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Lin L, Zhao J, Kubota N, Li Z, Lam YL, Nguyen LP, Yang L, Pokharel SP, Blue SM, Yee BA, Chen R, Yeo GW, Chen CW, Chen L, Zheng S. Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. Neuron 2024; 112:2157-2176.e12. [PMID: 38697111 DOI: 10.1016/j.neuron.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/14/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Mutations in human nonsense-mediated mRNA decay (NMD) factors are enriched in neurodevelopmental disorders. We show that deletion of key NMD factor Upf2 in mouse embryonic neural progenitor cells causes perinatal microcephaly but deletion in immature neurons does not, indicating NMD's critical roles in progenitors. Upf2 knockout (KO) prolongs the cell cycle of radial glia progenitor cells, promotes their transition into intermediate progenitors, and leads to reduced upper-layer neurons. CRISPRi screening identified Trp53 knockdown rescuing Upf2KO progenitors without globally reversing NMD inhibition, implying marginal contributions of most NMD targets to the cell cycle defect. Integrated functional genomics shows that NMD degrades selective TRP53 downstream targets, including Cdkn1a, which, without NMD suppression, slow the cell cycle. Trp53KO restores the progenitor cell pool and rescues the microcephaly of Upf2KO mice. Therefore, one physiological role of NMD in the developing brain is to degrade selective TRP53 targets to control progenitor cell cycle and brain size.
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Affiliation(s)
- Lin Lin
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Jingrong Zhao
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Naoto Kubota
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Zhelin Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Yi-Li Lam
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Lauren P Nguyen
- Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela P Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA; City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA; Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA.
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2
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Asthana S, Mott J, Tong M, Pei Z, Mao Y. The Exon Junction Complex Factor RBM8A in Glial Fibrillary Acid Protein-Expressing Astrocytes Modulates Locomotion Behaviors. Cells 2024; 13:498. [PMID: 38534343 DOI: 10.3390/cells13060498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The role of RNA Binding Motif Protein 8a (RBM8A), an exon junction complex (EJC) component, in neurodevelopmental disorders has been increasingly studied for its crucial role in regulating multiple levels of gene expression. It regulates mRNA splicing, translation, and mRNA degradation and influences embryonic development. RBM8A protein is expressed in both neurons and astrocytes, but little is known about RBM8A's specific role in glial fibrillary acid protein (GFAP)-positive astrocytes. To address the role of RBM8A in astrocytes, we generated a conditional heterozygous knockout (KO) mouse line of Rbm8a in astrocytes using a GFAP-cre line. We confirmed a decreased expression of RBM8A in astrocytes of heterozygous conditional KO mice via RT-PCR and Sanger sequencing, as well as qRT-PCR, immunohistochemistry, and Western blot. Interestingly, these mice exhibit significantly increased movement and mobility, alongside sex-specific altered anxiety in the open field test (OFT) and elevated plus maze (OPM) tests. These tests, along with the rotarod test, suggest that these mice have normal motor coordination but hyperactive phenotypes. In addition, the haploinsufficiency of Rbm8a in astrocytes leads to a sex-specific change in astrocyte density in the dentate gyrus. This study further reveals the contribution of Rbm8a deletion to CNS pathology, generating more insights via the glial lens of an Rbm8a model of neurodevelopmental disorder.
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Affiliation(s)
- Shravan Asthana
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA
| | - Jennifer Mott
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mabel Tong
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Zifei Pei
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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Ribeiro JH, Altinisik N, Rajan N, Verslegers M, Baatout S, Gopalakrishnan J, Quintens R. DNA damage and repair: underlying mechanisms leading to microcephaly. Front Cell Dev Biol 2023; 11:1268565. [PMID: 37881689 PMCID: PMC10597653 DOI: 10.3389/fcell.2023.1268565] [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: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
DNA-damaging agents and endogenous DNA damage constantly harm genome integrity. Under genotoxic stress conditions, the DNA damage response (DDR) machinery is crucial in repairing lesions and preventing mutations in the basic structure of the DNA. Different repair pathways are implicated in the resolution of such lesions. For instance, the non-homologous DNA end joining and homologous recombination pathways are central cellular mechanisms by which eukaryotic cells maintain genome integrity. However, defects in these pathways are often associated with neurological disorders, indicating the pivotal role of DDR in normal brain development. Moreover, the brain is the most sensitive organ affected by DNA-damaging agents compared to other tissues during the prenatal period. The accumulation of lesions is believed to induce cell death, reduce proliferation and premature differentiation of neural stem and progenitor cells, and reduce brain size (microcephaly). Microcephaly is mainly caused by genetic mutations, especially genes encoding proteins involved in centrosomes and DNA repair pathways. However, it can also be induced by exposure to ionizing radiation and intrauterine infections such as the Zika virus. This review explains mammalian cortical development and the major DNA repair pathways that may lead to microcephaly when impaired. Next, we discuss the mechanisms and possible exposures leading to DNA damage and p53 hyperactivation culminating in microcephaly.
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Affiliation(s)
- Jessica Honorato Ribeiro
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nazlican Altinisik
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Nicholas Rajan
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jay Gopalakrishnan
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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4
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Petrić Howe M, Patani R. Nonsense-mediated mRNA decay in neuronal physiology and neurodegeneration. Trends Neurosci 2023; 46:879-892. [PMID: 37543480 DOI: 10.1016/j.tins.2023.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/19/2023] [Accepted: 07/09/2023] [Indexed: 08/07/2023]
Abstract
The processes of mRNA export from the nucleus and subsequent mRNA translation in the cytoplasm are of particular relevance in eukaryotic cells. In highly polarised cells such as neurons, finely-tuned molecular regulation of these processes serves to safeguard the spatiotemporal fidelity of gene expression. Nonsense-mediated mRNA decay (NMD) is a cytoplasmic translation-dependent quality control process that regulates gene expression in a wide range of scenarios in the nervous system, including neurodevelopment, learning, and memory formation. Moreover, NMD dysregulation has been implicated in a broad range of neurodevelopmental and neurodegenerative disorders. We discuss how NMD and related aspects of mRNA translation regulate key neuronal functions and, in particular, we focus on evidence implicating these processes in the molecular pathogenesis of neurodegeneration. Finally, we discuss the therapeutic potential and challenges of targeting mRNA translation and NMD across the spectrum of largely untreatable neurological diseases.
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Affiliation(s)
- Marija Petrić Howe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London (UCL), Queen Square, WC1N 3BG London, UK.
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London (UCL), Queen Square, WC1N 3BG London, UK.
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5
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Strauss G, Mott K, Klopocki E, Schulze H. Thrombocytopenia Absent Radius (TAR)-Syndrome: From Current Genetics to Patient Self-Empowerment. Hamostaseologie 2023; 43:252-260. [PMID: 37611607 DOI: 10.1055/a-2088-1801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
Thrombocytopenia absent radius (TAR) syndrome is a rare form of hereditary thrombocytopenia associated with a bilateral radial aplasia. TAR syndrome is genetically defined by the combination of a microdeletion on chromosome 1 which includes the gene RBM8A, and a single nucleotide polymorphism (SNP) in the second RBM8A allele. While most patients with TAR syndrome harbor a SNP in either the 5' UTR region or in intron 1 of RBM8A, further SNPs associated with TAR syndrome are still being identified. Here, we report on the current understanding of the genetic basis, diagnosis, and therapy of TAR syndrome and discuss patient self-empowerment by enabling networking and exchange between affected individuals and families.
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Affiliation(s)
- Gabriele Strauss
- Department of Paediatric Haematology and Oncology, Helios-Klinikum Buch, Berlin, Germany
| | - Kristina Mott
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - Eva Klopocki
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Harald Schulze
- Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
- Center for Rare Blood Cell Disorders, Center for Rare Diseases, University Hospital Würzburg, Würzburg, Germany
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6
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Lupan BM, Solecki RA, Musso CM, Alsina FC, Silver DL. The exon junction complex component EIF4A3 is essential for mouse and human cortical progenitor mitosis and neurogenesis. Development 2023; 150:dev201619. [PMID: 37139782 PMCID: PMC10233715 DOI: 10.1242/dev.201619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 05/05/2023]
Abstract
Mutations in components of the exon junction complex (EJC) are associated with neurodevelopment and disease. In particular, reduced levels of the RNA helicase EIF4A3 cause Richieri-Costa-Pereira syndrome (RCPS) and copy number variations are linked to intellectual disability. Consistent with this, Eif4a3 haploinsufficient mice are microcephalic. Altogether, this implicates EIF4A3 in cortical development; however, the underlying mechanisms are poorly understood. Here, we use mouse and human models to demonstrate that EIF4A3 promotes cortical development by controlling progenitor mitosis, cell fate and survival. Eif4a3 haploinsufficiency in mice causes extensive cell death and impairs neurogenesis. Using Eif4a3;p53 compound mice, we show that apoptosis has the most impact on early neurogenesis, while additional p53-independent mechanisms contribute to later stages. Live imaging of mouse and human neural progenitors reveals that Eif4a3 controls mitosis length, which influences progeny fate and viability. These phenotypes are conserved, as cortical organoids derived from RCPS iPSCs exhibit aberrant neurogenesis. Finally, using rescue experiments we show that EIF4A3 controls neuron generation via the EJC. Altogether, our study demonstrates that EIF4A3 mediates neurogenesis by controlling mitosis duration and cell survival, implicating new mechanisms that underlie EJC-mediated disorders.
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Affiliation(s)
- Bianca M. Lupan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Rachel A. Solecki
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Camila M. Musso
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Fernando C. Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Debra L. Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
- Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Institute for Brain Sciences and Duke Regeneration Center, Duke University Medical Center, Durham, NC 27710, USA
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7
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McSweeney C, Chen M, Dong F, Sebastian A, Reynolds DJ, Mott J, Pei Z, Zou J, Shi Y, Mao Y. Transcriptomic Analyses of Brains of RBM8A Conditional Knockout Mice at Different Developmental Stages Reveal Conserved Signaling Pathways Contributing to Neurodevelopmental Diseases. Int J Mol Sci 2023; 24:4600. [PMID: 36902031 PMCID: PMC10003467 DOI: 10.3390/ijms24054600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
RNA-binding motif 8A (RBM8A) is a core component of the exon junction complex (EJC) that binds pre-mRNAs and regulates their splicing, transport, translation, and nonsense-mediated decay (NMD). Dysfunction in the core proteins has been linked to several detriments in brain development and neuropsychiatric diseases. To understand the functional role of Rbm8a in brain development, we have generated brain-specific Rbm8a knockout mice and used next-generation RNA-sequencing to identify differentially expressed genes (DEGs) in mice with heterozygous, conditional knockout (cKO) of Rbm8a in the brain at postnatal day 17 (P17) and at embryonic day 12. Additionally, we analyzed enriched gene clusters and signaling pathways within the DEGs. At the P17 time point, between the control and cKO mice, about 251 significant DEGs were identified. At E12, only 25 DEGs were identified in the hindbrain samples. Bioinformatics analyses have revealed many signaling pathways related to the central nervous system (CNS). When E12 and P17 results were compared, three DEGs, Spp1, Gpnmb, and Top2a, appeared to peak at different developmental time points in the Rbm8a cKO mice. Enrichment analyses suggested altered activity in pathways affecting cellular proliferation, differentiation, and survival. The results support the hypothesis that loss of Rbm8a causes decreased cellular proliferation, increased apoptosis, and early differentiation of neuronal subtypes, which may lead ultimately to an altered neuronal subtype composition in the brain.
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Affiliation(s)
- Colleen McSweeney
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Miranda Chen
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Fengping Dong
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aswathy Sebastian
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Derrick James Reynolds
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Jennifer Mott
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Zifei Pei
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jizhong Zou
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, Rockville, MD 20892, USA
| | - Yongsheng Shi
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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8
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Lupan BM, Solecki RA, Musso CM, Alsina FC, Silver DL. The exon junction complex component EIF4A3 is essential for mouse and human cortical progenitor mitosis and neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.524010. [PMID: 36711736 PMCID: PMC9882224 DOI: 10.1101/2023.01.13.524010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mutations in components of the exon junction complex (EJC) are associated with neurodevelopment and disease. In particular, reduced levels of the RNA helicase EIF4A3 cause Richieri-Costa-Pereira Syndrome (RCPS) and CNVs are linked to intellectual disability. Consistent with this, Eif4a3 haploinsufficient mice are microcephalic. Altogether, this implicates EIF4A3 in cortical development; however, the underlying mechanisms are poorly understood. Here, we use mouse and human models to demonstrate that EIF4A3 promotes cortical development by controlling progenitor mitosis, cell fate, and survival. Eif4a3 haploinsufficiency in mice causes extensive cell death and impairs neurogenesis. Using Eif4a3 ; p53 compound mice, we show that apoptosis is most impactful for early neurogenesis, while additional p53-independent mechanisms contribute to later stages. Live imaging of mouse and human neural progenitors reveals Eif4a3 controls mitosis length, which influences progeny fate and viability. These phenotypes are conserved as cortical organoids derived from RCPS iPSCs exhibit aberrant neurogenesis. Finally, using rescue experiments we show that EIF4A3 controls neuron generation via the EJC. Altogether, our study demonstrates that EIF4A3 mediates neurogenesis by controlling mitosis duration and cell survival, implicating new mechanisms underlying EJC-mediated disorders. Summary statement This study shows that EIF4A3 mediates neurogenesis by controlling mitosis duration in both mouse and human neural progenitors, implicating new mechanisms underlying neurodevelopmental disorders.
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9
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Chousal JN, Sohni A, Vitting-Seerup K, Cho K, Kim M, Tan K, Porse B, Wilkinson MF, Cook-Andersen H. Progression of the pluripotent epiblast depends upon the NMD factor UPF2. Development 2022; 149:dev200764. [PMID: 36255229 PMCID: PMC9687065 DOI: 10.1242/dev.200764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that degrades RNAs harboring in-frame stop codons in specific contexts. Loss of NMD factors leads to embryonic lethality in organisms spanning the phylogenetic scale, but the mechanism remains unknown. Here, we report that the core NMD factor, UPF2, is required for expansion of epiblast cells within the inner cell mass of mice in vivo. We identify NMD target mRNAs in mouse blastocysts - both canonical and alternatively processed mRNAs - including those encoding cell cycle arrest and apoptosis factors, raising the possibility that NMD is essential for embryonic cell proliferation and survival. In support, the inner cell mass of Upf2-null blastocysts rapidly regresses with outgrowth and is incompetent for embryonic stem cell derivation in vitro. In addition, we uncovered concordant temporal- and lineage-specific regulation of NMD factors and mRNA targets, indicative of a shift in NMD magnitude during peri-implantation development. Together, our results reveal developmental and molecular functions of the NMD pathway in the early embryo.
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Affiliation(s)
- Jennifer N. Chousal
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
- Section for Bioinformatics, Health Technology, Technical University of Denmark (DTU), 2800 Kongens Lyngby, Denmark
| | - Kyucheol Cho
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Kim
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kun Tan
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
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10
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Hoye ML, Calviello L, Poff AJ, Ejimogu NE, Newman CR, Montgomery MD, Ou J, Floor SN, Silver DL. Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model. eLife 2022; 11:e78203. [PMID: 35762573 PMCID: PMC9239684 DOI: 10.7554/elife.78203] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/25/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in the RNA helicase, DDX3X, are a leading cause of Intellectual Disability and present as DDX3X syndrome, a neurodevelopmental disorder associated with cortical malformations and autism. Yet, the cellular and molecular mechanisms by which DDX3X controls cortical development are largely unknown. Here, using a mouse model of Ddx3x loss-of-function we demonstrate that DDX3X directs translational and cell cycle control of neural progenitors, which underlies precise corticogenesis. First, we show brain development is sensitive to Ddx3x dosage; complete Ddx3x loss from neural progenitors causes microcephaly in females, whereas hemizygous males and heterozygous females show reduced neurogenesis without marked microcephaly. In addition, Ddx3x loss is sexually dimorphic, as its paralog, Ddx3y, compensates for Ddx3x in the developing male neocortex. Using live imaging of progenitors, we show that DDX3X promotes neuronal generation by regulating both cell cycle duration and neurogenic divisions. Finally, we use ribosome profiling in vivo to discover the repertoire of translated transcripts in neural progenitors, including those which are DDX3X-dependent and essential for neurogenesis. Our study reveals invaluable new insights into the etiology of DDX3X syndrome, implicating dysregulated progenitor cell cycle dynamics and translation as pathogenic mechanisms.
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Affiliation(s)
- Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Lorenzo Calviello
- Centre for Functional Genomics, Human TechnopoleMilanItaly
- Centre for Computational Biology, Human TechnopoleMilanItaly
| | - Abigail J Poff
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Nna-Emeka Ejimogu
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Carly R Newman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Maya D Montgomery
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Jianhong Ou
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
- Duke Regeneration Center, Duke University Medical CenterDurhamUnited States
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSFSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer CenterSan FranciscoUnited States
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
- Duke Regeneration Center, Duke University Medical CenterDurhamUnited States
- Department of Neurobiology, Duke University Medical CenterDurhamUnited States
- Duke Institute for Brain Sciences, Duke University Medical CenterDurhamUnited States
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11
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The Physiological Roles of the Exon Junction Complex in Development and Diseases. Cells 2022; 11:cells11071192. [PMID: 35406756 PMCID: PMC8997533 DOI: 10.3390/cells11071192] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 01/12/2023] Open
Abstract
The exon junction complex (EJC) becomes an increasingly important regulator of early gene expression in the central nervous system (CNS) and other tissues. The EJC is comprised of three core proteins: RNA-binding motif 8A (RBM8A), Mago homolog (MAGOH), eukaryotic initiation factor 4A3 (EIF4A3), and a peripheral EJC factor, metastatic lymph node 51 (MLN51), together with various auxiliary factors. The EJC is assembled specifically at exon-exon junctions on mRNAs, hence the name of the complex. The EJC regulates multiple levels of gene expression, from splicing to translation and mRNA degradation. The functional roles of the EJC have been established as crucial to the normal progress of embryonic and neurological development, with wide ranging implications on molecular, cellular, and organism level function. Dysfunction of the EJC has been implicated in multiple developmental and neurological diseases. In this review, we discuss recent progress on the EJC’s physiological roles.
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12
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Rocha C, Prinos P. Post-transcriptional and Post-translational Modifications of Primary Cilia: How to Fine Tune Your Neuronal Antenna. Front Cell Neurosci 2022; 16:809917. [PMID: 35295905 PMCID: PMC8918543 DOI: 10.3389/fncel.2022.809917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022] Open
Abstract
Primary cilia direct cellular signaling events during brain development and neuronal differentiation. The primary cilium is a dynamic organelle formed in a multistep process termed ciliogenesis that is tightly coordinated with the cell cycle. Genetic alterations, such as ciliary gene mutations, and epigenetic alterations, such as post-translational modifications and RNA processing of cilia related factors, give rise to human neuronal disorders and brain tumors such as glioblastoma and medulloblastoma. This review discusses the important role of genetics/epigenetics, as well as RNA processing and post-translational modifications in primary cilia function during brain development and cancer formation. We summarize mouse and human studies of ciliogenesis and primary cilia activity in the brain, and detail how cilia maintain neuronal progenitor populations and coordinate neuronal differentiation during development, as well as how cilia control different signaling pathways such as WNT, Sonic Hedgehog (SHH) and PDGF that are critical for neurogenesis. Moreover, we describe how post-translational modifications alter cilia formation and activity during development and carcinogenesis, and the impact of missplicing of ciliary genes leading to ciliopathies and cell cycle alterations. Finally, cilia genetic and epigenetic studies bring to light cellular and molecular mechanisms that underlie neurodevelopmental disorders and brain tumors.
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Affiliation(s)
- Cecilia Rocha
- Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
- *Correspondence: Cecilia Rocha,
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Panagiotis Prinos,
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13
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Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
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14
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Ho CH, Paolantoni C, Bawankar P, Tang Z, Brown S, Roignant J, Treisman JE. An exon junction complex-independent function of Barentsz in neuromuscular synapse growth. EMBO Rep 2022; 23:e53231. [PMID: 34726300 PMCID: PMC8728599 DOI: 10.15252/embr.202153231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/07/2023] Open
Abstract
The exon junction complex controls the translation, degradation, and localization of spliced mRNAs, and three of its core subunits also play a role in splicing. Here, we show that a fourth subunit, Barentsz, has distinct functions within and separate from the exon junction complex in Drosophila neuromuscular development. The distribution of mitochondria in larval muscles requires Barentsz as well as other exon junction complex subunits and is not rescued by a Barentsz transgene in which residues required for binding to the core subunit eIF4AIII are mutated. In contrast, interactions with the exon junction complex are not required for Barentsz to promote the growth of neuromuscular synapses. We find that the Activin ligand Dawdle shows reduced expression in barentsz mutants and acts downstream of Barentsz to control synapse growth. Both barentsz and dawdle are required in motor neurons, muscles, and glia for normal synapse growth, and exogenous Dawdle can rescue synapse growth in the absence of barentsz. These results identify a biological function for Barentsz that is independent of the exon junction complex.
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Affiliation(s)
- Cheuk Hei Ho
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Praveen Bawankar
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Zuojian Tang
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
Computational Biology at Ridgefield US, Global Computational Biology and Digital ScienceBoehringer IngelheimRidgefieldCTUSA
| | - Stuart Brown
- Center for Health Informatics and BioinformaticsNYU Langone Medical CenterNew YorkNYUSA
- Present address:
ExxonMobil Corporate Strategic ResearchAnnandaleNJUSA
| | - Jean‐Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- Institute of Pharmaceutical and Biomedical SciencesJohannes Gutenberg‐University MainzMainzGermany
| | - Jessica E Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell BiologyNYU School of MedicineNew YorkNYUSA
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15
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Marenda M, Lazarova E, Gilbert N. The role of SAF-A/hnRNP U in regulating chromatin structure. Curr Opin Genet Dev 2021; 72:38-44. [PMID: 34823151 DOI: 10.1016/j.gde.2021.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023]
Abstract
Scaffold attachment factor A (SAF-A) or hnRNP U is a nuclear RNA-binding protein with a well-documented role in processing newly transcribed RNA. Recent studies also indicate that SAF-A can oligomerise in an ATP-dependent manner and interact with RNA to form a dynamic nuclear mesh. This mesh is thought to regulate nuclear and chromatin architecture, yet a mechanistic understanding is lacking. Here, we review developments in the field to understand how the SAF-A/RNA mesh affects chromatin organisation in interphase and mitosis. As SAF-A has an intrinsically disordered domain we discuss how the chromatin mesh is related to nuclear phase-separated condensates, which in other situations have been shown to regulate transcription and cell functions. Finally, we infer possible links between diseases emerging from SAF-A mutations and its role in chromatin organisation and regulation.
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Affiliation(s)
- Mattia Marenda
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Elena Lazarova
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
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16
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Su CH, Liao WJ, Ke WC, Yang RB, Tarn WY. The Y14-p53 regulatory circuit in megakaryocyte differentiation and thrombocytopenia. iScience 2021; 24:103368. [PMID: 34816104 PMCID: PMC8593568 DOI: 10.1016/j.isci.2021.103368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/27/2021] [Accepted: 10/26/2021] [Indexed: 11/19/2022] Open
Abstract
Thrombocytopenia-absent radius (TAR) syndrome is caused by RBM8A insufficiency. We generated megakaryocyte-specific Rbm8a knockout (Rbm8aKOMK) mice that exhibited marked thrombocytopenia, internal hemorrhage, and splenomegaly, providing evidence that genetic deficiency of Rbm8a causes a disorder of platelet production. Rbm8aKOMK mice accumulated low-ploidy immature megakaryocytes in the bone marrow and exhibited defective platelet activation and aggregation. Accordingly, depletion of Y14 (RBM8A) in human erythroleukemia (HEL) cells compromised phorbol-ester-induced polyploidization. Notably, Y14/RBM8A deficiency induced both p53 and p21 in megakaryocytes and HEL cells. Treatment with a p53 inhibitor restored ex vivo differentiation of Rbm8aKOMK megakaryocytes and unexpectedly activated Y14 expression in HEL cells. Trp53 knockout partially restored megakaryocyte differentiation by reversing cell-cycle arrest and increased platelet counts of Rbm8aKOMK, indicating that excess p53 in part accounts for thrombocytopenia in TAR syndrome. This study provides evidence for the role of the Y14-p53 circuit in platelet production and a potential therapeutic strategy.
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Affiliation(s)
- Chun-Hao Su
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 11529, Taiwan
| | - Wei-Ju Liao
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 11529, Taiwan
| | - Wei-Chi Ke
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 11529, Taiwan
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 11529, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 11529, Taiwan
- Corresponding author
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17
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Brosens E, Brouwer RWW, Douben H, van Bever Y, Brooks AS, Wijnen RMH, van IJcken WFJ, Tibboel D, Rottier RJ, de Klein A. Heritability and De Novo Mutations in Oesophageal Atresia and Tracheoesophageal Fistula Aetiology. Genes (Basel) 2021; 12:genes12101595. [PMID: 34680991 PMCID: PMC8535313 DOI: 10.3390/genes12101595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 01/12/2023] Open
Abstract
Tracheoesophageal Fistula (TOF) is a congenital anomaly for which the cause is unknown in the majority of patients. OA/TOF is a variable feature in many (often mono-) genetic syndromes. Research using animal models targeting genes involved in candidate pathways often result in tracheoesophageal phenotypes. However, there is limited overlap in the genes implicated by animal models and those found in OA/TOF-related syndromic anomalies. Knowledge on affected pathways in animal models is accumulating, but our understanding on these pathways in patients lags behind. If an affected pathway is associated with both animals and patients, the mechanisms linking the genetic mutation, affected cell types or cellular defect, and the phenotype are often not well understood. The locus heterogeneity and the uncertainty of the exact heritability of OA/TOF results in a relative low diagnostic yield. OA/TOF is a sporadic finding with a low familial recurrence rate. As parents are usually unaffected, de novo dominant mutations seems to be a plausible explanation. The survival rates of patients born with OA/TOF have increased substantially and these patients start families; thus, the detection and a proper interpretation of these dominant inherited pathogenic variants are of great importance for these patients and for our understanding of OA/TOF aetiology.
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Affiliation(s)
- Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
- Correspondence:
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
| | - Rene M. H. Wijnen
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Center for Biomics, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (R.W.W.B.); (W.F.J.v.I.)
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (R.M.H.W.); (D.T.)
| | - Robbert J. Rottier
- Departments of Pediatric Surgery & Cell Biology, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (H.D.); (Y.v.B.); (A.S.B.); (A.d.K.)
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18
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Tsai YY, Su CH, Tarn WY. p53 Activation in Genetic Disorders: Different Routes to the Same Destination. Int J Mol Sci 2021; 22:9307. [PMID: 34502215 PMCID: PMC8430931 DOI: 10.3390/ijms22179307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/18/2022] Open
Abstract
The tumor suppressor p53 is critical for preventing neoplastic transformation and tumor progression. Inappropriate activation of p53, however, has been observed in a number of human inherited disorders that most often affect development of the brain, craniofacial region, limb skeleton, and hematopoietic system. Genes related to these developmental disorders are essentially involved in transcriptional regulation/chromatin remodeling, rRNA metabolism, DNA damage-repair pathways, telomere maintenance, and centrosome biogenesis. Perturbation of these activities or cellular processes may result in p53 accumulation in cell cultures, animal models, and perhaps humans as well. Mouse models of several p53 activation-associated disorders essentially recapitulate human traits, and inactivation of p53 in these models can alleviate disorder-related phenotypes. In the present review, we focus on how dysfunction of the aforementioned biological processes causes developmental defects via excessive p53 activation. Notably, several disease-related genes exert a pleiotropic effect on those cellular processes, which may modulate the magnitude of p53 activation and establish or disrupt regulatory loops. Finally, we discuss potential therapeutic strategies for genetic disorders associated with p53 misactivation.
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19
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Understanding microcephaly through the study of centrosome regulation in Drosophila neural stem cells. Biochem Soc Trans 2021; 48:2101-2115. [PMID: 32897294 DOI: 10.1042/bst20200261] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/30/2022]
Abstract
Microcephaly is a rare, yet devastating, neurodevelopmental condition caused by genetic or environmental insults, such as the Zika virus infection. Microcephaly manifests with a severely reduced head circumference. Among the known heritable microcephaly genes, a significant proportion are annotated with centrosome-related ontologies. Centrosomes are microtubule-organizing centers, and they play fundamental roles in the proliferation of the neuronal progenitors, the neural stem cells (NSCs), which undergo repeated rounds of asymmetric cell division to drive neurogenesis and brain development. Many of the genes, pathways, and developmental paradigms that dictate NSC development in humans are conserved in Drosophila melanogaster. As such, studies of Drosophila NSCs lend invaluable insights into centrosome function within NSCs and help inform the pathophysiology of human microcephaly. This mini-review will briefly survey causative links between deregulated centrosome functions and microcephaly with particular emphasis on insights learned from Drosophila NSCs.
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20
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Yoon J, Mao Y. Dissecting Molecular Genetic Mechanisms of 1q21.1 CNV in Neuropsychiatric Disorders. Int J Mol Sci 2021; 22:5811. [PMID: 34071723 PMCID: PMC8197994 DOI: 10.3390/ijms22115811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Pathogenic copy number variations (CNVs) contribute to the etiology of neurodevelopmental/neuropsychiatric disorders (NDs). Increased CNV burden has been found to be critically involved in NDs compared with controls in clinical studies. The 1q21.1 CNVs, rare and large chromosomal microduplications and microdeletions, are detected in many patients with NDs. Phenotypes of duplication and deletion appear at the two ends of the spectrum. Microdeletions are predominant in individuals with schizophrenia (SCZ) and microcephaly, whereas microduplications are predominant in individuals with autism spectrum disorder (ASD) and macrocephaly. However, its complexity hinders the discovery of molecular pathways and phenotypic networks. In this review, we summarize the recent genome-wide association studies (GWASs) that have identified candidate genes positively correlated with 1q21.1 CNVs, which are likely to contribute to abnormal phenotypes in carriers. We discuss the clinical data implicated in the 1q21.1 genetic structure that is strongly associated with neurodevelopmental dysfunctions like cognitive impairment and reduced synaptic plasticity. We further present variations reported in the phenotypic severity, genomic penetrance and inheritance.
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Affiliation(s)
| | - Yingwei Mao
- Department of Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA;
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21
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Edwards NA, Shacham-Silverberg V, Weitz L, Kingma PS, Shen Y, Wells JM, Chung WK, Zorn AM. Developmental basis of trachea-esophageal birth defects. Dev Biol 2021; 477:85-97. [PMID: 34023332 DOI: 10.1016/j.ydbio.2021.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 02/07/2023]
Abstract
Trachea-esophageal defects (TEDs), including esophageal atresia (EA), tracheoesophageal fistula (TEF), and laryngeal-tracheoesophageal clefts (LTEC), are a spectrum of life-threatening congenital anomalies in which the trachea and esophagus do not form properly. Up until recently, the developmental basis of these conditions and how the trachea and esophagus arise from a common fetal foregut was poorly understood. However, with significant advances in human genetics, organoids, and animal models, and integrating single cell genomics with high resolution imaging, we are revealing the molecular and cellular mechanisms that orchestrate tracheoesophageal morphogenesis and how disruption in these processes leads to birth defects. Here we review the current understanding of the genetic and developmental basis of TEDs. We suggest future opportunities for integrating developmental mechanisms elucidated from animals and organoids with human genetics and clinical data to gain insight into the genotype-phenotype basis of these heterogeneous birth defects. Finally, we envision how this will enhance diagnosis, improve treatment, and perhaps one day, lead to new tissue replacement therapy.
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Affiliation(s)
- Nicole A Edwards
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vered Shacham-Silverberg
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Leelah Weitz
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Paul S Kingma
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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22
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Wang B, Rong X, Zhou Y, Liu Y, Sun J, Zhao B, Deng B, Lu L, Lu L, Li Y, Zhou J. Eukaryotic initiation factor 4A3 inhibits Wnt/β-catenin signaling and regulates axis formation in zebrafish embryos. Development 2021; 148:261699. [PMID: 33914867 DOI: 10.1242/dev.198101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 12/31/2022]
Abstract
A key step in the activation of canonical Wnt signaling is the interaction between β-catenin and Tcf/Lefs that forms the transcription activation complex and facilitates the expression of target genes. Eukaryotic initiation factor 4A3 (EIF4A3) is an ATP-dependent DEAD box-family RNA helicase and acts as a core subunit of the exon junction complex (EJC) to control a series of RNA post-transcriptional processes. In this study, we uncover that EIF4A3 functions as a Wnt inhibitor by interfering with the formation of β-catenin/Tcf transcription activation complex. As Wnt stimulation increases, accumulated β-catenin displaces EIF4A3 from a transcriptional complex with Tcf/Lef, allowing the active complex to facilitate the expression of target genes. In zebrafish embryos, eif4a3 depletion inhibited the development of the dorsal organizer and pattern formation of the anterior neuroectoderm by increasing Wnt/β-catenin signaling. Conversely, overexpression of eif4a3 decreased Wnt/β-catenin signaling and inhibited the formation of the dorsal organizer before gastrulation. Our results reveal previously unreported roles of EIF4A3 in the inhibition of Wnt signaling and the regulation of embryonic development in zebrafish.
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Affiliation(s)
- Bo Wang
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiaozhi Rong
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
| | - Yumei Zhou
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yunzhang Liu
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiqin Sun
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Beibei Zhao
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Bei Deng
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Lei Lu
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China
| | - Ling Lu
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yun Li
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
| | - Jianfeng Zhou
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
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23
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Lee PJ, Yang S, Sun Y, Guo JU. Regulation of nonsense-mediated mRNA decay in neural development and disease. J Mol Cell Biol 2021; 13:269-281. [PMID: 33783512 PMCID: PMC8339359 DOI: 10.1093/jmcb/mjab022] [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: 10/12/2020] [Revised: 01/27/2021] [Accepted: 02/05/2021] [Indexed: 11/26/2022] Open
Abstract
Eukaryotes have evolved a variety of mRNA surveillance mechanisms to detect and degrade aberrant mRNAs with potential deleterious outcomes. Among them, nonsense-mediated mRNA decay (NMD) functions not only as a quality control mechanism targeting aberrant mRNAs containing a premature termination codon but also as a posttranscriptional gene regulation mechanism targeting numerous physiological mRNAs. Despite its well-characterized molecular basis, the regulatory scope and biological functions of NMD at an organismal level are incompletely understood. In humans, mutations in genes encoding core NMD factors cause specific developmental and neurological syndromes, suggesting a critical role of NMD in the central nervous system. Here, we review the accumulating biochemical and genetic evidence on the developmental regulation and physiological functions of NMD as well as an emerging role of NMD dysregulation in neurodegenerative diseases.
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Affiliation(s)
- Paul Jongseo Lee
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Yu Sun
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Junjie U Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.,Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
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24
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Kwon OS, Mishra R, Safieddine A, Coleno E, Alasseur Q, Faucourt M, Barbosa I, Bertrand E, Spassky N, Le Hir H. Exon junction complex dependent mRNA localization is linked to centrosome organization during ciliogenesis. Nat Commun 2021; 12:1351. [PMID: 33649372 PMCID: PMC7921557 DOI: 10.1038/s41467-021-21590-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 01/14/2021] [Indexed: 12/17/2022] Open
Abstract
Exon junction complexes (EJCs) mark untranslated spliced mRNAs and are crucial for the mRNA lifecycle. An imbalance in EJC dosage alters mouse neural stem cell (mNSC) division and is linked to human neurodevelopmental disorders. In quiescent mNSC and immortalized human retinal pigment epithelial (RPE1) cells, centrioles form a basal body for ciliogenesis. Here, we report that EJCs accumulate at basal bodies of mNSC or RPE1 cells and decline when these cells differentiate or resume growth. A high-throughput smFISH screen identifies two transcripts accumulating at centrosomes in quiescent cells, NIN and BICD2. In contrast to BICD2, the localization of NIN transcripts is EJC-dependent. NIN mRNA encodes a core component of centrosomes required for microtubule nucleation and anchoring. We find that EJC down-regulation impairs both pericentriolar material organization and ciliogenesis. An EJC-dependent mRNA trafficking towards centrosome and basal bodies might contribute to proper mNSC division and brain development. Exon junction complexes (EJCs) that mark untranslated mRNA are involved in transport, translation and nonsense-mediated mRNA decay. Here the authors show centrosomal localization of EJCs which appears to be required for both the localization of NIN mRNA around centrosomes and ciliogenesis.
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Affiliation(s)
- Oh Sung Kwon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Rahul Mishra
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Adham Safieddine
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Emeline Coleno
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Quentin Alasseur
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Marion Faucourt
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, University of Montpellier, CNRS, Montpellier, France
| | - Nathalie Spassky
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
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25
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Kweon H, Jung WB, Im GH, Ryoo J, Lee JH, Do H, Choi Y, Song YH, Jung H, Park H, Qiu LR, Ellegood J, Shim HJ, Yang E, Kim H, Lerch JP, Lee SH, Chung WS, Kim D, Kim SG, Kim E. Excitatory neuronal CHD8 in the regulation of neocortical development and sensory-motor behaviors. Cell Rep 2021; 34:108780. [PMID: 33626347 DOI: 10.1016/j.celrep.2021.108780] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 12/31/2022] Open
Abstract
CHD8 (chromodomain helicase DNA-binding protein 8) is a chromatin remodeler associated with autism spectrum disorders. Homozygous Chd8 deletion in mice leads to embryonic lethality, making it difficult to assess whether CHD8 regulates brain development and whether CHD8 haploinsufficiency-related macrocephaly reflects normal CHD8 functions. Here, we report that homozygous conditional knockout of Chd8 restricted to neocortical glutamatergic neurons causes apoptosis-dependent near-complete elimination of neocortical structures. These mice, however, display normal survival and hyperactivity, anxiolytic-like behavior, and increased social interaction. They also show largely normal auditory function and moderately impaired visual and motor functions but enhanced whisker-related somatosensory function. These changes accompany thalamic hyperactivity, revealed by 15.2-Tesla fMRI, and increased intrinsic excitability and decreased inhibitory synaptic transmission in thalamic ventral posterior medial (VPM) neurons involved in somatosensation. These results suggest that excitatory neuronal CHD8 critically regulates neocortical development through anti-apoptotic mechanisms, neocortical elimination distinctly affects cognitive behaviors and sensory-motor functions in mice, and Chd8 haploinsufficiency-related macrocephaly might represent compensatory responses.
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Affiliation(s)
- Hanseul Kweon
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Won Beom Jung
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Geun Ho Im
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea
| | - Jia Ryoo
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Joon-Hyuk Lee
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hogyeong Do
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Yeonsoo Choi
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - You-Hyang Song
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hwajin Jung
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Haram Park
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Lily R Qiu
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON M5T 3H7, Canada; Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford OX3 9DU, UK
| | - Jacob Ellegood
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON M5T 3H7, Canada; Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford OX3 9DU, UK
| | - Hyun-Ji Shim
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea
| | - Esther Yang
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul 02841, Korea
| | - Hyun Kim
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul 02841, Korea
| | - Jason P Lerch
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON M5T 3H7, Canada; Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford OX3 9DU, UK
| | - Seung-Hee Lee
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Won-Suk Chung
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Daesoo Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Seong-Gi Kim
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon 16419, Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea.
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea; Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon 34141, Korea.
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26
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McSweeney C, Dong F, Chen M, Vitale J, Xu L, Crowley N, Luscher B, Zou D, Mao Y. Full function of exon junction complex factor, Rbm8a, is critical for interneuron development. Transl Psychiatry 2020; 10:379. [PMID: 33154347 PMCID: PMC7644723 DOI: 10.1038/s41398-020-01065-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/16/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
The formation of the nervous system requires a balance between proliferation, differentiation, and migration of neural progenitors (NPs). Mutations in genes regulating development impede neurogenesis and lead to neuropsychiatric diseases, including autism spectrum disorders (ASDs) and schizophrenia (SZ). Recently, mutations in nonsense-mediated mRNA decay genes have been associated with ASDs, intellectual disability (ID), and SZ. Here, we examine the function of a gene in the exon junction complex, Rbm8a, in the cortical development. When Rbm8a is selectively knocked out in neural stem cells, the resulting mice exhibit microcephaly, early postnatal lethality, and altered distribution of excitatory neurons in the neocortex. Moreover, Rbm8a haploinsufficiency in the central nervous system decreases cell proliferation in the ganglionic eminences. Parvalbumin+ and neuropeptide Y+ interneurons in the cortex are significantly reduced, and distribution of interneurons are altered. Consistently, neurons in the cortex of conditional knockout (cKO) mice show a significant decrease in GABA frequency. Transcriptomic analysis revealed differentially expressed genes enriched in telencephalon development and mitosis. To further investigate the role of Rbm8a in interneuron differentiation, conditional KO of Rbm8a in NKX2.1 interneuron progenitor cells reduces progenitor proliferation and alters interneuron distributions. Taken together, these data reveal a critical role of Rbm8a in interneuron development, and establish that perturbation of this gene leads to profound cortical deficits.
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Affiliation(s)
- Colleen McSweeney
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Fengping Dong
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Miranda Chen
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Jessica Vitale
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Li Xu
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, University Park, PA 16802 USA ,grid.268505.c0000 0000 8744 8924Zhejiang Chinese Medical University, 310053 Hangzhou, Zhejiang China
| | - Nicole Crowley
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Bernhard Luscher
- grid.29857.310000 0001 2097 4281Department of Biology, Pennsylvania State University, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Donghua Zou
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, 530021, Nanning, Guangxi, China.
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
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27
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Griffin C, Saint-Jeannet JP. Spliceosomopathies: Diseases and mechanisms. Dev Dyn 2020; 249:1038-1046. [PMID: 32506634 DOI: 10.1002/dvdy.214] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
The spliceosome is a complex of RNA and proteins that function together to identify intron-exon junctions in precursor messenger-RNAs, splice out the introns, and join the flanking exons. Mutations in any one of the genes encoding the proteins that make up the spliceosome may result in diseases known as spliceosomopathies. While the spliceosome is active in all cell types, with the majority of the proteins presumably expressed ubiquitously, spliceosomopathies tend to be tissue-specific as a result of germ line or somatic mutations, with phenotypes affecting primarily the retina in retinitis pigmentosa, hematopoietic lineages in myelodysplastic syndromes, or the craniofacial skeleton in mandibulofacial dysostosis. Here we describe the major spliceosomopathies, review the proposed mechanisms underlying retinitis pigmentosa and myelodysplastic syndromes, and discuss how this knowledge may inform our understanding of craniofacial spliceosomopathies.
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Affiliation(s)
- Casey Griffin
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, USA
| | - Jean-Pierre Saint-Jeannet
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, USA
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28
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Gangras P, Gallagher TL, Parthun MA, Yi Z, Patton RD, Tietz KT, Deans NC, Bundschuh R, Amacher SL, Singh G. Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3'UTR intron-containing NMD targets. PLoS Genet 2020; 16:e1008830. [PMID: 32502192 PMCID: PMC7310861 DOI: 10.1371/journal.pgen.1008830] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 06/23/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
Many post-transcriptional mechanisms operate via mRNA 3'UTRs to regulate protein expression, and such controls are crucial for development. We show that homozygous mutations in two zebrafish exon junction complex (EJC) core genes rbm8a and magoh leads to muscle disorganization, neural cell death, and motor neuron outgrowth defects, as well as dysregulation of mRNAs subjected to nonsense-mediated mRNA decay (NMD) due to translation termination ≥ 50 nts upstream of the last exon-exon junction. Intriguingly, we find that EJC-dependent NMD also regulates a subset of transcripts that contain 3'UTR introns (3'UI) < 50 nts downstream of a stop codon. Some transcripts containing such stop codon-proximal 3'UI are also NMD-sensitive in cultured human cells and mouse embryonic stem cells. We identify 167 genes that contain a conserved proximal 3'UI in zebrafish, mouse and humans. foxo3b is one such proximal 3'UI-containing gene that is upregulated in zebrafish EJC mutant embryos, at both mRNA and protein levels, and loss of foxo3b function in EJC mutant embryos significantly rescues motor axon growth defects. These data are consistent with EJC-dependent NMD regulating foxo3b mRNA to control protein expression during zebrafish development. Our work shows that the EJC is critical for normal zebrafish development and suggests that proximal 3'UIs may serve gene regulatory function in vertebrates.
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Affiliation(s)
- Pooja Gangras
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Thomas L. Gallagher
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Michael A. Parthun
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Zhongxia Yi
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Robert D. Patton
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Physics, The Ohio State University, Ohio, United States of America
| | - Kiel T. Tietz
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Natalie C. Deans
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Physics, The Ohio State University, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Ohio, United States of America
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Ohio, United States of America
| | - Sharon L. Amacher
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Ohio, United States of America
- Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children’s Hospital, Ohio, United States of America
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
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29
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Lennox AL, Hoye ML, Jiang R, Johnson-Kerner BL, Suit LA, Venkataramanan S, Sheehan CJ, Alsina FC, Fregeau B, Aldinger KA, Moey C, Lobach I, Afenjar A, Babovic-Vuksanovic D, Bézieau S, Blackburn PR, Bunt J, Burglen L, Campeau PM, Charles P, Chung BHY, Cogné B, Curry C, D'Agostino MD, Di Donato N, Faivre L, Héron D, Innes AM, Isidor B, Keren B, Kimball A, Klee EW, Kuentz P, Küry S, Martin-Coignard D, Mirzaa G, Mignot C, Miyake N, Matsumoto N, Fujita A, Nava C, Nizon M, Rodriguez D, Blok LS, Thauvin-Robinet C, Thevenon J, Vincent M, Ziegler A, Dobyns W, Richards LJ, Barkovich AJ, Floor SN, Silver DL, Sherr EH. Pathogenic DDX3X Mutations Impair RNA Metabolism and Neurogenesis during Fetal Cortical Development. Neuron 2020; 106:404-420.e8. [PMID: 32135084 PMCID: PMC7331285 DOI: 10.1016/j.neuron.2020.01.042] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 11/05/2019] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
De novo germline mutations in the RNA helicase DDX3X account for 1%-3% of unexplained intellectual disability (ID) cases in females and are associated with autism, brain malformations, and epilepsy. Yet, the developmental and molecular mechanisms by which DDX3X mutations impair brain function are unknown. Here, we use human and mouse genetics and cell biological and biochemical approaches to elucidate mechanisms by which pathogenic DDX3X variants disrupt brain development. We report the largest clinical cohort to date with DDX3X mutations (n = 107), demonstrating a striking correlation between recurrent dominant missense mutations, polymicrogyria, and the most severe clinical outcomes. We show that Ddx3x controls cortical development by regulating neuron generation. Severe DDX3X missense mutations profoundly disrupt RNA helicase activity, induce ectopic RNA-protein granules in neural progenitors and neurons, and impair translation. Together, these results uncover key mechanisms underlying DDX3X syndrome and highlight aberrant RNA metabolism in the pathogenesis of neurodevelopmental disease.
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Affiliation(s)
- Ashley L Lennox
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ruiji Jiang
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Lindsey A Suit
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Charles J Sheehan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Fernando C Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Ching Moey
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Iryna Lobach
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alexandra Afenjar
- Centre de référence des malformations et maladies congénitales du cervelet et Département de génétique et embryologie médicale, APHP, Sorbonne Université, Hôpital Armand Trousseau, 75012 Paris, France
| | - Dusica Babovic-Vuksanovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jens Bunt
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Lydie Burglen
- Centre de référence des malformations et maladies congénitales du cervelet et Département de génétique et embryologie médicale, APHP, Sorbonne Université, Hôpital Armand Trousseau, 75012 Paris, France
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal and CHU Sainte-Justine, Montreal, QC, Canada
| | - Perrine Charles
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Cynthia Curry
- Genetic Medicine, University of California San Francisco/Fresno, Fresno, CA 93701, USA
| | - Maria Daniela D'Agostino
- Division of Medical Genetics, Departments of Specialized Medicine and Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Laurence Faivre
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, INSERM UMR 1231 GAD, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Delphine Héron
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Boris Keren
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Amy Kimball
- Harvey Institute of Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul Kuentz
- UMR-INSERM 1231 GAD, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | | | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Caroline Nava
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | - Diana Rodriguez
- Centre de Référence Neurogénétique & Service de Neurologie Pédiatrique, APHP, Sorbonne Université, Hôpital Armand Trousseau, 75012 Paris, France
| | - Lot Snijders Blok
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Christel Thauvin-Robinet
- Centre de référence Déficience Intellectuelle, INSERM UMR 1231 GAD, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Julien Thevenon
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, INSERM UMR 1231 GAD, CHU de Dijon et Université de Bourgogne, Dijon, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000 Nantes, France
| | | | - William Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Departments of Pediatrics and Neurology, University of Washington, Seattle, WA 98101, USA
| | - Linda J Richards
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia; The University of Queensland, School of Biomedical Sciences, Brisbane 4072, QLD, Australia
| | - A James Barkovich
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA.
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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30
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Kurosaki T, Popp MW, Maquat LE. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat Rev Mol Cell Biol 2020; 20:406-420. [PMID: 30992545 DOI: 10.1038/s41580-019-0126-2] [Citation(s) in RCA: 421] [Impact Index Per Article: 105.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is one of the best characterized and most evolutionarily conserved cellular quality control mechanisms. Although NMD was first found to target one-third of mutated, disease-causing mRNAs, it is now known to also target ~10% of unmutated mammalian mRNAs to facilitate appropriate cellular responses - adaptation, differentiation or death - to environmental changes. Mutations in NMD genes in humans are associated with intellectual disability and cancer. In this Review, we discuss how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal mRNAs to control the quantities of unmutated transcripts.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. .,Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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31
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Sheehan CJ, McMahon JJ, Serdar LD, Silver DL. Dosage-dependent requirements of Magoh for cortical interneuron generation and survival. Development 2020; 147:dev.182295. [PMID: 31857347 DOI: 10.1242/dev.182295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/30/2019] [Indexed: 12/15/2022]
Abstract
Embryonic interneuron development underlies cortical function and its disruption contributes to neurological disease. Yet the mechanisms by which viable interneurons are produced from progenitors remain poorly understood. Here, we demonstrate dosage-dependent requirements of the exon junction complex component Magoh for interneuron genesis in mouse. Conditional Magoh ablation from interneuron progenitors, but not post-mitotic neurons, depletes cortical interneuron number through adulthood, with increased severity in homozygotes. Using live imaging, we discover that Magoh deficiency delays progenitor mitotic progression in a dosage-sensitive fashion, with 40% of homozygous progenitors failing to divide. This shows that Magoh is required in progenitors for both generation and survival of newborn progeny. Transcriptome analysis implicates p53 signaling; moreover, p53 ablation in Magoh haploinsufficient progenitors rescues apoptosis, completely recovering interneuron number. In striking contrast, in Magoh homozygotes, p53 loss fails to rescue interneuron number and mitotic delay, further implicating mitotic defects in interneuron loss. Our results demonstrate that interneuron development is intimately dependent upon progenitor mitosis duration and uncover a crucial post-transcriptional regulator of interneuron fate relevant for neurodevelopmental pathologies.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Charles J Sheehan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - John J McMahon
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lucas D Serdar
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA .,Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.,Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 27710, USA
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32
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Kimball C, Powers K, Dustin J, Poirier V, Pellettieri J. The exon junction complex is required for stem and progenitor cell maintenance in planarians. Dev Biol 2020; 457:119-127. [PMID: 31557470 PMCID: PMC8544814 DOI: 10.1016/j.ydbio.2019.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/31/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022]
Abstract
Named for its assembly near exon-exon junctions during pre-mRNA splicing, the exon junction complex (EJC) regulates multiple aspects of RNA biochemistry, including export of spliced mRNAs from the nucleus and translation. Transcriptome analyses have revealed broad EJC occupancy of spliced metazoan transcripts, yet inhibition of core subunits has been linked to surprisingly specific phenotypes and a growing number of studies support gene-specific regulatory roles. Here we report results from a classroom-based RNAi screen revealing the EJC is necessary for regeneration in the planarian flatworm Schmidtea mediterranea. RNAi animals rapidly lost the stem and progenitor cells that drive formation of new tissue during both regeneration and cell turnover, but exhibited normal amputation-induced changes in gene expression in differentiated tissues. Together with previous reports that partial loss of EJC function causes stem cell defects in Drosophila and mice, our observations implicate the EJC as a conserved, posttranscriptional regulator of gene expression in stem cell lineages. This work also highlights the combined educational and scientific impacts of discovery-based research in the undergraduate biology curriculum.
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Affiliation(s)
- Casey Kimball
- Department of Biology, Keene State College, Keene, NH, USA
| | - Kaleigh Powers
- Department of Biology, Keene State College, Keene, NH, USA
| | - John Dustin
- Department of Biology, Keene State College, Keene, NH, USA
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33
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Translating neural stem cells to neurons in the mammalian brain. Cell Death Differ 2019; 26:2495-2512. [PMID: 31551564 DOI: 10.1038/s41418-019-0411-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/05/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
The mammalian neocortex underlies our perception of sensory information, performance of motor activities, and higher-order cognition. During mammalian embryogenesis, radial glial precursor cells sequentially give rise to diverse populations of excitatory cortical neurons, followed by astrocytes and oligodendrocytes. A subpopulation of these embryonic neural precursors persists into adulthood as neural stem cells, which give rise to inhibitory interneurons and glia. Although the intrinsic mechanisms instructing the genesis of these distinct progeny have been well-studied, most work to date has focused on transcriptional, epigenetic, and cell-cycle control. Recent studies, however, have shown that posttranscriptional mechanisms also regulate the cell fate choices of transcriptionally primed neural precursors during cortical development. These mechanisms are mediated primarily by RNA-binding proteins and microRNAs that coordinately regulate mRNA translation, stability, splicing, and localization. Together, these findings point to an extensive network of posttranscriptional control and provide insight into both normal cortical development and disease. They also add another layer of complexity to brain development and raise important biological questions for future investigation.
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34
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Bartkowska K, Tepper B, Turlejski K, Djavadian RL. Roles of the exon junction complex components in the central nervous system: a mini review. Rev Neurosci 2019; 29:817-824. [PMID: 29791316 DOI: 10.1515/revneuro-2017-0113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/22/2018] [Indexed: 01/02/2023]
Abstract
The exon junction complex (EJC) consists of four core proteins: Magoh, RNA-binding motif 8A (Rbm8a, also known as Y14), eukaryotic initiation factor 4A3 (eIF4A3, also known as DDX48), and metastatic lymph node 51 (MLN51, also known as Casc3 or Barentsz), which are involved in the regulation of many processes occurring between gene transcription and protein translation. Its main role is to assemble into spliceosomes at the exon-exon junction of mRNA during splicing. It is, therefore, a range of functions concerning post-splicing events such as mRNA translocation, translation, and nonsense-mediated mRNA decay (NMD). Apart from this, proteins of the EJC control the splicing of specific pre-mRNAs, for example, splicing of the mapk transcript. Recent studies support essential functions of EJC proteins in oocytes and, after fertilization, in all stages of zygote development, as well as the growth of the embryo, including the development of the nervous system. During the development of the central nervous system (CNS), the EJC controls mitosis, regulating both symmetric and asymmetric cell divisions. Reduced levels of EJC components cause microcephaly. In the adult brain, Y14 and eIF4A3 appear to be involved in synaptic plasticity and in learning and memory. In this review, we focus on the involvement of EJC components in brain development and its functioning under normal conditions.
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Affiliation(s)
- Katarzyna Bartkowska
- Department of Molecular and Cellular Biology, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw, Poland
| | - Beata Tepper
- Department of Molecular and Cellular Biology, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw, Poland
| | - Kris Turlejski
- Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszynski University, Warsaw, Poland
| | - Ruzanna L Djavadian
- Department of Molecular and Cellular Biology, Nencki Institute of Experimental Biology Polish Academy of Sciences, Warsaw 02-093, Poland
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Nonsense-mediated RNA decay in the brain: emerging modulator of neural development and disease. Nat Rev Neurosci 2019; 19:715-728. [PMID: 30410025 DOI: 10.1038/s41583-018-0079-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Steady-state RNA levels are controlled by the balance between RNA synthesis and RNA turnover. A selective RNA turnover mechanism that has received recent attention in neurons is nonsense-mediated RNA decay (NMD). NMD has been shown to influence neural development, neural stem cell differentiation decisions, axon guidance and synaptic plasticity. In humans, NMD factor gene mutations cause some forms of intellectual disability and are associated with neurodevelopmental disorders, including schizophrenia and autism spectrum disorder. Impairments in NMD are linked to neurodegenerative disorders, including amyotrophic lateral sclerosis. We discuss these findings, their clinical implications and challenges for the future.
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36
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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37
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Chuang TW, Lu CC, Su CH, Wu PY, Easwvaran S, Lee CC, Kuo HC, Hung KY, Lee KM, Tsai CY, Tarn WY. The RNA Processing Factor Y14 Participates in DNA Damage Response and Repair. iScience 2019; 13:402-415. [PMID: 30901577 PMCID: PMC6428943 DOI: 10.1016/j.isci.2019.03.005] [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: 08/19/2018] [Revised: 01/08/2019] [Accepted: 03/04/2019] [Indexed: 02/01/2023] Open
Abstract
DNA repair deficiency leads to genome instability and hence human disease. Depletion of the RNA processing factor Y14/RBM8A in cultured cells or Rbm8a haplodeficiency in the developing mouse cortex results in the accumulation of DNA damage. Y14 depletion differentially affected the expression of DNA damage response (DDR) factors and induced R-loops, both of which threaten genomic stability. Immunoprecipitation coupled with mass spectrometry revealed DDR factors as potential Y14-interacting partners. Further results confirmed that Y14 interacts with Ku and several DDR factors in an ATM-dependent manner. Y14 co-fractionated with Ku in chromatin-enriched fractions and further accumulated on chromatin upon DNA damage. Y14 knockdown delayed recruitment of DDR factors to DNA damage sites and formation of γH2AX foci and also led to Ku retention on chromatin. Accordingly, Y14 depletion compromised the efficiency of DNA end joining. Therefore Y14 likely plays a direct role in DNA damage repair via its interaction with DDR factors. Y14 deficiency leads to DNA damage accumulation Y14 depletion disturbs DNA damage response and induces R-loops Y14 promotes Ku70/80 recruitment to DNA damage sites Y14 participates in DNA damage repair
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Affiliation(s)
- Tzu-Wei Chuang
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Chia-Chen Lu
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan; Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Chun-Hao Su
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Pei-Yu Wu
- Institute of Biochemistry, Academia Sinica, Taipei, Taiwan
| | - Sarasvathi Easwvaran
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Chi-Chieh Lee
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Hung-Che Kuo
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuan-Yang Hung
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuo-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
| | - Ching-Yen Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan.
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38
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Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection. Nat Microbiol 2019; 4:985-995. [PMID: 30833725 PMCID: PMC6533143 DOI: 10.1038/s41564-019-0375-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022]
Abstract
West Nile virus (WNV) is an emerging mosquito-borne flavivirus, related to dengue virus and Zika virus. To gain insight into host pathways involved in WNV infection, we performed a systematic affinity-tag purification mass spectrometry (AP-MS) study to identify 259 WNV-interacting human proteins. RNAi screening revealed 26 genes that both interact with WNV proteins and influence WNV infection. We found that WNV, dengue and Zika virus capsids interact with a conserved subset of proteins that impact infection. These include the exon-junction complex (EJC) recycling factor, PYM1, which is antiviral against all three viruses. The EJC has roles in nonsense-mediated decay (NMD), and we found that both the EJC and NMD are antiviral and the EJC protein RBM8A directly binds WNV RNA. To counteract this, flavivirus infection inhibits NMD and the capsid-PYM1 interaction interferes with EJC protein function and localization. Depletion of PYM1 attenuates RBM8A binding to viral RNA, suggesting that WNV sequesters PYM1 to protect viral RNA from decay. Together, these data suggest a complex interplay between the virus and host in regulating NMD and the EJC.
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39
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Ma Q, Tatsuno T, Nakamura Y, Ishigaki Y. The stability of Magoh and Y14 depends on their heterodimer formation and nuclear localization. Biochem Biophys Res Commun 2019; 511:631-636. [PMID: 30826064 DOI: 10.1016/j.bbrc.2019.02.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 01/10/2023]
Abstract
Reduced expression of the Y14 gene is a cause of Thrombocytopenia-absent radius (TAR) syndrome. This gene contains a conserved RNA recognition motif (RRM) in the central region and nuclear localization/export sequences (NLS/NES) in the N-terminal. Y14 and Magoh proteins form tight heterodimers and are the core of exon junction complexes (EJCs), which mediate various processes of mRNA metabolism after transcription. In this report, we found that protein expression levels of exogenously expressed Magoh L136R and Y14 L118R (leucine-to-arginine substitution at amino acid residue 136 and 118 respectively, that results in the formation of the complex being lost) are lower than their wild-types. This reduction is likely caused by protein levels, as no difference in mRNA levels was detected. Meanwhile, a cycloheximide chase assay determined that the degradation rates of Magoh L136R and Y14 L118R were faster than their wild-types. Both Y14 L118R and Magoh L136R lost the ability to form heterodimers with corresponding wild-type proteins. However, Y14 L118R is able to still localize in the nucleus which causes the stability of Y14 L118R to be higher than Magoh L136R. These results reveal that the stability of Magoh and Y14 is not only dependent on the heterodimer structure, but also dependent on nuclear localization.
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Affiliation(s)
- Qingfeng Ma
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan; Department of Clinical Laboratory, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Takanori Tatsuno
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan
| | - Yuka Nakamura
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan
| | - Yasuhito Ishigaki
- Medical Research Institute, Kanazawa Medical University, Uchinada, Kahoku, Japan.
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40
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Vevera J, Zarrei M, Hartmannová H, Jedličková I, Mušálková D, Přistoupilová A, Oliveriusová P, Trešlová H, Nosková L, Hodaňová K, Stránecký V, Jiřička V, Preiss M, Příhodová K, Šaligová J, Wei J, Woodbury-Smith M, Bleyer AJ, Scherer SW, Kmoch S. Rare copy number variation in extremely impulsively violent males. GENES BRAIN AND BEHAVIOR 2018; 18:e12536. [DOI: 10.1111/gbb.12536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jan Vevera
- Department of Psychiatry; Faculty of Medicine and University Hospital in Pilsen, Charles University; Prague Czech Republic
- Department of Psychiatry, First Faculty of Medicine; Charles University and General University Hospital in Prague; Prague Czech Republic
- Institute for Postgraduate Medical Education; Prague Czech Republic
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Petra Oliveriusová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Václav Jiřička
- Prison Service of the Czech Republic, Directorate General; Department of Psychology; Prague Czech Republic
| | - Marek Preiss
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
- Psychology Department; University of New York in Prague; Prague Czech Republic
| | - Kateřina Příhodová
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Jana Šaligová
- Children's Faculty Hospital; Department of Pediatrics and Adolescent Medicine; Kosice Slovakia
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine of Pavel Jozef Šafárik University Kosice; Kosice Slovakia
| | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Neuroscience, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary; Newcastle upon Tyne UK
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
- Section on Nephrology, Wake Forest School of Medicine; Medical Center Blvd.; Winston-Salem North Carolina USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Department of Molecular Genetics and McLaughlin Centre; University of Toronto; Toronto Ontario Canada
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
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41
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Chen YC, Chang YW, Huang YS. Dysregulated Translation in Neurodevelopmental Disorders: An Overview of Autism-Risk Genes Involved in Translation. Dev Neurobiol 2018; 79:60-74. [PMID: 30430754 DOI: 10.1002/dneu.22653] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/17/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Abstract
Regulated local translation-whereby specific mRNAs are transported and localized in subcellular domains where they are translated in response to regional signals-allows for remote control of gene expression to concentrate proteins in subcellular compartments. Neurons are highly polarized cells with unique features favoring local control for axonal pathfinding and synaptic plasticity, which are key processes involved in constructing functional circuits in the developing brain. Neurodevelopmental disorders are caused by genetic or environmental factors that disturb the nervous system's development during prenatal and early childhood periods. The growing list of genetic mutations that affect mRNA translation raises the question of whether aberrant translatomes in individuals with neurodevelopmental disorders share common molecular features underlying their stereotypical phenotypes and, vice versa, cause a certain degree of phenotypic heterogeneity. Here, we briefly give an overview of the role of local translation during neuronal development. We take the autism-risk gene list and discuss the molecules that (perhaps) are involved in mRNA transport and translation. Both exaggerated and suppressed translation caused by mutations in those genes have been identified or suggested. Finally, we discuss some proof-of-principle regimens for use in autism mouse models to correct dysregulated translation.
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Affiliation(s)
- Yan-Chu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Wei Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
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42
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Hetman M, Slomnicki LP. Ribosomal biogenesis as an emerging target of neurodevelopmental pathologies. J Neurochem 2018; 148:325-347. [PMID: 30144322 DOI: 10.1111/jnc.14576] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 12/17/2022]
Abstract
Development of the nervous system is carried out by complex gene expression programs that are regulated at both transcriptional and translational level. In addition, quality control mechanisms such as the TP53-mediated apoptosis or neuronal activity-stimulated survival ensure successful neurogenesis and formation of functional circuitries. In the nucleolus, production of ribosomes is essential for protein synthesis. In addition, it participates in chromatin organization and regulates the TP53 pathway via the ribosomal stress response. Its tight regulation is required for maintenance of genomic integrity. Mutations in several ribosomal components and trans-acting ribosomal biogenesis factors result in neurodevelopmental syndromes that present with microcephaly, autism, intellectual deficits and/or progressive neurodegeneration. Furthermore, ribosomal biogenesis is perturbed by exogenous factors that disrupt neurodevelopment including alcohol or Zika virus. In this review, we present recent literature that argues for a role of dysregulated ribosomal biogenesis in pathogenesis of various neurodevelopmental syndromes. We also discuss potential mechanisms through which such dysregulation may lead to cellular pathologies of the developing nervous system including insufficient proliferation and/or loss of neuroprogenitors cells, apoptosis of immature neurons, altered neuronal morphogenesis, and neurodegeneration.
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Affiliation(s)
- Michal Hetman
- Departments of Neurological Surgery, Kentucky Spinal Cord Injury Research Center, Louisville, Kentucky, USA.,Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Lukasz P Slomnicki
- Departments of Neurological Surgery, Kentucky Spinal Cord Injury Research Center, Louisville, Kentucky, USA
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43
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Abstract
Zika virus (ZIKV) is a significant global health threat, as infection has been linked to serious neurological complications, including microcephaly. Using a human stem cell-derived neural progenitor model system, we find that a critical cellular quality control process called the nonsense-mediated mRNA decay (NMD) pathway is disrupted during ZIKV infection. Importantly, disruption of the NMD pathway is a known cause of microcephaly and other neurological disorders. We further identify an interaction between the capsid protein of ZIKV and up-frameshift protein 1 (UPF1), the master regulator of NMD, and show that ZIKV capsid targets UPF1 for degradation. Together, these results offer a new mechanism for how ZIKV infection can cause neuropathology in the developing brain. Zika virus (ZIKV) infection of neural progenitor cells (NPCs) in utero is associated with neurological disorders, such as microcephaly, but a detailed molecular understanding of ZIKV-induced pathogenesis is lacking. Here we show that in vitro ZIKV infection of human cells, including NPCs, causes disruption of the nonsense-mediated mRNA decay (NMD) pathway. NMD is a cellular mRNA surveillance mechanism that is required for normal brain size in mice. Using affinity purification-mass spectrometry, we identified multiple cellular NMD factors that bind to the viral capsid protein, including the central NMD regulator up-frameshift protein 1 (UPF1). Endogenous UPF1 interacted with the ZIKV capsid protein in coimmunoprecipitation experiments, and capsid expression posttranscriptionally downregulated UPF1 protein levels, a process that we confirmed occurs during ZIKV infection. Cellular fractionation studies show that the ZIKV capsid protein specifically targets nuclear UPF1 for degradation via the proteasome. A further decrease in UPF1 levels by RNAi significantly enhanced ZIKV infection in NPC cultures, consistent with a model in which NMD restricts ZIKV infection in the fetal brain. We propose that ZIKV, via the capsid protein, has evolved a strategy to lower UPF1 levels and dampen antiviral activities of NMD, which in turn contributes to neuropathology in vivo.
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44
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Zhou Y, Dong F, Mao Y. Control of CNS functions by RNA-binding proteins in neurological diseases. ACTA ACUST UNITED AC 2018; 4:301-313. [PMID: 30410853 DOI: 10.1007/s40495-018-0140-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarizes recent studies on the molecular mechanisms of RNA binding proteins (RBPs) that control neurological functions and pathogenesis in various neurodevelopmental and neurodegenerative diseases, including autism spectrum disorders, schizophrenia, Alzheimer's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and spinocerebellar ataxia. Recent Findings RBPs are critical players in gene expression that regulate every step of posttranscriptional modifications. Recent genome-wide approaches revealed that many proteins associate with RNA, but do not contain any known RNA binding motifs. Additionally, many causal and risk genes of neurodevelopmental and neurodegenerative diseases are RBPs. Development of high-throughput sequencing methods has mapped out the fingerprints of RBPs on transcripts and provides unprecedented potential to discover new mechanisms of neurological diseases. Insights into how RBPs modulate neural development are important for designing effective therapies for numerous neurodevelopmental and neurodegenerative diseases. Summary RBPs have diverse mechanisms for modulating RNA processing and, thereby, controlling neurogenesis. Understanding the role of disease-associated RBPs in neurogenesis is vital for developing novel treatments for neurological diseases.
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Affiliation(s)
- Yijing Zhou
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Fengping Dong
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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45
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Slomnicki LP, Chung DH, Parker A, Hermann T, Boyd NL, Hetman M. Ribosomal stress and Tp53-mediated neuronal apoptosis in response to capsid protein of the Zika virus. Sci Rep 2017; 7:16652. [PMID: 29192272 PMCID: PMC5709411 DOI: 10.1038/s41598-017-16952-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
We report here that in rat and human neuroprogenitor cells as well as rat embryonic cortical neurons Zika virus (ZIKV) infection leads to ribosomal stress that is characterized by structural disruption of the nucleolus. The anti-nucleolar effects were most pronounced in postmitotic neurons. Moreover, in the latter system, nucleolar presence of ZIKV capsid protein (ZIKV-C) was associated with ribosomal stress and apoptosis. Deletion of 22 C-terminal residues of ZIKV-C prevented nucleolar localization, ribosomal stress and apoptosis. Consistent with a casual relationship between ZIKV-C-induced ribosomal stress and apoptosis, ZIKV-C-overexpressing neurons were protected by loss-of-function manipulations targeting the ribosomal stress effector Tp53 or knockdown of the ribosomal stress mediator RPL11. Finally, capsid protein of Dengue virus, but not West Nile virus, induced ribosomal stress and apoptosis. Thus, anti-nucleolar and pro-apoptotic effects of protein C are flavivirus-species specific. In the case of ZIKV, capsid protein-mediated ribosomal stress may contribute to neuronal death, neurodevelopmental disruption and microcephaly.
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Affiliation(s)
- Lukasz P Slomnicki
- Kentucky Spinal Cord Injury Research Center and the Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Dong-Hoon Chung
- Center of Predictive Medicine and the Department of Microbiology & Immunology, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Austin Parker
- Kentucky Spinal Cord Injury Research Center and the Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Taylor Hermann
- Kentucky Spinal Cord Injury Research Center and the Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Nolan L Boyd
- Cardiovascular Innovation Institute and the Department of Physiology, University of Louisville, Louisville, Kentucky, 40292, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center and the Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, 40292, USA.
- Pharmacology & Toxicology, University of Louisville, Louisville, Kentucky, 40292, USA.
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46
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Popovitchenko T, Rasin MR. Transcriptional and Post-Transcriptional Mechanisms of the Development of Neocortical Lamination. Front Neuroanat 2017; 11:102. [PMID: 29170632 PMCID: PMC5684109 DOI: 10.3389/fnana.2017.00102] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022] Open
Abstract
The neocortex is a laminated brain structure that is the seat of higher cognitive capacity and responses, long-term memory, sensory and emotional functions, and voluntary motor behavior. Proper lamination requires that progenitor cells give rise to a neuron, that the immature neuron can migrate away from its mother cell and past other cells, and finally that the immature neuron can take its place and adopt a mature identity characterized by connectivity and gene expression; thus lamination proceeds through three steps: genesis, migration, and maturation. Each neocortical layer contains pyramidal neurons that share specific morphological and molecular characteristics that stem from their prenatal birth date. Transcription factors are dynamic proteins because of the cohort of downstream factors that they regulate. RNA-binding proteins are no less dynamic, and play important roles in every step of mRNA processing. Indeed, recent screens have uncovered post-transcriptional mechanisms as being integral regulatory mechanisms to neocortical development. Here, we summarize major aspects of neocortical laminar development, emphasizing transcriptional and post-transcriptional mechanisms, with the aim of spurring increased understanding and study of its intricacies.
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Affiliation(s)
- Tatiana Popovitchenko
- Neuroscience and Cell Biology, Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Mladen-Roko Rasin
- Neuroscience and Cell Biology, Robert Wood Johnson Medical School, New Brunswick, NJ, United States
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47
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Miller EE, Kobayashi GS, Musso CM, Allen M, Ishiy FAA, de Caires LC, Goulart E, Griesi-Oliveira K, Zechi-Ceide RM, Richieri-Costa A, Bertola DR, Passos-Bueno MR, Silver DL. EIF4A3 deficient human iPSCs and mouse models demonstrate neural crest defects that underlie Richieri-Costa-Pereira syndrome. Hum Mol Genet 2017; 26:2177-2191. [PMID: 28334780 DOI: 10.1093/hmg/ddx078] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/28/2017] [Indexed: 11/14/2022] Open
Abstract
Biallelic loss-of-function mutations in the RNA-binding protein EIF4A3 cause Richieri-Costa-Pereira syndrome (RCPS), an autosomal recessive condition mainly characterized by craniofacial and limb malformations. However, the pathogenic cellular mechanisms responsible for this syndrome are entirely unknown. Here, we used two complementary approaches, patient-derived induced pluripotent stem cells (iPSCs) and conditional Eif4a3 mouse models, to demonstrate that defective neural crest cell (NCC) development explains RCPS craniofacial abnormalities. RCPS iNCCs have decreased migratory capacity, a distinct phenotype relative to other craniofacial disorders. Eif4a3 haploinsufficient embryos presented altered mandibular process fusion and micrognathia, thus recapitulating the most penetrant phenotypes of the syndrome. These defects were evident in either ubiquitous or NCC-specific Eif4a3 haploinsufficient animals, demonstrating an autonomous requirement of Eif4a3 in NCCs. Notably, RCPS NCC-derived mesenchymal stem-like cells (nMSCs) showed premature bone differentiation, a phenotype paralleled by premature clavicle ossification in Eif4a3 haploinsufficient embryos. Likewise, nMSCs presented compromised in vitro chondrogenesis, and Meckel's cartilage was underdeveloped in vivo. These findings indicate novel and essential requirements of EIF4A3 for NCC migration and osteochondrogenic differentiation during craniofacial development. Altogether, complementary use of iPSCs and mouse models pinpoint unique cellular mechanisms by which EIF4A3 mutation causes RCPS, and provide a paradigm to study craniofacial disorders.
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Affiliation(s)
- Emily E Miller
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Gerson S Kobayashi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Camila M Musso
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Miranda Allen
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Felipe A A Ishiy
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Luiz Carlos de Caires
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Ernesto Goulart
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Karina Griesi-Oliveira
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Roseli M Zechi-Ceide
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies (HRCA), University of São Paulo, Bauru, Brazil
| | - Antonio Richieri-Costa
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies (HRCA), University of São Paulo, Bauru, Brazil
| | - Debora R Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology.,Department of Cell Biology.,Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
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48
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Lennox AL, Mao H, Silver DL. RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28837264 DOI: 10.1002/wdev.290] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Embryonic development is a critical period during which neurons of the brain are generated and organized. In the developing cerebral cortex, this requires complex processes of neural progenitor proliferation, neuronal differentiation, and migration. Each step relies upon highly regulated control of gene expression. In particular, RNA splicing, stability, localization, and translation have emerged as key post-transcriptional regulatory nodes of mouse corticogenesis. Trans-regulators of RNA metabolism, including microRNAs (miRs) and RNA-binding proteins (RBPs), orchestrate diverse steps of cortical development. These trans-factors function either individually or cooperatively to influence RNAs, often of similar classes, termed RNA regulons. New technological advances raise the potential for an increasingly sophisticated understanding of post-transcriptional control in the developing neocortex. Many RNA-binding factors are also implicated in neurodevelopmental diseases of the cortex. Therefore, elucidating how RBPs and miRs converge to influence mRNA expression in progenitors and neurons will give valuable insights into mechanisms of cortical development and disease. WIREs Dev Biol 2018, 7:e290. doi: 10.1002/wdev.290 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory RNA Nervous System Development > Vertebrates: Regional Development Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease.
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Affiliation(s)
- Ashley L Lennox
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Hanqian Mao
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
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49
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Lu CC, Lee CC, Tseng CT, Tarn WY. Y14 governs p53 expression and modulates DNA damage sensitivity. Sci Rep 2017; 7:45558. [PMID: 28361991 PMCID: PMC5374521 DOI: 10.1038/srep45558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/27/2017] [Indexed: 01/29/2023] Open
Abstract
Y14 is a core component of the exon junction complex (EJC), while it also exerts cellular functions independent of the EJC. Depletion of Y14 causes G2/M arrest, DNA damage and apoptosis. Here we show that knockdown of Y14 induces the expression of an alternative spliced isoform of p53, namely p53β, in human cells. Y14, in the context of the EJC, inhibited aberrant exon inclusion during the splicing of p53 pre-mRNA, and thus prevent p53β expression. The anti-cancer agent camptothecin specifically suppressed p53β induction. Intriguingly, both depletion and overexpression of Y14 increased overall p53 protein levels, suggesting that Y14 governs the quality and quantity control of p53. Moreover, Y14 depletion unexpectedly reduced p21 protein levels, which in conjunction with aberrant p53 expression accordingly increased cell sensitivity to genotoxic agents. This study establishes a direct link between Y14 and p53 expression and suggests a function for Y14 in DNA damage signaling.
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Affiliation(s)
- Chia-Chen Lu
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chi-Chieh Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ching-Tzu Tseng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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50
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Disruptions in asymmetric centrosome inheritance and WDR62-Aurora kinase B interactions in primary microcephaly. Sci Rep 2017; 7:43708. [PMID: 28272472 PMCID: PMC5341122 DOI: 10.1038/srep43708] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/26/2017] [Indexed: 12/11/2022] Open
Abstract
Recessive mutations in WD repeat domain 62 (WDR62) cause microcephaly and a wide spectrum of severe brain malformations. Disruption of the mouse ortholog results in microcephaly underlain by reduced proliferation of neocortical progenitors during late neurogenesis, abnormalities in asymmetric centrosome inheritance leading to neuronal migration delays, and altered neuronal differentiation. Spindle pole localization of WDR62 and mitotic progression are defective in patient-derived fibroblasts, which, similar to mouse neocortical progenitors, transiently arrest at prometaphase. Expression of WDR62 is closely correlated with components of the chromosome passenger complex (CPC), a key regulator of mitosis. Wild type WDR62, but not disease-associated mutant forms, interacts with the CPC core enzyme Aurora kinase B and staining of CPC components at centromeres is altered in patient-derived fibroblasts. Our findings demonstrate critical and diverse functions of WDR62 in neocortical development and provide insight into the mechanisms by which its disruption leads to a plethora of structural abnormalities.
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