1
|
Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
Collapse
Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
2
|
He D, Sun H, Zhang M, Li Y, Liu F, Zhang Y, He M, Ban B. Clinical Manifestations, Genetic Variants and Therapeutic Evaluation in Sporadic Chinese Patients with Idiopathic Hypogonadotropic Hypogonadism. Int J Gen Med 2023; 16:4429-4439. [PMID: 37799300 PMCID: PMC10547821 DOI: 10.2147/ijgm.s430904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Purpose Genetic factors account for a large proportion of idiopathic hypogonadotropic hypogonadism (IHH) etiologies, although not necessarily a complete genetic basis. This study aimed to characterize the clinical presentations, genetic variants, and therapeutic outcomes of patients with sporadic IHH, which may be helpful for genetic counseling and treatment decisions. Patients and Methods Eleven Chinese patients with IHH were retrospectively analyzed. Rare genetic variants were evaluated using whole-exome sequencing and bioinformatics analysis and were further classified according to the ACMG-AMP guidelines. The therapeutic responses of patients were further evaluated. Results Six heterozygous variants of SOX10, WDR11, PROKR2, CHD7 and FGF17 were detected in five Kallmann syndrome (KS) patients, whereas two heterozygous variants of CHD7 and PROKR2 were detected in two normosmic IHH (nIHH) patients. Among these variants, a novel likely pathogenic variant in the SOX10 (c.429-1G>C) was considered to cause the KS phenotype in patient 02, and two potential variants of uncertain significance (VUS) in CHD7 (c.3344G>A and c.7391A>G) possibly contributed to the KS phenotype in patient 05 and the nIHH phenotype in patient 07, which need to be confirmed by further evidence. Additionally, long-term testosterone or estradiol replacement treatment effectively improved the development of sexual characteristics in patients with IHH. Conclusion Next-generation sequencing is a powerful tool for identifying the molecular etiology and early diagnosis of IHH. Efficient therapeutic outcomes strongly indicate a need for timely treatment.
Collapse
Affiliation(s)
- Dongye He
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
| | - Hailing Sun
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
| | - Mei Zhang
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, 272029, People’s Republic of China
| | - Yanying Li
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, 272029, People’s Republic of China
| | - Fupeng Liu
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
| | - Yanhong Zhang
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, 272029, People’s Republic of China
| | - Mingming He
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
| | - Bo Ban
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, 272029, People’s Republic of China
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, 272029, People’s Republic of China
| |
Collapse
|
3
|
Collins SC, Vancollie VE, Mikhaleva A, Wagner C, Balz R, Lelliott CJ, Yalcin B. Characterization of Two Mouse Chd7 Heterozygous Loss-of-Function Models Shows Dysgenesis of the Corpus Callosum and Previously Unreported Features of CHARGE Syndrome. Int J Mol Sci 2022; 23:11509. [PMID: 36232804 PMCID: PMC9569499 DOI: 10.3390/ijms231911509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
CHARGE syndrome is a rare congenital disorder frequently caused by mutations in the chromodomain helicase DNA-binding protein-7 CHD7. Here, we developed and systematically characterized two genetic mouse models with identical, heterozygous loss-of-function mutation of the Chd7 gene engineered on inbred and outbred genetic backgrounds. We found that both models showed consistent phenotypes with the core clinical manifestations seen in CHARGE syndrome, but the phenotypes in the inbred Chd7 model were more severe, sometimes having reduced penetrance and included dysgenesis of the corpus callosum, hypoplasia of the hippocampus, abnormal retrosplenial granular cortex, ventriculomegaly, hyperactivity, growth delays, impaired grip strength and repetitive behaviors. Interestingly, we also identified previously unreported features including reduced levels of basal insulin and reduced blood lipids. We suggest that the phenotypic variation reported in individuals diagnosed with CHARGE syndrome is likely due to the genetic background and modifiers. Finally, our study provides a valuable resource, making it possible for mouse biologists interested in Chd7 to make informed choices on which mouse model they should use to study phenotypes of interest and investigate in more depth the underlying cellular and molecular mechanisms.
Collapse
Affiliation(s)
- Stephan C. Collins
- Inserm UMR1231, University of Burgundy Franche-Comté, 15 Boulevard Maréchal de Lattre de Tassigny, 21070 Dijon, France
| | | | - Anna Mikhaleva
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christel Wagner
- Institute of Genetics and Molecular and Cellular Biology, UMR7104, 67400 Illkirch, France
| | - Rebecca Balz
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | | | - Binnaz Yalcin
- Inserm UMR1231, University of Burgundy Franche-Comté, 15 Boulevard Maréchal de Lattre de Tassigny, 21070 Dijon, France
| |
Collapse
|
4
|
Liu C, Kang N, Guo Y, Gong P. Advances in Chromodomain Helicase DNA-Binding (CHD) Proteins Regulating Stem Cell Differentiation and Human Diseases. Front Cell Dev Biol 2021; 9:710203. [PMID: 34616726 PMCID: PMC8488160 DOI: 10.3389/fcell.2021.710203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Regulation of gene expression is critical for stem cell differentiation, tissue development, and human health maintenance. Recently, epigenetic modifications of histone and chromatin remodeling have been verified as key controllers of gene expression and human diseases. Objective: In this study, we review the role of chromodomain helicase DNA-binding (CHD) proteins in stem cell differentiation, cell fate decision, and several known human developmental disorders and cancers. Conclusion: CHD proteins play a crucial role in stem cell differentiation and human diseases.
Collapse
Affiliation(s)
- Caojie Liu
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ning Kang
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Yuchen Guo
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ping Gong
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
5
|
Haug P, Koller S, Maggi J, Lang E, Feil S, Wlodarczyk A, Bähr L, Steindl K, Rohrbach M, Gerth-Kahlert C, Berger W. Whole Exome Sequencing in Coloboma/Microphthalmia: Identification of Novel and Recurrent Variants in Seven Genes. Genes (Basel) 2021; 12:65. [PMID: 33418956 PMCID: PMC7825129 DOI: 10.3390/genes12010065] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/25/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022] Open
Abstract
Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.
Collapse
Affiliation(s)
- Patricia Haug
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Elena Lang
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
- Department of Ophthalmology, University Hospital and University of Zurich, 8091 Zurich, Switzerland;
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Agnès Wlodarczyk
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland;
| | - Marianne Rohrbach
- Division of Metabolism and Children’s Research Centre, University Children’s Hospital Zurich, 8032 Zurich, Switzerland;
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital and University of Zurich, 8091 Zurich, Switzerland;
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8006 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8006 Zurich, Switzerland
| |
Collapse
|