1
|
Ming Y, Deng Z, Tian X, Jia Y, Ning M, Cheng S. Anti-apoptotic capacity of MALAT1 on hippocampal neurons correlates with CASP3 DNA methylation in a mouse model of autism. Metab Brain Dis 2023; 38:2591-2602. [PMID: 37751122 DOI: 10.1007/s11011-023-01285-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/29/2023] [Indexed: 09/27/2023]
Abstract
Prior evidence has suggested the alleviatory effect of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) on neuroinflammation in neurodegenerative diseases. This study primarily investigates the underlying mechanism of how the long non-coding RNA MALAT1 affects neuronal apoptosis in the hippocampus of mice with autism spectrum disorder (ASD). The findings demonstrate that CASP3 is highly expressed while MALAT1 is downregulated in the hippocampal neurons of autistic mice. MALAT1 mainly localizes within the cell nucleus and recruits DNA methyltransferases (including DNMT1, DNMT3a, and DNMT3b) to the promoter region of CASP3, promoting its methylation and further inhibiting its expression. In vitro experiments reveal that reducing MALAT1 expression promotes the expression of CASP3 and Bax while suppressing Bcl-2 expression, thereby enhancing cellular apoptosis. Conversely, increasing MALAT1 expression yields the opposite effect. Consequently, these results further confirm the role of MALAT1 in suppressing neuronal apoptosis in the hippocampus of mice with ASD through the regulation of CASP3 promoter methylation. Thus, this research unveils the significant roles of MALAT1 and CASP3 in the pathogenesis of ASD, offering new possibilities for future therapeutic interventions.
Collapse
Affiliation(s)
- Yue Ming
- Department of Applied Psychology, College of Teacher Education, Qiqihar University, No. 32, Zhonghua West Road, Jianhua District, Qiqihar, Heilongjiang Province, 161006, P.R. China
| | - Zhihui Deng
- Institute of Medicine and Pharmacy, Qiqihar Medical University, Qiqihar, 161006, P.R. China
| | - Xianhua Tian
- Department of Applied Psychology, College of Teacher Education, Qiqihar University, No. 32, Zhonghua West Road, Jianhua District, Qiqihar, Heilongjiang Province, 161006, P.R. China
| | - Yuerong Jia
- Department of Applied Psychology, College of Teacher Education, Qiqihar University, No. 32, Zhonghua West Road, Jianhua District, Qiqihar, Heilongjiang Province, 161006, P.R. China
| | - Meng Ning
- Department of Applied Psychology, College of Teacher Education, Qiqihar University, No. 32, Zhonghua West Road, Jianhua District, Qiqihar, Heilongjiang Province, 161006, P.R. China
| | - Shuhua Cheng
- Department of Applied Psychology, College of Teacher Education, Qiqihar University, No. 32, Zhonghua West Road, Jianhua District, Qiqihar, Heilongjiang Province, 161006, P.R. China.
| |
Collapse
|
2
|
Cabej NR. On the origin and nature of nongenetic information in eumetazoans. Ann N Y Acad Sci 2023. [PMID: 37154677 DOI: 10.1111/nyas.15001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.
Collapse
Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
| |
Collapse
|
3
|
Disintegration of the NuRD Complex in Primary Human Muscle Stem Cells in Critical Illness Myopathy. Int J Mol Sci 2023; 24:ijms24032772. [PMID: 36769095 PMCID: PMC9916927 DOI: 10.3390/ijms24032772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Critical illness myopathy (CIM) is an acquired, devastating, multifactorial muscle-wasting disease with incomplete recovery. The impact on hospital costs and permanent loss of quality of life is enormous. Incomplete recovery might imply that the function of muscle stem cells (MuSC) is impaired. We tested whether epigenetic alterations could be in part responsible. We characterized human muscle stem cells (MuSC) isolated from early CIM and analyzed epigenetic alterations (CIM n = 15, controls n = 21) by RNA-Seq, immunofluorescence, analysis of DNA repair, and ATAC-Seq. CIM-MuSC were transplanted into immunodeficient NOG mice to assess their regenerative potential. CIM-MuSC exhibited significant growth deficits, reduced ability to differentiate into myotubes, and impaired DNA repair. The chromatin structure was damaged, as characterized by alterations in mRNA of histone 1, depletion or dislocation of core proteins of nucleosome remodeling and deacetylase complex, and loosening of multiple nucleosome-spanning sites. Functionally, CIM-MuSC had a defect in building new muscle fibers. Further, MuSC obtained from the electrically stimulated muscle of CIM patients was very similar to control MuSC, indicating the impact of muscle contraction in the onset of CIM. CIM not only affects working skeletal muscle but has a lasting and severe epigenetic impact on MuSC.
Collapse
|
4
|
Raven F, Aton SJ. The Engram's Dark Horse: How Interneurons Regulate State-Dependent Memory Processing and Plasticity. Front Neural Circuits 2021; 15:750541. [PMID: 34588960 PMCID: PMC8473837 DOI: 10.3389/fncir.2021.750541] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022] Open
Abstract
Brain states such as arousal and sleep play critical roles in memory encoding, storage, and recall. Recent studies have highlighted the role of engram neurons–populations of neurons activated during learning–in subsequent memory consolidation and recall. These engram populations are generally assumed to be glutamatergic, and the vast majority of data regarding the function of engram neurons have focused on glutamatergic pyramidal or granule cell populations in either the hippocampus, amygdala, or neocortex. Recent data suggest that sleep and wake states differentially regulate the activity and temporal dynamics of engram neurons. Two potential mechanisms for this regulation are either via direct regulation of glutamatergic engram neuron excitability and firing, or via state-dependent effects on interneuron populations–which in turn modulate the activity of glutamatergic engram neurons. Here, we will discuss recent findings related to the roles of interneurons in state-regulated memory processes and synaptic plasticity, and the potential therapeutic implications of understanding these mechanisms.
Collapse
Affiliation(s)
- Frank Raven
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI, United States
| | - Sara J Aton
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI, United States
| |
Collapse
|
5
|
Espeso-Gil S, Holik AZ, Bonnin S, Jhanwar S, Chandrasekaran S, Pique-Regi R, Albaigès-Ràfols J, Maher M, Permanyer J, Irimia M, Friedländer MR, Pons-Espinal M, Akbarian S, Dierssen M, Maass PG, Hor CN, Ossowski S. Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition. Front Mol Neurosci 2021; 14:664912. [PMID: 34025350 PMCID: PMC8131874 DOI: 10.3389/fnmol.2021.664912] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/09/2021] [Indexed: 01/11/2023] Open
Abstract
In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the epigenome and genome organization, we used the paradigm of environmental enrichment (EE) in young mice constantly receiving novel stimulation. We profiled epigenome and chromatin architecture in whole cortex and sorted neurons by deep-sequencing techniques. Specifically, we studied chromatin accessibility, gene and protein regulation, and 3D genome conformation, combined with predicted enhancer and chromatin interactions. We identified increased chromatin accessibility, transcription factor binding including CTCF-mediated insulation, differential occupancy of H3K36me3 and H3K79me2, and changes in transcriptional programs required for neuronal development. EE stimuli led to local genome re-organization by inducing increased contacts between chromosomes 7 and 17 (inter-chromosomal). Our findings support the notion that EE-induced learning and memory processes are directly associated with the epigenome and genome organization.
Collapse
Affiliation(s)
- Sergio Espeso-Gil
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
| | - Aliaksei Z. Holik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sarah Bonnin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Shalu Jhanwar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandhya Chandrasekaran
- MD/PhD Program in the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Júlia Albaigès-Ràfols
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Michael Maher
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona, Spain
| | - Marc R. Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Meritxell Pons-Espinal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Schahram Akbarian
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Philipp G. Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charlotte N. Hor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
6
|
Egervari G. Chromatin accessibility in neuropsychiatric disorders. Neurobiol Learn Mem 2021; 181:107438. [PMID: 33845131 DOI: 10.1016/j.nlm.2021.107438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Epigenetic mechanisms have recently emerged as critical regulators of brain function in health and disease. By controlling the accessibility and the expression of specific genes, these pathways can mediate transient and long-lasting changes in neuronal function in both physiological and pathological contexts. Due to the extreme complexity of the epigenetic regulatory landscape, emerging methods that directly assay chromatin accessibility are of particular interest. Here, I review recent insights gained on open and closed chromatin states in the brain, with emphasis on neuropsychiatric disorders. These advances generated an invaluable wealth of information that can help us better understand gene regulation in the brain and its impairments that contribute to the development of disease.
Collapse
Affiliation(s)
- Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
7
|
Myosin XVI in the Nervous System. Cells 2020; 9:cells9081903. [PMID: 32824179 PMCID: PMC7464383 DOI: 10.3390/cells9081903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/07/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
The myosin family is a large inventory of actin-associated motor proteins that participate in a diverse array of cellular functions. Several myosin classes are expressed in neural cells and play important roles in neural functioning. A recently discovered member of the myosin superfamily, the vertebrate-specific myosin XVI (Myo16) class is expressed predominantly in neural tissues and appears to be involved in the development and proper functioning of the nervous system. Accordingly, the alterations of MYO16 has been linked to neurological disorders. Although the role of Myo16 as a generic actin-associated motor is still enigmatic, the N-, and C-terminal extensions that flank the motor domain seem to confer unique structural features and versatile interactions to the protein. Recent biochemical and physiological examinations portray Myo16 as a signal transduction element that integrates cell signaling pathways to actin cytoskeleton reorganization. This review discusses the current knowledge of the structure-function relation of Myo16. In light of its prevalent localization, the emphasis is laid on the neural aspects.
Collapse
|
8
|
Mattos BDS, Soares MSP, Spohr L, Pedra NS, Teixeira FC, Souza AA, Stefanello FM, Baldissarelli J, Gamaro GD, Spanevello RM. Quercetin prevents alterations of behavioral parameters, delta‐aminolevulinic dehydratase activity, and oxidative damage in brain of rats in a prenatal model of autism. Int J Dev Neurosci 2020; 80:287-302. [DOI: 10.1002/jdn.10025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/01/2020] [Indexed: 12/27/2022] Open
Affiliation(s)
- Bruna da Silveira Mattos
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Mayara Sandrielly Pereira Soares
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Luiza Spohr
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Nathalia Stark Pedra
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Fernanda Cardoso Teixeira
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Anita Avila Souza
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Francieli Moro Stefanello
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Biomarcadores Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Jucimara Baldissarelli
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Giovana Duzzo Gamaro
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| | - Roselia Maria Spanevello
- Programa de Pós‐Graduação em Bioquímica e Bioprospecção ‐ Laboratório de Neuroquímica Inflamação e Câncer Centro de Ciências Químicas Farmacêuticas e de Alimentos Universidade Federal de Pelotas Pelotas Brazil
| |
Collapse
|
9
|
Heavner WE, Smith SEP. Resolving the Synaptic versus Developmental Dichotomy of Autism Risk Genes. Trends Neurosci 2020; 43:227-241. [PMID: 32209454 DOI: 10.1016/j.tins.2020.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 12/28/2022]
Abstract
Genes that are mutated in Autism Spectrum Disorders (ASD) can be classified broadly as either synaptic or developmental. But what if this is a false distinction? A recent spate of publications has provided evidence for developmental mechanisms that rely on neural activity for proper cortical development. Conversely, a growing body of evidence indicates a role for developmental mechanisms, particularly chromatin remodeling, during learning or in response to neural activity. Here, we review these recent publications and propose a model in which genes that confer ASD risk operate in signal transduction networks critical for both cortical development and synaptic homeostasis.
Collapse
Affiliation(s)
- Whitney E Heavner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
| |
Collapse
|
10
|
Hegde AN, Smith SG. Recent developments in transcriptional and translational regulation underlying long-term synaptic plasticity and memory. ACTA ACUST UNITED AC 2019; 26:307-317. [PMID: 31416904 PMCID: PMC6699410 DOI: 10.1101/lm.048769.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/20/2019] [Indexed: 12/16/2022]
Abstract
Formation of long-term synaptic plasticity that underlies long-term memory requires new protein synthesis. Years of research has elucidated some of the transcriptional and translational mechanisms that contribute to the production of new proteins. Early research on transcription focused on the transcription factor cAMP-responsive element binding protein. Since then, other transcription factors, such as the Nuclear Receptor 4 family of proteins that play a role in memory formation and maintenance have been identified. In addition, several studies have revealed details of epigenetic mechanisms consisting of new types of chemical alterations of DNA such as hydroxymethylation, and various histone modifications in long-term synaptic plasticity and memory. Our understanding of translational control critical for memory formation began with the identification of molecules that impinge on the 5′ and 3′ untranslated regions of mRNAs and continued with the appreciation for local translation near synaptic sites. Lately, a role for noncoding RNAs such as microRNAs in regulating translation factors and other molecules critical for memory has been found. This review describes the past research in brief and mainly focuses on the recent work on molecular mechanisms of transcriptional and translational regulation that form the underpinnings of long-term synaptic plasticity and memory.
Collapse
Affiliation(s)
- Ashok N Hegde
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, Georgia 31061, USA
| | - Spencer G Smith
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, Georgia 31061, USA
| |
Collapse
|
11
|
Roesler MK, Lombino FL, Freitag S, Schweizer M, Hermans-Borgmeyer I, Schwarz JR, Kneussel M, Wagner W. Myosin XVI Regulates Actin Cytoskeleton Dynamics in Dendritic Spines of Purkinje Cells and Affects Presynaptic Organization. Front Cell Neurosci 2019; 13:330. [PMID: 31474830 PMCID: PMC6705222 DOI: 10.3389/fncel.2019.00330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/04/2019] [Indexed: 11/29/2022] Open
Abstract
The actin cytoskeleton is crucial for function and morphology of neuronal synapses. Moreover, altered regulation of the neuronal actin cytoskeleton has been implicated in neuropsychiatric diseases such as autism spectrum disorder (ASD). Myosin XVI is a neuronally expressed unconventional myosin known to bind the WAVE regulatory complex (WRC), a regulator of filamentous actin (F-actin) polymerization. Notably, the gene encoding the myosin’s heavy chain (MYO16) shows genetic association with neuropsychiatric disorders including ASD. Here, we investigated whether myosin XVI plays a role for actin cytoskeleton regulation in the dendritic spines of cerebellar Purkinje cells (PCs), a neuronal cell type crucial for motor learning, social cognition and vocalization. We provide evidence that both myosin XVI and the WRC component WAVE1 localize to PC spines. Fluorescence recovery after photobleaching (FRAP) analysis of GFP-actin in cultured PCs shows that Myo16 knockout as well as PC-specific Myo16 knockdown, lead to faster F-actin turnover in the dendritic spines of PCs. We also detect accelerated F-actin turnover upon interference with the WRC, and upon inhibition of Arp2/3 that drives formation of branched F-actin downstream of the WRC. In contrast, inhibition of formins that are responsible for polymerization of linear actin filaments does not cause faster F-actin turnover. Together, our data establish myosin XVI as a regulator of the postsynaptic actin cytoskeleton and suggest that it is an upstream activator of the WRC-Arp2/3 pathway in PC spines. Furthermore, ultra-structural and electrophysiological analyses of Myo16 knockout cerebellum reveals the presence of reduced numbers of synaptic vesicles at presynaptic terminals in the absence of the myosin. Therefore, we here define myosin XVI as an F-actin regulator important for presynaptic organization in the cerebellum.
Collapse
Affiliation(s)
- Mona Katrin Roesler
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franco Luis Lombino
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Freitag
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michaela Schweizer
- Electron Microscopy Unit, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irm Hermans-Borgmeyer
- Transgenic Animal Unit, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jürgen R Schwarz
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Kneussel
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang Wagner
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
12
|
Talebizadeh Z, Shah A, DiTacchio L. The potential role of a retrotransposed gene and a long noncoding RNA in regulating an X-linked chromatin gene (KDM5C): Novel epigenetic mechanism in autism. Autism Res 2019; 12:1007-1021. [PMID: 31087518 DOI: 10.1002/aur.2116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/11/2019] [Accepted: 03/25/2019] [Indexed: 12/22/2022]
Abstract
A growing body of evidence supports the potential role of the circadian system and chromatin remodeling genes in autism. Considering the heterogeneity and gender discrepancy in autism, and the complex nature of the epigenetic landscape, identification of biologically relevant epigenetic factors requires reducing heterogeneity using proper subtyping. For this study, we used X chromosome inactivation (XCI) status in females with autism as an epigenetic marker for subtyping and examined the expression level of members of KDM5, a chromatin remodeling gene family. KDM5 are histone demethylases involved in the circadian molecular machinery. We used human blood samples to characterize alternatively spliced KDM5 isoforms and noticed that KDM5C undergoes a complex splicing process. We also identified a KDM5C isoform (KDM5C-3'UTR-lncRNA) containing a novel 3'UTR originated from a retrotransposed gene (retro-SUV39H2) of an autosomal methyltransferase (SUV39H2). This 3'UTR shows 84% sequence homology with long ncRNAs (lncRNAs) and is located 32 kb downstream of KDM5C. The KDM5C-3'UTR-lncRNA isoform was differentially expressed in autistic females with XCI skewness compared with controls. KDM5C plays a crucial role in balancing histone H3K4 methylation states. The identified retro-SUV39H2 originated lncRNA also shows H3K4 marks. By assessing the expression level of alternatively spliced Kdm5 isoforms at different circadian time-points, we showed that some isoforms follow a circadian oscillation pattern in wild type mouse brain.This study provides the first evidence and a suggestive model for the potential role of retrotransposed elements in autism through linking methylases and demethylases, two functionally complementary components of chromatin remodeling, which may collectively contribute to disease etiology through lncRNAs. Autism Res 2019, 12: 1007-1021. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Genes do not function in isolated conditions and their proper expression level also depends on a mechanism called gene regulation. An example of gene regulation is when changes outside DNA sequences influence the function of autism susceptibility genes. Alternative splicing is one type of gene regulation, which produces several versions of a gene (called variants) that may slightly differ from each other and be expressed at different levels in response to environmental changes. The circadian clock is an essential timing mechanism that enables organisms to maintain internal processes in sync with the dynamic environment brought about by the day-night cycle. The goal of this study was to assess if a subset of females with autism with certain genetic marker had a unique pattern of alternative splicing of three circadian genes. We identified a novel variant that is differentially expressed in this subset. Our study provides a novel subject stratification strategy, and a suggestive model of how biologically relevant components of a gene regulatory process may be linked and, possibly, collectively contribute to the etiology of autism.
Collapse
Affiliation(s)
- Zohreh Talebizadeh
- Children's Mercy Hospital and University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Ayten Shah
- Children's Mercy Hospital and University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | | |
Collapse
|
13
|
Sun MW, Gupta* A, Varma M, Paskov KM, Jung JY, Stockham NT, Wall DP. Coalitional Game Theory Facilitates Identification of Non-Coding Variants Associated With Autism. BIOMEDICAL INFORMATICS INSIGHTS 2019; 11:1178222619832859. [PMID: 30886520 PMCID: PMC6410388 DOI: 10.1177/1178222619832859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/17/2018] [Indexed: 12/18/2022]
Abstract
Studies on autism spectrum disorder (ASD) have amassed substantial evidence for the role of genetics in the disease's phenotypic manifestation. A large number of coding and non-coding variants with low penetrance likely act in a combinatorial manner to explain the variable forms of ASD. However, many of these combined interactions, both additive and epistatic, remain undefined. Coalitional game theory (CGT) is an approach that seeks to identify players (individual genetic variants or genes) who tend to improve the performance-association to a disease phenotype of interest-of any coalition (subset of co-occurring genetic variants) they join. This method has been previously applied to boost biologically informative signal from gene expression data and exome sequencing data but remains to be explored in the context of cooperativity among non-coding genomic regions. We describe our extension of previous work, highlighting non-coding chromosomal regions relevant to ASD using CGT on alteration data of 4595 fully sequenced genomes from 756 multiplex families. Genomes were encoded into binary matrices for three types of non-coding regions previously implicated in ASD and separated into ASD (case) and unaffected (control) samples. A player metric, the Shapley value, enabled determination of individual variant contributions in both sets of cohorts. A total of 30 non-coding positions were found to have significantly elevated player scores and likely represent significant contributors to the genetic coordination underlying ASD. Cross-study analyses revealed that a subset of mutated non-coding regions (all of which are in human accelerated regions (HARs)) and related genes are involved in biological pathways or behavioral outcomes known to be affected in autism, suggesting the importance of single nucleotide polymorphisms (SNPs) within HARs in ASD. These findings support the use of CGT in identifying hidden yet influential non-coding players from large-scale genomic data, to better understand the precise underpinnings of complex neurodevelopmental disorders such as autism.
Collapse
Affiliation(s)
- Min Woo Sun
- Departments of Pediatrics (Division of Systems Medicine), Psychiatry (by courtesy), and Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Anika Gupta*
- Departments of Pediatrics (Division of Systems Medicine), Psychiatry (by courtesy), and Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Maya Varma
- Departments of Pediatrics (Division of Systems Medicine), Psychiatry (by courtesy), and Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kelley M Paskov
- Departments of Pediatrics (Division of Systems Medicine), Psychiatry (by courtesy), and Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Jae-Yoon Jung
- Departments of Pediatrics (Division of Systems Medicine), Psychiatry (by courtesy), and Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Nate T Stockham
- Departments of Pediatrics (Division of Systems Medicine), Psychiatry (by courtesy), and Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Dennis P Wall
- Departments of Pediatrics (Division of Systems Medicine), Psychiatry (by courtesy), and Biomedical Data Science, Stanford University, Stanford, CA, USA
| |
Collapse
|
14
|
Genome-wide profiling reveals functional diversification of ∆FosB gene targets in the hippocampus of an Alzheimer's disease mouse model. PLoS One 2018; 13:e0192508. [PMID: 29408867 PMCID: PMC5800686 DOI: 10.1371/journal.pone.0192508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/24/2018] [Indexed: 01/20/2023] Open
Abstract
The activity-induced transcription factor ∆FosB has been implicated in Alzheimer’s disease (AD) as a critical regulator of hippocampal function and cognition downstream of seizures and network hyperexcitability. With its long half-life (> 1 week), ∆FosB is well-poised to modulate hippocampal gene expression over extended periods of time, enabling effects to persist even during seizure-free periods. However, the transcriptional mechanisms by which ∆FosB regulates hippocampal function are poorly understood due to lack of identified hippocampal gene targets. To identify putative ∆FosB gene targets, we employed high-throughput sequencing of genomic DNA bound to ∆FosB after chromatin immunoprecipitation (ChIP-sequencing). We compared ChIP-sequencing results from hippocampi of transgenic mice expressing mutant human amyloid precursor protein (APP) and nontransgenic (NTG) wild-type littermates. Surprisingly, only 52 ∆FosB gene targets were shared between NTG and APP mice; the vast majority of targets were unique to one genotype or the other. We also found a functional shift in the repertoire of ∆FosB gene targets between NTG and APP mice. A large number of targets in NTG mice are involved in neurodevelopment and/or cell morphogenesis, whereas in APP mice there is an enrichment of targets involved in regulation of membrane potential and neuronal excitability. RNA-sequencing and quantitative PCR experiments confirmed that expression of putative ∆FosB gene targets were altered in the hippocampus of APP mice. This study provides key insights into functional domains regulated by ∆FosB in the hippocampus, emphasizing remarkably different programs of gene regulation under physiological and pathological conditions.
Collapse
|
15
|
Ferrarelli LK. New connections: Signaling in learning disability. Sci Signal 2018. [DOI: 10.1126/scisignal.aas9779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Research in this issue of
Science Signaling
and the Archives brings us steps closer to understanding the origins of learning disability.
Collapse
|