 8–23% are conserved across ant subfamilies and likely to have been important for the evolution of eusociality in ants. The level of editing varies for the same site between castes, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants. Post-translational mRNA editing has the potential to enhance the diversity of gene products and alter the functional properties of proteins. Here, Li et al. provide evidence that RNA editing is involved in generating caste-specific contrasting phenotypes in the leaf-cutting ant Acromyrmex echinatior.
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Affiliation(s)
- Qiye Li
- 1] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China [2] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zongji Wang
- 1] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China [2] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Jinmin Lian
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Lijun Jin
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Pei Zhang
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | | | - Sanne Nygaard
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | | | - Yang Zhou
- 1] School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China [2] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yuan Deng
- China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | | | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Guojie Zhang
- 1] China National GeneBank, BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China [2] Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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Norling A, Hirschberg AL, Rodriguez-Wallberg KA, Iwarsson E, Wedell A, Barbaro M. Identification of a duplication within the GDF9 gene and novel candidate genes for primary ovarian insufficiency (POI) by a customized high-resolution array comparative genomic hybridization platform. Hum Reprod 2014; 29:1818-27. [PMID: 24939957 PMCID: PMC4093997 DOI: 10.1093/humrep/deu149] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
STUDY QUESTION Can high-resolution array comparative genomic hybridization (CGH) analysis of DNA samples from women with primary ovarian insufficiency (POI) improve the diagnosis of the condition and identify novel candidate genes for POI? SUMMARY ANSWER A mutation affecting the regulatory region of growth differentiation factor 9 (GDF9) was identified for the first time together with several novel candidate genes for POI. WHAT IS KNOWN ALREADY Most patients with POI do not receive a molecular diagnosis despite a significant genetic component in the pathogenesis. STUDY DESIGN, SIZE, DURATION We performed a case–control study. Twenty-six patients were analyzed by array CGH for identification of copy number variants. Novel changes were investigated in 95 controls and in a separate population of 28 additional patients with POI. The experimental procedures were performed during a 1-year period. PARTICIPANTS/MATERIALS, SETTING, METHODS DNA samples from 26 patients with POI were analyzed by a customized 1M array-CGH platform with whole genome coverage and probe enrichment targeting 78 genes in sex development. By PCR amplification and sequencing, the breakpoint of an identified partial GDF9 gene duplication was characterized. A multiplex ligation-dependent probe amplification (MLPA) probe set for specific identification of deletions/duplications affecting GDF9 was developed. An MLPA probe set for the identification of additional cases or controls carrying novel candidate regions identified by array-CGH was developed. Sequencing of three candidate genes was performed. MAIN RESULTS AND THE ROLE OF CHANCE Eleven unique copy number changes were identified in a total of 11 patients, including a tandem duplication of 475 bp, containing part of the GDF9 gene promoter region. The duplicated region contains three NOBOX-binding elements and an E-box, important for GDF9 gene regulation. This aberration is likely causative of POI. Fifty-four patients were investigated for copy number changes within GDF9, but no additional cases were found. Ten aberrations constituting novel candidate regions were detected, including a second DNAH6 deletion in a patient with POI. Other identified candidate genes were TSPYL6, SMARCC1, CSPG5 and ZFR2. LIMITATIONS, REASONS FOR CAUTION This is a descriptive study and no functional experiments were performed. WIDER IMPLICATIONS OF THE FINDINGS The study illustrates the importance of analyzing small copy number changes in addition to sequence alterations in the genetic investigation of patients with POI. Also, promoter regions should be included in the investigation. STUDY FUNDING/COMPETING INTEREST(S) The study was supported by grants from the Swedish Research council (project no 12198 to A.W. and project no 20324 to A.L.H.), Stockholm County Council (E.I., A.W. and K.R.W.), Foundation Frimurare Barnhuset (A.N., A.W. and M.B.), Karolinska Institutet (A.N., A.L.H., E.I., A.W. and M.B.), Novo Nordic Foundation (A.W.) and Svenska Läkaresällskapet (M.B.). The funding sources had no involvement in the design or analysis of the study. The authors have no competing interests to declare. TRIAL REGISTRATION NUMBER Not applicable.
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Affiliation(s)
- A Norling
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 76, Sweden Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 76, Sweden Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - A L Hirschberg
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 76, Sweden
| | - K A Rodriguez-Wallberg
- Department of Clinical Science, Intervention and Technology, Section for Obstetrics and Gynaecology and Fertility Unit, Karolinska University Hospital, Stockholm, Sweden
| | - E Iwarsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 76, Sweden Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - A Wedell
- Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Department of Molecular Medicine and Surgery, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden Centre for Inherited Metabolic Diseases (CMMS), Karolinska University Hospital, Stockholm 171 76, Sweden
| | - M Barbaro
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 76, Sweden Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden Centre for Inherited Metabolic Diseases (CMMS), Karolinska University Hospital, Stockholm 171 76, Sweden
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Ramaseshadri P, Segers G, Flannagan R, Wiggins E, Clinton W, Ilagan O, McNulty B, Clark T, Bolognesi R. Physiological and cellular responses caused by RNAi- mediated suppression of Snf7 orthologue in western corn rootworm (Diabrotica virgifera virgifera) larvae. PLoS One 2013; 8:e54270. [PMID: 23349844 PMCID: PMC3548817 DOI: 10.1371/journal.pone.0054270] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 12/11/2012] [Indexed: 11/19/2022] Open
Abstract
Ingestion of double stranded RNA (dsRNA) has been previously demonstrated to be effective in triggering RNA interference (RNAi) in western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte), providing potential novel opportunities for insect pest control. The putative Snf7 homolog of WCR (DvSnf7) has previously been shown to be an effective RNAi target for insect control, as DvSnf7 RNAi leads to lethality of WCR larvae. Snf7 functions as a part of the ESCRT (Endosomal Sorting Complex Required for Transport) pathway which plays a crucial role in cellular housekeeping by internalization, transport, sorting and lysosomal degradation of transmembrane proteins. To understand the effects that lead to death of WCR larvae by DvSnf7 RNAi, we examined some of the distinct cellular processes associated with ESCRT functions such as de-ubiquitination of proteins and autophagy. Our data indicate that ubiquitinated proteins accumulate in DvSnf7 dsRNA-fed larval tissues and that the autophagy process seems to be impaired. These findings suggest that the malfunctioning of these cellular processes in both midgut and fat body tissues triggered by DvSnf7 RNAi were the main effects leading to the death of WCR. This study also illustrates that Snf7 is an essential gene in WCR and its functions are consistent with biological functions described for other eukaryotes.
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Affiliation(s)
| | - Gerrit Segers
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Ronald Flannagan
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Elizabeth Wiggins
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
| | - William Clinton
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Oliver Ilagan
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Brian McNulty
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Thomas Clark
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
| | - Renata Bolognesi
- Department of Biotechnology, Monsanto Company, Chesterfield, Missouri, United States of America
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Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE. Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech 2012; 6:358-72. [PMID: 23104991 PMCID: PMC3597018 DOI: 10.1242/dmm.010322] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Numerous disease syndromes are associated with regions of copy number variation (CNV) in the human genome and, in most cases, the pathogenicity of the CNV is thought to be related to altered dosage of the genes contained within the affected segment. However, establishing the contribution of individual genes to the overall pathogenicity of CNV syndromes is difficult and often relies on the identification of potential candidates through manual searches of the literature and online resources. We describe here the development of a computational framework to comprehensively search phenotypic information from model organisms and single-gene human hereditary disorders, and thus speed the interpretation of the complex phenotypes of CNV disorders. There are currently more than 5000 human genes about which nothing is known phenotypically but for which detailed phenotypic information for the mouse and/or zebrafish orthologs is available. Here, we present an ontology-based approach to identify similarities between human disease manifestations and the mutational phenotypes in characterized model organism genes; this approach can therefore be used even in cases where there is little or no information about the function of the human genes. We applied this algorithm to detect candidate genes for 27 recurrent CNV disorders and identified 802 gene-phenotype associations, approximately half of which involved genes that were previously reported to be associated with individual phenotypic features and half of which were novel candidates. A total of 431 associations were made solely on the basis of model organism phenotype data. Additionally, we observed a striking, statistically significant tendency for individual disease phenotypes to be associated with multiple genes located within a single CNV region, a phenomenon that we denote as pheno-clustering. Many of the clusters also display statistically significant similarities in protein function or vicinity within the protein-protein interaction network. Our results provide a basis for understanding previously un-interpretable genotype-phenotype correlations in pathogenic CNVs and for mobilizing the large amount of model organism phenotype data to provide insights into human genetic disorders.
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Affiliation(s)
- Sandra C Doelken
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome. Nat Genet 2012; 44:639-41. [PMID: 22544363 DOI: 10.1038/ng.2262] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 04/06/2012] [Indexed: 12/23/2022]
Abstract
We show that haploinsufficiency of KANSL1 is sufficient to cause the 17q21.31 microdeletion syndrome, a multisystem disorder characterized by intellectual disability, hypotonia and distinctive facial features. The KANSL1 protein is an evolutionarily conserved regulator of the chromatin modifier KAT8, which influences gene expression through histone H4 lysine 16 (H4K16) acetylation. RNA sequencing studies in cell lines derived from affected individuals and the presence of learning deficits in Drosophila melanogaster mutants suggest a role for KANSL1 in neuronal processes.
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