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Bai Y, Wang H, Li C. SAPAP Scaffold Proteins: From Synaptic Function to Neuropsychiatric Disorders. Cells 2022; 11:cells11233815. [PMID: 36497075 PMCID: PMC9740047 DOI: 10.3390/cells11233815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Excitatory (glutamatergic) synaptic transmission underlies many aspects of brain activity and the genesis of normal human behavior. The postsynaptic scaffolding proteins SAP90/PSD-95-associated proteins (SAPAPs), which are abundant components of the postsynaptic density (PSD) at excitatory synapses, play critical roles in synaptic structure, formation, development, plasticity, and signaling. The convergence of human genetic data with recent in vitro and in vivo animal model data indicates that mutations in the genes encoding SAPAP1-4 are associated with neurological and psychiatric disorders, and that dysfunction of SAPAP scaffolding proteins may contribute to the pathogenesis of various neuropsychiatric disorders, such as schizophrenia, autism spectrum disorders, obsessive compulsive disorders, Alzheimer's disease, and bipolar disorder. Here, we review recent major genetic, epigenetic, molecular, behavioral, electrophysiological, and circuitry studies that have advanced our knowledge by clarifying the roles of SAPAP proteins at the synapses, providing new insights into the mechanistic links to neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
- Yunxia Bai
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
- Shanghai Changning Mental Health Center, Shanghai 200335, China
| | - Huimin Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
- Shanghai Changning Mental Health Center, Shanghai 200335, China
- NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai 200062, China
| | - Chunxia Li
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
- Shanghai Changning Mental Health Center, Shanghai 200335, China
- Correspondence:
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Eiberg H, Mikkelsen AF, Bak M, Tommerup N, Lund AM, Wenzel A, Sabarinathan R, Gorodkin J, Bang-Berthelsen CH, Hansen L. A splice-site variant in the lncRNA gene RP1-140A9.1 cosegregates in the large Volkmann cataract family. Mol Vis 2019; 25:1-11. [PMID: 30820140 PMCID: PMC6377377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 01/17/2019] [Indexed: 11/12/2022] Open
Abstract
Purpose To identify the mutation for Volkmann cataract (CTRCT8) at 1p36.33. Methods The genes in the candidate region 1p36.33 were Sanger and parallel deep sequenced, and informative single nucleotide polymorphisms (SNPs) were identified for linkage analysis. Expression analysis with reverse transcription polymerase chain reaction (RT-PCR) of the candidate gene was performed using RNA from different human tissues. Quantitative transcription polymerase chain reaction (qRT-PCR) analysis of the GNB1 gene was performed in affected and healthy individuals. Bioinformatic analysis of the linkage regions including the candidate gene was performed. Results Linkage analysis of the 1p36.33 CCV locus applying new marker systems obtained with Sanger and deep sequencing reduced the candidate locus from 2.1 Mb to 0.389 Mb flanked by the markers STS-22AC and rs549772338 and resulted in an logarithm of the odds (LOD) score of Z = 21.67. The identified mutation, rs763295804, affects the donor splice site in the long non-coding RNA gene RP1-140A9.1 (ENSG00000231050). The gene including splice-site junctions is conserved in primates but not in other mammalian genomes, and two alternative transcripts were shown with RT-PCR. One of these transcripts represented a lens cell-specific transcript. Meta-analysis of the Cross-Linking-Immuno-Precipitation sequencing (CLIP-Seq) data suggested the RNA binding protein (RBP) eIF4AIII is an active counterpart for RP1-140A9.1, and several miRNA and transcription factors binding sites were predicted in the proximity of the mutation. ENCODE DNase I hypersensitivity and histone methylation and acetylation data suggest the genomic region may have regulatory functions. Conclusions The mutation in RP1-140A9.1 suggests the long non-coding RNA as the candidate cataract gene associated with the autosomal dominant inherited congenital cataract from CCV. The mutation has the potential to destroy exon/intron splicing of both transcripts of RP1-140A9.1. Sanger and massive deep resequencing of the linkage region failed to identify alternative candidates suggesting the mutation in RP1-140A9.1 is causative for the CCV phenotype.
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Affiliation(s)
- Hans Eiberg
- RCLINK, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Copenhagen N, Denmark
| | - Annemette F. Mikkelsen
- RCLINK, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Copenhagen N, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johansen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Copenhagen N, Denmark,Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Allan M. Lund
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Anne Wenzel
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Radhakrishnan Sabarinathan
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Claus H. Bang-Berthelsen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Copenhagen N, Denmark
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A novel de novo 20q13.32-q13.33 deletion in a 2-year-old child with poor growth, feeding difficulties and low bone mass. J Hum Genet 2015; 60:313-7. [PMID: 25761574 DOI: 10.1038/jhg.2015.22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/30/2015] [Accepted: 02/04/2015] [Indexed: 11/08/2022]
Abstract
Interstitial deletions of the long arm of chromosome 20 are rarely reported in the literature. We report a 2-year-old child with a 2.6 Mb deletion of 20q13.32-q13.33, detected by microarray-based comparative genomic hybridization, who presented with poor growth, feeding difficulties, abnormal subcutaneous fat distribution with the lack of adipose tissue on clinical examination, facial dysmorphism and low bone mass. This report adds to rare publications describing constitutional aberrations of chromosome 20q, and adds further evidence to the fact that deletion of the GNAS complex may not always be associated with an Albright's hereditary osteodystrophy phenotype as described previously.
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Minocherhomji S, Hansen C, Kim HG, Mang Y, Bak M, Guldberg P, Papadopoulos N, Eiberg H, Doh GD, Møllgård K, Hertz JM, Nielsen JE, Ropers HH, Tümer Z, Tommerup N, Kalscheuer VM, Silahtaroglu A. Epigenetic remodelling and dysregulation of DLGAP4 is linked with early-onset cerebellar ataxia. Hum Mol Genet 2014; 23:6163-76. [PMID: 24986922 PMCID: PMC4222360 DOI: 10.1093/hmg/ddu337] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genome instability, epigenetic remodelling and structural chromosomal rearrangements are hallmarks of cancer. However, the coordinated epigenetic effects of constitutional chromosomal rearrangements that disrupt genes associated with congenital neurodevelopmental diseases are poorly understood. To understand the genetic-epigenetic interplay at breakpoints of chromosomal translocations disrupting CG-rich loci, we quantified epigenetic modifications at DLGAP4 (SAPAP4), a key post-synaptic density 95 (PSD95) associated gene, truncated by the chromosome translocation t(8;20)(p12;q11.23), co-segregating with cerebellar ataxia in a five-generation family. We report significant epigenetic remodelling of the DLGAP4 locus triggered by the t(8;20)(p12;q11.23) translocation and leading to dysregulation of DLGAP4 expression in affected carriers. Disruption of DLGAP4 results in monoallelic hypermethylation of the truncated DLGAP4 promoter CpG island. This induced hypermethylation is maintained in somatic cells of carriers across several generations in a t(8;20) dependent-manner however, is erased in the germ cells of the translocation carriers. Subsequently, chromatin remodelling of the locus-perturbed monoallelic expression of DLGAP4 mRNAs and non-coding RNAs in haploid cells having the translocation. Our results provide new mechanistic insight into the way a balanced chromosomal rearrangement associated with a neurodevelopmental disorder perturbs allele-specific epigenetic mechanisms at breakpoints leading to the deregulation of the truncated locus.
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Affiliation(s)
- Sheroy Minocherhomji
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Claus Hansen
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Hyung-Goo Kim
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Yuan Mang
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Per Guldberg
- Danish Cancer Society, Institute of Cancer Biology, Copenhagen DK-2100, Denmark
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Gerald Dayebga Doh
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Kjeld Møllgård
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense C DK-5000, Denmark
| | - Jørgen E Nielsen
- Section for Neurogenetics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark, Danish Dementia Research Centre, Neurogenetics Clinic, Department of Neurology, Rigshospitalet, Copenhagen University Hospital, Copenhagen Ø 2100, Denmark and
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Zeynep Tümer
- Wilhelm Johannsen Centre for Functional Genome Research, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup DK-2600, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Asli Silahtaroglu
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark,
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Pan Y, Deng Y, Lin H, Kudrna DA, Wing RA, Li L, Zhang Q, Luo M. Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:795-805. [PMID: 24330235 DOI: 10.1111/tpj.12412] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 05/10/2023]
Abstract
Reference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole-genome shotgun/next-generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole-genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub-species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93-11. Through BAC end sequence alignments and tri-assembly comparisons of the 93-11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone-by-clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93-11 reference sequence generated using the whole-genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93-11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93-11 reference sequences.
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Affiliation(s)
- Yonglong Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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