301
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Li Y, Stockton ME, Bhuiyan I, Eisinger BE, Gao Y, Miller JL, Bhattacharyya A, Zhao X. MDM2 inhibition rescues neurogenic and cognitive deficits in a mouse model of fragile X syndrome. Sci Transl Med 2017; 8:336ra61. [PMID: 27122614 DOI: 10.1126/scitranslmed.aad9370] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/08/2016] [Indexed: 12/15/2022]
Abstract
Fragile X syndrome, the most common form of inherited intellectual disability, is caused by loss of the fragile X mental retardation protein (FMRP). However, the mechanism remains unclear, and effective treatment is lacking. We show that loss of FMRP leads to activation of adult mouse neural stem cells (NSCs) and a subsequent reduction in the production of neurons. We identified the ubiquitin ligase mouse double minute 2 homolog (MDM2) as a target of FMRP. FMRP regulates Mdm2 mRNA stability, and loss of FMRP resulted in elevated MDM2 mRNA and protein. Further, we found that increased MDM2 expression led to reduced P53 expression in adult mouse NSCs, leading to alterations in NSC proliferation and differentiation. Treatment with Nutlin-3, a small molecule undergoing clinical trials for treating cancer, specifically inhibited the interaction of MDM2 with P53, and rescued neurogenic and cognitive deficits in FMRP-deficient mice. Our data reveal a potential regulatory role for FMRP in the balance between adult NSC activation and quiescence, and identify a potential new treatment for fragile X syndrome.
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Affiliation(s)
- Yue Li
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA. Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Ismat Bhuiyan
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Brian E Eisinger
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA. Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yu Gao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA. Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jessica L Miller
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA. Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA.
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302
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Munshi K, Pawlowski K, Gonzalez-Heydrich J, Picker JD. Review of Salient Investigational Drugs for the Treatment of Fragile X Syndrome. J Child Adolesc Psychopharmacol 2017; 27:850-863. [PMID: 28475355 DOI: 10.1089/cap.2016.0200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability, in addition to being the commonest diagnosable cause of autism. The identification of the biochemical mechanism underlying this disorder has provided amenable targets for therapy. This review aims to provide an overview of investigational drug therapies for FXS. METHODS The authors carried out a search of clinical and preclinical trials for FXS in PubMed and on the U.S. National Institutes of Health index of clinical trials ( www.clinicaltrials.gov ). We limited our review to Phase II trials or more preliminary and reviewed the associated publications for these studies, complemented by a review of the literature on PubMed. RESULTS The review of the preclinical, Phase I, and Phase II trials of agents with therapeutic potential in FXS revolves around an understanding of the putative pathways in the pathogenesis of FXS. While there is significant overlap between some of these pathways, the agents can be categorized as modulators of the metabotropic glutamate receptor system, GABAergic agents, and miscellaneous modulators affecting other pathways. CONCLUSION As trials involving agents targeting different aspects of the molecular biology proceed, common themes have emerged. With the great hope came great disappointment as the initial trials failed to demonstrate sufficient significance. In particular, the differences in outcome between the animal models and humans have highlighted the unique challenges of carrying out trials in these cognitively and behaviorally challenged individuals, as well as a dearth of clinically relevant outcome measures for use in medication trials. However, in reviewing and reframing the studies of the last decade, many important lessons have been learned, which will ultimately have a greater impact on therapeutic research in the field of developmental delay as a whole.
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Affiliation(s)
- Kaizad Munshi
- 1 Department of Psychiatry, Boston Children's Hospital , Boston, Massachusetts.,2 Harvard Medical School , Boston, Massachusetts
| | - Katherine Pawlowski
- 3 Division of Genetics and Genomics, Boston Children's Hospital , Boston, Massachusetts.,4 Division of Developmental Medicine, Department of Medicine, Boston Children's Hospital , Boston, Massachusetts
| | - Joseph Gonzalez-Heydrich
- 1 Department of Psychiatry, Boston Children's Hospital , Boston, Massachusetts.,2 Harvard Medical School , Boston, Massachusetts
| | - Jonathan D Picker
- 1 Department of Psychiatry, Boston Children's Hospital , Boston, Massachusetts.,2 Harvard Medical School , Boston, Massachusetts.,3 Division of Genetics and Genomics, Boston Children's Hospital , Boston, Massachusetts
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303
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Lowther C, Merico D, Costain G, Waserman J, Boyd K, Noor A, Speevak M, Stavropoulos DJ, Wei J, Lionel AC, Marshall CR, Scherer SW, Bassett AS. Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia. Genome Med 2017; 9:105. [PMID: 29187259 PMCID: PMC5708103 DOI: 10.1186/s13073-017-0488-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Schizophrenia is a severe psychiatric disorder associated with IQ deficits. Rare copy number variations (CNVs) have been established to play an important role in the etiology of schizophrenia. Several of the large rare CNVs associated with schizophrenia have been shown to negatively affect IQ in population-based controls where no major neuropsychiatric disorder is reported. The aim of this study was to examine the diagnostic yield of microarray testing and the functional impact of genome-wide rare CNVs in a community ascertained cohort of adults with schizophrenia and low (< 85) or average (≥ 85) IQ. Methods We recruited 546 adults of European ancestry with schizophrenia from six community psychiatric clinics in Canada. Each individual was assigned to the low or average IQ group based on standardized tests and/or educational attainment. We used rigorous methods to detect genome-wide rare CNVs from high-resolution microarray data. We compared the burden of rare CNVs classified as pathogenic or as a variant of unknown significance (VUS) between each of the IQ groups and the genome-wide burden and functional impact of rare CNVs after excluding individuals with a pathogenic CNV. Results There were 39/546 (7.1%; 95% confidence interval [CI] = 5.2–9.7%) schizophrenia participants with at least one pathogenic CNV detected, significantly more of whom were from the low IQ group (odds ratio [OR] = 5.01 [2.28–11.03], p = 0.0001). Secondary analyses revealed that individuals with schizophrenia and average IQ had the lowest yield of pathogenic CNVs (n = 9/325; 2.8%), followed by those with borderline intellectual functioning (n = 9/130; 6.9%), non-verbal learning disability (n = 6/29; 20.7%), and co-morbid intellectual disability (n = 15/62; 24.2%). There was no significant difference in the burden of rare CNVs classified as a VUS between any of the IQ subgroups. There was a significantly (p=0.002) increased burden of rare genic duplications in individuals with schizophrenia and low IQ that persisted after excluding individuals with a pathogenic CNV. Conclusions Using high-resolution microarrays we were able to demonstrate for the first time that the burden of pathogenic CNVs in schizophrenia differs significantly between IQ subgroups. The results of this study have implications for clinical practice and may help inform future rare variant studies of schizophrenia using next-generation sequencing technologies. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0488-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chelsea Lowther
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Daniele Merico
- Deep Genomics Inc, Toronto, ON, Canada.,The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gregory Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Kerry Boyd
- Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Abdul Noor
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Marsha Speevak
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anath C Lionel
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1. .,Institute of Medical Science, University of Toronto, Toronto, ON, Canada. .,Toronto General Research Institute, University Health Network, Toronto, ON, Canada. .,Cambell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada. .,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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304
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Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions. Molecules 2017; 22:molecules22122027. [PMID: 29186753 PMCID: PMC6149999 DOI: 10.3390/molecules22122027] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins and proteins with intrinsically disordered regions have been shown to be highly prevalent in disease. Furthermore, disease-causing expansions of the regions containing tandem amino acid repeats often push repetitive proteins towards formation of irreversible aggregates. In fact, in disease-relevant proteins, the increased repeat length often positively correlates with the increased aggregation efficiency and the increased disease severity and penetrance, being negatively correlated with the age of disease onset. The major categories of repeat extensions involved in disease include poly-glutamine and poly-alanine homorepeats, which are often times located in the intrinsically disordered regions, as well as repeats in non-coding regions of genes typically encoding proteins with ordered structures. Repeats in such non-coding regions of genes can be expressed at the mRNA level. Although they can affect the expression levels of encoded proteins, they are not translated as parts of an affected protein and have no effect on its structure. However, in some cases, the repetitive mRNAs can be translated in a non-canonical manner, generating highly repetitive peptides of different length and amino acid composition. The repeat extension-caused aggregation of a repetitive protein may represent a pivotal step for its transformation into a proteotoxic entity that can lead to pathology. The goals of this article are to systematically analyze molecular mechanisms of the proteinopathies caused by the poly-glutamine and poly-alanine homorepeat expansion, as well as by the polypeptides generated as a result of the microsatellite expansions in non-coding gene regions and to examine the related proteins. We also present results of the analysis of the prevalence and functional roles of intrinsic disorder in proteins associated with pathological repeat expansions.
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305
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Smidak R, Sialana FJ, Kristofova M, Stojanovic T, Rajcic D, Malikovic J, Feyissa DD, Korz V, Hoeger H, Wackerlig J, Mechtcheriakova D, Lubec G. Reduced Levels of the Synaptic Functional Regulator FMRP in Dentate Gyrus of the Aging Sprague-Dawley Rat. Front Aging Neurosci 2017; 9:384. [PMID: 29218006 PMCID: PMC5703695 DOI: 10.3389/fnagi.2017.00384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/09/2017] [Indexed: 11/15/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) encoded by Fragile X mental retardation 1 (FMR1) gene is a RNA-binding regulator of mRNA translation, transport and stability with multiple targets responsible for proper synaptic function. Epigenetic silencing of FMR1 gene expression leads to the development of Fragile X syndrome (FXS) that is characterized by intellectual disability and other behavioral problems including autism. In the rat FXS model, the lack of FMRP caused a deficit in hippocampal-dependent memory. However, the hippocampal changes of FMRP in aging rats are not fully elucidated. The current study addresses the changes in FMRP levels in dentate gyrus (DG) from young (17 weeks) and aging (22 months) Sprague – Dawley rats. The aging animal group showed significant decline in spatial reference memory. Protein samples from five rats per each group were analyzed by quantitative proteomic analysis resulting in 153 significantly changed proteins. FMRP showed significant reduction in aging animals which was confirmed by immunoblotting and immunofluorescence microscopy. Furthermore, bioinformatic analysis of the differential protein dataset revealed several functionally related protein groups with individual interactions with FMRP. These include high representation of the RNA translation and processing machinery connected to FMRP and other RNA-binding regulators including CAPRIN1, the members of Pumilio (PUM) and CUG-BP, Elav-like (CELF) family, and YTH N(6)-methyladenosine RNA-binding proteins (YTHDF). The results of the current study point to the important role of FMRP and regulation of RNA processing in the rat DG and memory decline during the aging process.
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Affiliation(s)
- Roman Smidak
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Fernando J Sialana
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Martina Kristofova
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Tamara Stojanovic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Dragana Rajcic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Jovana Malikovic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Daniel D Feyissa
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Volker Korz
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Vienna, Austria
| | - Harald Hoeger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Vienna, Austria
| | - Judit Wackerlig
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Diana Mechtcheriakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
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306
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Benhalevy D, Gupta SK, Danan CH, Ghosal S, Sun HW, Kazemier HG, Paeschke K, Hafner M, Juranek SA. The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation. Cell Rep 2017; 18:2979-2990. [PMID: 28329689 DOI: 10.1016/j.celrep.2017.02.080] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 07/18/2016] [Accepted: 02/27/2017] [Indexed: 12/16/2022] Open
Abstract
The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs. CNBP preferentially bound G-rich elements in the target mRNA coding sequences, most of which were previously found to form G-quadruplex and other stable structures in vitro. Functional analyses, including RNA sequencing, ribosome profiling, and quantitative mass spectrometry, revealed that CNBP binding did not influence target mRNA abundance but rather increased their translational efficiency. Considering that CNBP binding prevented G-quadruplex structure formation in vitro, we hypothesize that CNBP is supporting translation by resolving stable structures on mRNAs.
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Affiliation(s)
- Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Sanjay K Gupta
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Charles H Danan
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Suman Ghosal
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biostatistics and Datamining Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands
| | - Katrin Paeschke
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA.
| | - Stefan A Juranek
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands.
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307
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Arguello AE, DeLiberto AN, Kleiner RE. RNA Chemical Proteomics Reveals the N 6-Methyladenosine (m 6A)-Regulated Protein-RNA Interactome. J Am Chem Soc 2017; 139:17249-17252. [PMID: 29140688 DOI: 10.1021/jacs.7b09213] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Epitranscriptomic RNA modifications can regulate mRNA function; however, there is a major gap in our understanding of the biochemical mechanisms mediating their effects. Here, we develop a chemical proteomics approach relying upon photo-cross-linking with synthetic diazirine-containing RNA probes and quantitative proteomics to profile RNA-protein interactions regulated by N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic RNA. In addition to identifying YTH domain-containing proteins and ALKBH5, known interactors of this modification, we find that FMR1 and LRPPRC, two proteins associated with human disease, "read" this modification. Surprisingly, we also find that m6A disrupts RNA binding by the stress granule proteins G3BP1/2, USP10, CAPRIN1, and RBM42. Our work provides a general strategy for interrogating the interactome of RNA modifications and reveals the biochemical mechanisms underlying m6A function in the cell.
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Affiliation(s)
- A Emilia Arguello
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Amanda N DeLiberto
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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308
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Chu M, Novak SM, Cover C, Wang AA, Chinyere IR, Juneman EB, Zarnescu DC, Wong PK, Gregorio CC. Increased Cardiac Arrhythmogenesis Associated With Gap Junction Remodeling With Upregulation of RNA-Binding Protein FXR1. Circulation 2017; 137:605-618. [PMID: 29101288 DOI: 10.1161/circulationaha.117.028976] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/23/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Gap junction remodeling is well established as a consistent feature of human heart disease involving spontaneous ventricular arrhythmia. The mechanisms responsible for gap junction remodeling that include alterations in the distribution of, and protein expression within, gap junctions are still debated. Studies reveal that multiple transcriptional and posttranscriptional regulatory pathways are triggered in response to cardiac disease, such as those involving RNA-binding proteins. The expression levels of FXR1 (fragile X mental retardation autosomal homolog 1), an RNA-binding protein, are critical to maintain proper cardiac muscle function; however, the connection between FXR1 and disease is not clear. METHODS To identify the mechanisms regulating gap junction remodeling in cardiac disease, we sought to identify the functional properties of FXR1 expression, direct targets of FXR1 in human left ventricle dilated cardiomyopathy (DCM) biopsy samples and mouse models of DCM through BioID proximity assay and RNA immunoprecipitation, how FXR1 regulates its targets through RNA stability and luciferase assays, and functional consequences of altering the levels of this important RNA-binding protein through the analysis of cardiac-specific FXR1 knockout mice and mice injected with 3xMyc-FXR1 adeno-associated virus. RESULTS FXR1 expression is significantly increased in tissue samples from human and mouse models of DCM via Western blot analysis. FXR1 associates with intercalated discs, and integral gap junction proteins Cx43 (connexin 43), Cx45 (connexin 45), and ZO-1 (zonula occludens-1) were identified as novel mRNA targets of FXR1 by using a BioID proximity assay and RNA immunoprecipitation. Our findings show that FXR1 is a multifunctional protein involved in translational regulation and stabilization of its mRNA targets in heart muscle. In addition, introduction of 3xMyc-FXR1 via adeno-associated virus into mice leads to the redistribution of gap junctions and promotes ventricular tachycardia, showing the functional significance of FXR1 upregulation observed in DCM. CONCLUSIONS In DCM, increased FXR1 expression appears to play an important role in disease progression by regulating gap junction remodeling. Together this study provides a novel function of FXR1, namely, that it directly regulates major gap junction components, contributing to proper cell-cell communication in the heart.
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Affiliation(s)
- Miensheng Chu
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Stefanie Mares Novak
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Cathleen Cover
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Anne A Wang
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | | | | | | | - Pak Kin Wong
- University of Arizona, Tucson. Department of Biomedical Engineering at Pennsylvania State University, University Park (P.K.W.)
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
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309
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Lapointe CP, Preston MA, Wilinski D, Saunders HAJ, Campbell ZT, Wickens M. Architecture and dynamics of overlapped RNA regulatory networks. RNA (NEW YORK, N.Y.) 2017; 23:1636-1647. [PMID: 28768715 PMCID: PMC5648032 DOI: 10.1261/rna.062687.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/28/2017] [Indexed: 06/07/2023]
Abstract
A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is known about the architecture or dynamics of overlapped networks. We focused on three proteins with similar structures and related RNA-binding specificities-Puf3p, Puf4p, and Puf5p of S. cerevisiae Using RNA Tagging, we identified a "super-network" comprised of four subnetworks: Puf3p, Puf4p, and Puf5p subnetworks, and one controlled by both Puf4p and Puf5p. The architecture of individual subnetworks, and thus the super-network, is determined by competition among particular PUF proteins to bind mRNAs, their affinities for binding elements, and the abundances of the proteins. The super-network responds dramatically: The remaining network can either expand or contract. These strikingly opposite outcomes are determined by an interplay between the relative abundance of the RNAs and proteins, and their affinities for one another. The diverse interplay between overlapping RNA-protein networks provides versatile opportunities for regulation and evolution.
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Affiliation(s)
- Christopher P Lapointe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Melanie A Preston
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Daniel Wilinski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Harriet A J Saunders
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Zachary T Campbell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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310
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Lovastatin suppresses hyperexcitability and seizure in Angelman syndrome model. Neurobiol Dis 2017; 110:12-19. [PMID: 29097328 DOI: 10.1016/j.nbd.2017.10.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 10/27/2017] [Indexed: 11/22/2022] Open
Abstract
Epilepsy is prevalent and often medically intractable in Angelman syndrome (AS). AS mouse model (Ube3am-/p+) shows reduced excitatory neurotransmission but lower seizure threshold. The neural mechanism linking the synaptic dysfunction to the seizure remains elusive. We show that the local circuits of Ube3am-/p+in vitro are hyperexcitable and display a unique epileptiform activity, a phenomenon that is reminiscent of the finding in fragile X syndrome (FXS) mouse model. Similar to the FXS model, lovastatin suppressed the epileptiform activity and audiogenic seizures in Ube3am-/p+. The in vitro model of Ube3am-/p+ is valuable for dissection of neural mechanism and epilepsy drug screening in vivo.
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311
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Zhang K, Li YJ, Guo Y, Zheng KY, Yang Q, Yang L, Wang XS, Song Q, Chen T, Zhuo M, Zhao MG. Elevated progranulin contributes to synaptic and learning deficit due to loss of fragile X mental retardation protein. Brain 2017; 140:3215-3232. [DOI: 10.1093/brain/awx265] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/20/2017] [Indexed: 01/09/2023] Open
Affiliation(s)
- Kun Zhang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
| | - Yu-jiao Li
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
| | - Yanyan Guo
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
| | - Kai-yin Zheng
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
| | - Qi Yang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
| | - Le Yang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
| | - Xin-shang Wang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
| | - Qian Song
- Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi’an Jiaotong University, Xi’an, 710032, China
| | - Tao Chen
- Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi’an Jiaotong University, Xi’an, 710032, China
- Department of Anatomy, Histology and Embryology and K.K. Leung Brain Research Center, Fourth Military Medical University, Xi’an, 710032, China
| | - Min Zhuo
- Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi’an Jiaotong University, Xi’an, 710032, China
| | - Ming-gao Zhao
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi’an, 710032l, China
- Center for Neuron and Disease, Frontier Institutes of Life Science and of Science and Technology, Xi’an Jiaotong University, Xi’an, 710032, China
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312
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Abstract
Fragile X syndrome (FXS) is the leading inherited form of intellectual disability and autism spectrum disorder, and patients can present with severe behavioural alterations, including hyperactivity, impulsivity and anxiety, in addition to poor language development and seizures. FXS is a trinucleotide repeat disorder, in which >200 repeats of the CGG motif in FMR1 leads to silencing of the gene and the consequent loss of its product, fragile X mental retardation 1 protein (FMRP). FMRP has a central role in gene expression and regulates the translation of potentially hundreds of mRNAs, many of which are involved in the development and maintenance of neuronal synaptic connections. Indeed, disturbances in neuroplasticity is a key finding in FXS animal models, and an imbalance in inhibitory and excitatory neuronal circuits is believed to underlie many of the clinical manifestations of this disorder. Our knowledge of the proteins that are regulated by FMRP is rapidly growing, and this has led to the identification of multiple targets for therapeutic intervention, some of which have already moved into clinical trials or clinical practice.
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313
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Savisaar R, Hurst LD. Both Maintenance and Avoidance of RNA-Binding Protein Interactions Constrain Coding Sequence Evolution. Mol Biol Evol 2017; 34:1110-1126. [PMID: 28138077 PMCID: PMC5400389 DOI: 10.1093/molbev/msx061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
While the principal force directing coding sequence (CDS) evolution is selection on protein function, to ensure correct gene expression CDSs must also maintain interactions with RNA-binding proteins (RBPs). Understanding how our genes are shaped by these RNA-level pressures is necessary for diagnostics and for improving transgenes. However, the evolutionary impact of the need to maintain RBP interactions remains unresolved. Are coding sequences constrained by the need to specify RBP binding motifs? If so, what proportion of mutations are affected? Might sequence evolution also be constrained by the need not to specify motifs that might attract unwanted binding, for instance because it would interfere with exon definition? Here, we have scanned human CDSs for motifs that have been experimentally determined to be recognized by RBPs. We observe two sets of motifs-those that are enriched over nucleotide-controlled null and those that are depleted. Importantly, the depleted set is enriched for motifs recognized by non-CDS binding RBPs. Supporting the functional relevance of our observations, we find that motifs that are more enriched are also slower-evolving. The net effect of this selection to preserve is a reduction in the over-all rate of synonymous evolution of 2-3% in both primates and rodents. Stronger motif depletion, on the other hand, is associated with stronger selection against motif gain in evolution. The challenge faced by our CDSs is therefore not only one of attracting the right RBPs but also of avoiding the wrong ones, all while also evolving under selection pressures related to protein structure.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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314
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Fujita R, Zismanov V, Jacob JM, Jamet S, Asiev K, Crist C. Fragile X mental retardation protein regulates skeletal muscle stem cell activity by regulating the stability of Myf5 mRNA. Skelet Muscle 2017; 7:18. [PMID: 28882193 PMCID: PMC5588675 DOI: 10.1186/s13395-017-0136-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/01/2017] [Indexed: 01/08/2023] Open
Abstract
Background Regeneration of adult tissues relies on adult stem cells that are primed to enter a differentiation program, while typically remaining quiescent. In mouse skeletal muscle, these features are reconciled by multiple translational control mechanisms that ensure primed muscle stem cells (MuSCs) are not activated. In quiescent MuSCs, this concept is illustrated by reversible microRNA silencing of Myf5 translation, mediated by microRNA-31 and fragile X mental retardation protein (FMRP). Methods In this work, we take advantage of FMRP knockout (Fmr1−/−) mice to support the role for FMRP in maintaining stem cell properties of the MuSC. We compare the activity of MuSCs in vivo after acute injury and engraftment, as well as ex vivo during culture. We use RNA immunoprecipitation and 3’UTR poly-adenine (poly(A)) length assays to assess the impact of FMRP on the stability of transcripts for myogenic regulatory factors. Results We show that RNA-binding FMRP is required to maintain the MuSC pool. More specifically, FMRP is required for stem cell properties of muscle stem cells, which include MuSC capacity to prime the myogenic program, their self-renewal, and their capacity to efficiently regenerate muscle. We provide evidence that FMRP regulation of MuSC activity occurs in part by the capacity of FMRP to directly bind Myf5 transcripts and impact rates of Myf5 deadenylation. Conclusions Our results provide further evidence supporting a role for post-transcriptional silencing platforms by RNA-binding proteins in maintaining stemness properties of adult stem cells. In addition, deregulated MuSC activity in the absence of Fmr1 may have implications for fragile X syndrome, which is associated with muscle hypotonia during infancy.
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Affiliation(s)
- Ryo Fujita
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, H3A 1B1, Canada
| | - Victoria Zismanov
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, H3A 1B1, Canada
| | - Jean-Marie Jacob
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, H3A 1B1, Canada.,Current address: Unité Stroma, Inflammation and Tissue Repair, Institut Pasteur, Paris, 75724, France
| | - Solène Jamet
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
| | - Krum Asiev
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada.,Department of Radiation Oncology, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
| | - Colin Crist
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada. .,Department of Human Genetics, McGill University, Montreal, Quebec, H3A 1B1, Canada.
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315
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Filippini A, Bonini D, Lacoux C, Pacini L, Zingariello M, Sancillo L, Bosisio D, Salvi V, Mingardi J, La Via L, Zalfa F, Bagni C, Barbon A. Absence of the Fragile X Mental Retardation Protein results in defects of RNA editing of neuronal mRNAs in mouse. RNA Biol 2017. [PMID: 28640668 PMCID: PMC5785225 DOI: 10.1080/15476286.2017.1338232] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The fragile X syndrome (FXS), the most common form of inherited intellectual disability, is due to the absence of FMRP, a protein regulating RNA metabolism. Recently, an unexpected function of FMRP in modulating the activity of Adenosine Deaminase Acting on RNA (ADAR) enzymes has been reported both in Drosophila and Zebrafish. ADARs are RNA-binding proteins that increase transcriptional complexity through a post-transcriptional mechanism called RNA editing. To evaluate the ADAR2-FMRP interaction in mammals we analyzed several RNA editing re-coding sites in the fmr1 knockout (KO) mice. Ex vivo and in vitro analysis revealed that absence of FMRP leads to an increase in the editing levels of brain specific mRNAs, indicating that FMRP might act as an inhibitor of editing activity. Proximity Ligation Assay (PLA) in mouse primary cortical neurons and in non-neuronal cells revealed that ADAR2 and FMRP co-localize in the nucleus. The ADAR2-FMRP co-localization was further observed by double-immunogold Electron Microscopy (EM) in the hippocampus. Moreover, ADAR2-FMRP interaction appeared to be RNA independent. Because changes in the editing pattern are associated with neuropsychiatric and neurodevelopmental disorders, we propose that the increased editing observed in the fmr1-KO mice might contribute to the FXS molecular phenotypes.
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Affiliation(s)
- Alice Filippini
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Daniela Bonini
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Caroline Lacoux
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy
| | - Laura Pacini
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy
| | - Maria Zingariello
- c Department of Medicine , Campus Bio-Medico University , via Álvaro del Portillo 21, Rome , Italy
| | - Laura Sancillo
- d Department of Medicine and Aging Sciences, Section of Human Morphology , University G. D'Annunzio of Chieti-Pescara , Chieti , Italy
| | - Daniela Bosisio
- e Immunology Unit; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Valentina Salvi
- e Immunology Unit; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Jessica Mingardi
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Luca La Via
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
| | - Francesca Zalfa
- c Department of Medicine , Campus Bio-Medico University , via Álvaro del Portillo 21, Rome , Italy
| | - Claudia Bagni
- b Department of Biomedicine and Prevention , University of Rome Tor Vergata , Rome , Italy.,f VIB Center for the Biology of Disease and Center for Human Genetics , Leuven , Belgium.,g Department of Fundamental Neuroscience , University of Lausanne , Lausanne , Switzerland
| | - Alessandro Barbon
- a Biology and Genetic Division; Department of Molecular and Translational Medicine; University of Brescia ; Brescia , Italy
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316
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N 6-methyladenosine (m 6A) recruits and repels proteins to regulate mRNA homeostasis. Nat Struct Mol Biol 2017; 24:870-878. [PMID: 28869609 DOI: 10.1038/nsmb.3462] [Citation(s) in RCA: 379] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022]
Abstract
RNA modifications are integral to the regulation of RNA metabolism. One abundant mRNA modification is N6-methyladenosine (m6A), which affects various aspects of RNA metabolism, including splicing, translation and degradation. Current knowledge about the proteins recruited to m6A to carry out these molecular processes is still limited. Here we describe comprehensive and systematic mass-spectrometry-based screening of m6A interactors in various cell types and sequence contexts. Among the main findings, we identified G3BP1 as a protein that is repelled by m6A and positively regulates mRNA stability in an m6A-regulated manner. Furthermore, we identified FMR1 as a sequence-context-dependent m6A reader, thus revealing a connection between an mRNA modification and an autism spectrum disorder. Collectively, our data represent a rich resource and shed further light on the complex interplay among m6A, m6A interactors and mRNA homeostasis.
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317
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Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning. Cell Syst 2017; 5:212-220.e6. [DOI: 10.1016/j.cels.2017.08.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/27/2017] [Accepted: 08/04/2017] [Indexed: 01/16/2023]
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318
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Dendritic transport of tick-borne flavivirus RNA by neuronal granules affects development of neurological disease. Proc Natl Acad Sci U S A 2017; 114:9960-9965. [PMID: 28847946 DOI: 10.1073/pnas.1704454114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neurological diseases caused by encephalitic flaviviruses are severe and associated with high levels of mortality. However, little is known about the detailed mechanisms of viral replication and pathogenicity in the brain. Previously, we reported that the genomic RNA of tick-borne encephalitis virus (TBEV), a member of the genus Flavivirus, is transported and replicated in the dendrites of neurons. In the present study, we analyzed the transport mechanism of the viral genome to dendrites. We identified specific sequences of the 5' untranslated region of TBEV genomic RNA that act as a cis-acting element for RNA transport. Mutated TBEV with impaired RNA transport in dendrites caused a reduction in neurological symptoms in infected mice. We show that neuronal granules, which regulate the transport and local translation of dendritic mRNAs, are involved in TBEV genomic RNA transport. TBEV genomic RNA bound an RNA-binding protein of neuronal granules and disturbed the transport of dendritic mRNAs. These results demonstrated a neuropathogenic virus hijacking the neuronal granule system for the transport of viral genomic RNA in dendrites, resulting in severe neurological disease.
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319
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Tian Y, Zhang ZC, Han J. Drosophila Studies on Autism Spectrum Disorders. Neurosci Bull 2017; 33:737-746. [PMID: 28795356 DOI: 10.1007/s12264-017-0166-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/23/2017] [Indexed: 02/07/2023] Open
Abstract
In the past decade, numerous genes associated with autism spectrum disorders (ASDs) have been identified. These genes encode key regulators of synaptogenesis, synaptic function, and synaptic plasticity. Drosophila is a prominent model system for ASD studies to define novel genes linked to ASDs and decipher their molecular roles in synaptogenesis, synaptic function, synaptic plasticity, and neural circuit assembly and consolidation. Here, we review Drosophila studies on ASD genes that regulate synaptogenesis, synaptic function, and synaptic plasticity through modulating chromatin remodeling, transcription, protein synthesis and degradation, cytoskeleton dynamics, and synaptic scaffolding.
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Affiliation(s)
- Yao Tian
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China
| | - Zi Chao Zhang
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China
| | - Junhai Han
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.
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320
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Fan Y, Yue J, Xiao M, Han-Zhang H, Wang YV, Ma C, Deng Z, Li Y, Yu Y, Wang X, Niu S, Hua Y, Weng Z, Atadja P, Li E, Xiang B. FXR1 regulates transcription and is required for growth of human cancer cells with TP53/FXR2 homozygous deletion. eLife 2017; 6:26129. [PMID: 28767039 PMCID: PMC5595435 DOI: 10.7554/elife.26129] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/01/2017] [Indexed: 11/25/2022] Open
Abstract
Tumor suppressor p53 prevents cell transformation by inducing apoptosis and other responses. Homozygous TP53 deletion occurs in various types of human cancers for which no therapeutic strategies have yet been reported. TCGA database analysis shows that the TP53 homozygous deletion locus mostly exhibits co-deletion of the neighboring gene FXR2, which belongs to the Fragile X gene family. Here, we demonstrate that inhibition of the remaining family member FXR1 selectively blocks cell proliferation in human cancer cells containing homozygous deletion of both TP53 and FXR2 in a collateral lethality manner. Mechanistically, in addition to its RNA-binding function, FXR1 recruits transcription factor STAT1 or STAT3 to gene promoters at the chromatin interface and regulates transcription thus, at least partially, mediating cell proliferation. Our study anticipates that inhibition of FXR1 is a potential therapeutic approach to targeting human cancers harboring TP53 homozygous deletion. Healthy human cells employ many tricks to avoid becoming cancerous. For example, they produce proteins known as tumor suppressors, which sense if a cell shows early signs of cancer and instruct the cell to die. A gene known as TP53 produces one of the most important tumor suppressor proteins, and this gene is inactive or missing in many types of human cancer. Treating cancers that have completely lost the TP53 gene is particularly difficult. One way to develop new treatments for these conditions would be to target other proteins that these cancers need to survive; but these proteins first need to be identified. Fan et al. have now identified one such protein in human cancer cells lacking TP53. Searching databases of DNA sequences from human cancer cells revealed that those without the TP53 gene often also lose a neighboring gene called FXR2. Cancer cells survive without FXR2 because a similar gene, called FXR1, can compensate. Fan et al. therefore decided to experimentally lower the activity of the FXR1 gene and, as expected, cancer cells without TP53 and FXR2 stopped growing. Normal cells, on the other hand, were unaffected by the deletion of the FXR1 gene since FXR2 is still there. This phenomenon, in which cancer cells become vulnerable after the loss of certain genes but only because they have already lost important tumor suppressors, is called “collateral lethality”. Further experiments showed that the protein encoded by FXR1 coordinates with other proteins to activate genes that contribute to cell growth. These findings suggest new ways to treat human cancers that have lost TP53. For example, if scientists can find small molecules that inhibit the protein encoded by FXR1 and show that these molecules can block the growth of tumors lacking TP53 and FXR2, this could eventually lead to a new anticancer drug. However, like any new drug, these small molecule inhibitors would also need to be extensively tested before they could be taken into human clinical trials.
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Affiliation(s)
- Yichao Fan
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Jiao Yue
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Mengtao Xiao
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Han Han-Zhang
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Yao Vickie Wang
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Chun Ma
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Zhilin Deng
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Yingxiang Li
- Department of Bioinformatics, Tongji University, Shanghai, China
| | - Yanyan Yu
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Xinghao Wang
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Shen Niu
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Youjia Hua
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Zhiping Weng
- Department of Bioinformatics, Tongji University, Shanghai, China
| | - Peter Atadja
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - En Li
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Bin Xiang
- Epigenetic Discovery, China Novartis Institutes for BioMedical Research, Shanghai, China
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321
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Singh T, Walters JTR, Johnstone M, Curtis D, Suvisaari J, Torniainen M, Rees E, Iyegbe C, Blackwood D, McIntosh AM, Kirov G, Geschwind D, Murray RM, Di Forti M, Bramon E, Gandal M, Hultman CM, Sklar P, Palotie A, Sullivan PF, O'Donovan MC, Owen MJ, Barrett JC. The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability. Nat Genet 2017; 49:1167-1173. [PMID: 28650482 PMCID: PMC5533219 DOI: 10.1038/ng.3903] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
By performing a meta-analysis of rare coding variants in whole-exome sequences from 4,133 schizophrenia cases and 9,274 controls, de novo mutations in 1,077 family trios, and copy number variants from 6,882 cases and 11,255 controls, we show that individuals with schizophrenia carry a significant burden of rare, damaging variants in 3,488 genes previously identified as having a near-complete depletion of loss-of-function variants. In patients with schizophrenia who also have intellectual disability, this burden is concentrated in risk genes associated with neurodevelopmental disorders. After excluding known risk genes for neurodevelopmental disorders, a significant rare variant burden persists in other genes intolerant of loss-of-function variants; although this effect is notably stronger in patients with both schizophrenia and intellectual disability, it is also seen in patients with schizophrenia who do not have intellectual disability. Together, our results show that rare, damaging variants contribute to the risk of schizophrenia both with and without intellectual disability and support an overlap of genetic risk between schizophrenia and other neurodevelopmental disorders.
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Affiliation(s)
- Tarjinder Singh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, Cambridge, UK
| | - James T. R. Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Mandy Johnstone
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK
| | - David Curtis
- University College London (UCL) Genetics Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
- Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK
| | - Jaana Suvisaari
- National Institute for Health and Welfare (THL), Helsinki FI-00271, Finland
| | - Minna Torniainen
- National Institute for Health and Welfare (THL), Helsinki FI-00271, Finland
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Conrad Iyegbe
- Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, UK
| | - Douglas Blackwood
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK
| | - Andrew M. McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
| | - Georg Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Daniel Geschwind
- UCLA David Geffen School of Medicine, Los Angeles, California 90095, USA
| | - Robin M. Murray
- Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, UK
| | - Marta Di Forti
- Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, UK
| | - Elvira Bramon
- Division of Psychiatry, University College London, Charles Bell House, Riding House Street, London W1W 7EJ, UK
| | - Michael Gandal
- UCLA David Geffen School of Medicine, Los Angeles, California 90095, USA
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | | | | | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014 Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge MA 02132, USA
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177 Stockholm, Sweden
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, 27599-7264, USA
| | - Michael C. O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Michael J. Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, Cambridge, UK
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322
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McAninch DS, Heinaman AM, Lang CN, Moss KR, Bassell GJ, Rita Mihailescu M, Evans TL. Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR. MOLECULAR BIOSYSTEMS 2017; 13:1448-1457. [PMID: 28612854 PMCID: PMC5544254 DOI: 10.1039/c7mb00070g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
G quadruplex structures have been predicted by bioinformatics to form in the 5'- and 3'-untranslated regions (UTRs) of several thousand mature mRNAs and are believed to play a role in translation regulation. Elucidation of these roles has primarily been focused on the 3'-UTR, with limited focus on characterizing the G quadruplex structures and functions in the 5'-UTR. Investigation of the affinity and specificity of RNA binding proteins for 5'-UTR G quadruplexes and the resulting regulatory effects have also been limited. Among the mRNAs predicted to form a G quadruplex structure within the 5'-UTR is the survival motor neuron domain containing 1 (SMNDC1) mRNA, encoding a protein that is critical to the spliceosome. Additionally, this mRNA has been identified as a potential target of the fragile X mental retardation protein (FMRP), whose loss of expression leads to fragile X syndrome. FMRP is an RNA binding protein involved in translation regulation that has been shown to bind mRNA targets that form G quadruplex structures. In this study we have used biophysical methods to investigate G quadruplex formation in the 5'-UTR of SMNDC1 mRNA and analyzed its interactions with FMRP. Our results show that SMNDC1 mRNA 5'-UTR forms an intramolecular, parallel G quadruplex structure comprised of three G quartet planes, which is bound specifically by FMRP both in vitro and in mouse brain lysates. These findings suggest a model by which FMRP might regulate the translation of a subset of its mRNA targets by recognizing the G quadruplex structure present in their 5'-UTR, and affecting their accessibility by the protein synthesis machinery.
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Affiliation(s)
- Damian S McAninch
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
| | - Ashley M Heinaman
- Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
| | - Cara N Lang
- Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
| | - Kathryn R Moss
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
| | - Timothy L Evans
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA. and Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, Pennsylvania 15904, USA
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323
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Sakano H, Zorio DAR, Wang X, Ting YS, Noble WS, MacCoss MJ, Rubel EW, Wang Y. Proteomic analyses of nucleus laminaris identified candidate targets of the fragile X mental retardation protein. J Comp Neurol 2017; 525:3341-3359. [PMID: 28685837 DOI: 10.1002/cne.24281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/23/2017] [Accepted: 07/04/2017] [Indexed: 12/17/2022]
Abstract
The avian nucleus laminaris (NL) is a brainstem nucleus necessary for binaural processing, analogous in structure and function to the mammalian medial superior olive. In chickens (Gallus gallus), NL is a well-studied model system for activity-dependent neural plasticity. Its neurons have bipolar extension of dendrites, which receive segregated inputs from two ears and display rapid and compartment-specific reorganization in response to unilateral changes in auditory input. More recently, fragile X mental retardation protein (FMRP), an RNA-binding protein that regulates local protein translation, has been shown to be enriched in NL dendrites, suggesting its potential role in the structural dynamics of these dendrites. To explore the molecular role of FMRP in this nucleus, we performed proteomic analysis of NL, using micro laser capture and liquid chromatography tandem mass spectrometry. We identified 657 proteins, greatly represented in pathways involved in mitochondria, translation and metabolism, consistent with high levels of activity of NL neurons. Of these, 94 are potential FMRP targets, by comparative analysis with previously proposed FMRP targets in mammals. These proteins are enriched in pathways involved in cellular growth, cellular trafficking and transmembrane transport. Immunocytochemistry verified the dendritic localization of several proteins in NL. Furthermore, we confirmed the direct interaction of FMRP with one candidate, RhoC, by in vitro RNA binding assays. In summary, we provide a database of highly expressed proteins in NL and in particular a list of potential FMRP targets, with the goal of facilitating molecular characterization of FMRP signaling in future studies.
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Affiliation(s)
- Hitomi Sakano
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology-Head and Neck Surgery, University of Washington, School of Medicine, Seattle, Washington
| | - Diego A R Zorio
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida
| | - Xiaoyu Wang
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida
| | - Ying S Ting
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Edwin W Rubel
- Virginia Merrill Bloedel Hearing Research Center, Department of Otolaryngology-Head and Neck Surgery, University of Washington, School of Medicine, Seattle, Washington
| | - Yuan Wang
- Department of Biomedical Sciences, Florida State University, Tallahassee, Florida.,Program in Neuroscience, Florida State University, Tallahassee, Florida
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324
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Vidaki M, Drees F, Saxena T, Lanslots E, Taliaferro MJ, Tatarakis A, Burge CB, Wang ET, Gertler FB. A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons. Neuron 2017; 95:608-622.e5. [PMID: 28735747 DOI: 10.1016/j.neuron.2017.06.048] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 05/17/2017] [Accepted: 06/29/2017] [Indexed: 12/16/2022]
Abstract
During neuronal development, local mRNA translation is required for axon guidance and synaptogenesis, and dysregulation of this process contributes to multiple neurodevelopmental and cognitive disorders. However, regulation of local protein synthesis in developing axons remains poorly understood. Here, we uncover a novel role for the actin-regulatory protein Mena in the formation of a ribonucleoprotein complex that involves the RNA-binding proteins HnrnpK and PCBP1 and regulates local translation of specific mRNAs in developing axons. We find that translation of dyrk1a, a Down syndrome- and autism spectrum disorders-related gene, is dependent on Mena, both in steady-state conditions and upon BDNF stimulation. We identify hundreds of additional mRNAs that associate with the Mena complex, suggesting that it plays broader role(s) in post-transcriptional gene regulation. Our work establishes a dual role for Mena in neurons, providing a potential link between regulation of actin dynamics and local translation.
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Affiliation(s)
- Marina Vidaki
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Frauke Drees
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tanvi Saxena
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erwin Lanslots
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew J Taliaferro
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Antonios Tatarakis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric T Wang
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Frank B Gertler
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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325
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Cheng GR, Li XY, Xiang YD, Liu D, McClintock SM, Zeng Y. The implication of AMPA receptor in synaptic plasticity impairment and intellectual disability in fragile X syndrome. Physiol Res 2017; 66:715-727. [PMID: 28730825 DOI: 10.33549/physiolres.933473] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fragile X syndrome (FXS) is the most frequently inherited form of intellectual disability and prevalent single-gene cause of autism. A priority of FXS research is to determine the molecular mechanisms underlying the cognitive and social functioning impairments in humans and the FXS mouse model. Glutamate ionotropic alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors (AMPARs) mediate a majority of fast excitatory neurotransmission in the central nervous system and are critically important for nearly all aspects of brain function, including neuronal development, synaptic plasticity, and learning and memory. Both preclinical and clinical studies have indicated that expression, trafficking, and functions of AMPARs are altered and result in altered synapse development and plasticity, cognitive impairment, and poor mental health in FXS. In this review, we discuss the contribution of AMPARs to disorders of FXS by highlighting recent research advances with a specific focus on change in AMPARs expression, trafficking, and dependent synaptic plasticity. Since changes in synaptic strength underlie the basis of learning, development, and disease, we suggest that the current knowledge base of AMPARs has reached a unique point to permit a comprehensive re-evaluation of their roles in FXS.
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Affiliation(s)
- Gui-Rong Cheng
- Brain and Cognition Research Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan, China, Hubei Key Laboratory of Hazard Identification and Control for Occupational Disease, Wuhan, China.
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326
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Dysregulation of mRNA Localization and Translation in Genetic Disease. J Neurosci 2017; 36:11418-11426. [PMID: 27911744 DOI: 10.1523/jneurosci.2352-16.2016] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 11/21/2022] Open
Abstract
RNA-binding proteins (RBPs) acting at various steps in the post-transcriptional regulation of gene expression play crucial roles in neuronal development and synaptic plasticity. Genetic mutations affecting several RBPs and associated factors lead to diverse neurological symptoms, as characterized by neurodevelopmental and neuropsychiatric disorders, neuromuscular and neurodegenerative diseases, and can often be multisystemic diseases. We will highlight the physiological roles of a few specific proteins in molecular mechanisms of cytoplasmic mRNA regulation, and how these processes are dysregulated in genetic disease. Recent advances in computational biology and genomewide analysis, integrated with diverse experimental approaches and model systems, have provided new insights into conserved mechanisms and the shared pathobiology of mRNA dysregulation in disease. Progress has been made to understand the pathobiology of disease mechanisms for myotonic dystrophy, spinal muscular atrophy, and fragile X syndrome, with broader implications for other RBP-associated genetic neurological diseases. This gained knowledge of underlying basic mechanisms has paved the way to the development of therapeutic strategies targeting disease mechanisms.
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327
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Uemura Y, Oshima T, Yamamoto M, Reyes CJ, Costa Cruz PH, Shibuya T, Kawahara Y. Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing. Genes Cells 2017; 22:785-798. [PMID: 28695676 DOI: 10.1111/gtc.12512] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/11/2017] [Indexed: 12/13/2022]
Abstract
Matrin3 is an RNA-binding protein that is localized in the nuclear matrix. Although various roles in RNA metabolism have been reported for Matrin3, in vivo target RNAs to which Matrin3 binds directly have not been investigated comprehensively so far. Here, we show that Matrin3 binds predominantly to intronic regions of pre-mRNAs. Photoactivatable Ribonucleoside-Enhanced Cross-linking and Immunoprecipitation (PAR-CLIP) analysis using human neuronal cells showed that Matrin3 recognized pyrimidine-rich sequences as binding motifs, including the polypyrimidine tract, a splicing regulatory element. Splicing-sensitive microarray analysis showed that depletion of Matrin3 preferentially increased the inclusion of cassette exons that were adjacent to introns that contained Matrin3-binding sites. We further found that although most of the genes targeted by polypyrimidine tract binding protein 1 (PTBP1) were also bound by Matrin3, Matrin3 could control alternative splicing in a PTBP1-independent manner, at least in part. These findings suggest that Matrin3 is a splicing regulator that targets intronic pyrimidine-rich sequences.
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Affiliation(s)
- Yuri Uemura
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takuya Oshima
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Munetaka Yamamoto
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Charles Jourdan Reyes
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshiharu Shibuya
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
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328
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Zhang X, Lin Y, Eschmann NA, Zhou H, Rauch JN, Hernandez I, Guzman E, Kosik KS, Han S. RNA stores tau reversibly in complex coacervates. PLoS Biol 2017; 15:e2002183. [PMID: 28683104 PMCID: PMC5500003 DOI: 10.1371/journal.pbio.2002183] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/24/2017] [Indexed: 12/17/2022] Open
Abstract
Nonmembrane-bound organelles that behave like liquid droplets are widespread among eukaryotic cells. Their dysregulation appears to be a critical step in several neurodegenerative conditions. Here, we report that tau protein, the primary constituent of Alzheimer neurofibrillary tangles, can form liquid droplets and therefore has the necessary biophysical properties to undergo liquid-liquid phase separation (LLPS) in cells. Consonant with the factors that induce LLPS, tau is an intrinsically disordered protein that complexes with RNA to form droplets. Uniquely, the pool of RNAs to which tau binds in living cells are tRNAs. This phase state of tau is held in an approximately 1:1 charge balance across the protein and the nucleic acid constituents, and can thus be maximal at different RNA:tau mass ratios, depending on the biopolymer constituents involved. This feature is characteristic of complex coacervation. We furthermore show that the LLPS process is directly and sensitively tuned by salt concentration and temperature, implying it is modulated by both electrostatic interactions between the involved protein and nucleic acid constituents, as well as net changes in entropy. Despite the high protein concentration within the complex coacervate phase, tau is locally freely tumbling and capable of diffusing through the droplet interior. In fact, tau in the condensed phase state does not reveal any immediate changes in local protein packing, local conformations and local protein dynamics from that of tau in the dilute solution state. In contrast, the population of aggregation-prone tau as induced by the complexation with heparin is accompanied by large changes in local tau conformations and irreversible aggregation. However, prolonged residency within the droplet state eventually results in the emergence of detectable β-sheet structures according to thioflavin-T assay. These findings suggest that the droplet state can incubate tau and predispose the protein toward the formation of insoluble fibrils. Tau is a common neuronal protein that, under circumstances and conditions not well understood to date, self-assembles into intracellular aggregates in several neurodegenerative diseases including Alzheimer disease. These aggregates are formed of fibrous polymers. The mechanism by which this critical transition from a soluble protein to insoluble fibrous material occurs is unknown. We have discovered a novel state in which many tau molecules become compacted into a protein-rich droplet while maintaining their solubility and native-like protein conformations. Chemists refer to this dense liquid droplet state as a complex coacervate phase, and it is held together by the opposite charges of their constituents, ions, and water. In the case of the tau protein, the oppositely charged constituent is RNA. Indeed, we found that in human neuronal cell culture, tau selectively binds to a category of RNA known as tRNA. Interestingly, tau and RNA favorably condense to a complex coacervate phase when the charges between them are matched and at elevated temperatures, such that tau-RNA droplets could be observed at physiologically viable protein concentrations simply by increasing the temperature from room to physiological temperatures. When the tau-RNA–dense droplets are incubated together over time, tau transitions to a conformation similar to that found in pathological fibers. Our experiments therefore demonstrate physicochemical properties of tau that may predispose it to undergo changes associated with neurodegenerative disease.
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Affiliation(s)
- Xuemei Zhang
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Yanxian Lin
- Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Neil A. Eschmann
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Hongjun Zhou
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Jennifer N. Rauch
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Israel Hernandez
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Elmer Guzman
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Kenneth S. Kosik
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail: (KSK); (SH)
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, United States of America
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail: (KSK); (SH)
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329
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Tang J, Fan Y, Li H, Xiang Q, Zhang DF, Li Z, He Y, Liao Y, Wang Y, He F, Zhang F, Shugart YY, Liu C, Tang Y, Chan RCK, Wang CY, Yao YG, Chen X. Whole-genome sequencing of monozygotic twins discordant for schizophrenia indicates multiple genetic risk factors for schizophrenia. J Genet Genomics 2017. [PMID: 28645778 DOI: 10.1016/j.jgg.2017.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight non-synonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p.V24689I mutation in TTN, p.S2506T mutation in GCN1L1, IVS3+1G > T in DOCK1) or had a benign to damaging effect according to in silico prediction analysis. By searching the inherited rare damaging or loss-of-function (LOF) variants and common susceptible alleles from three classes of schizophrenia candidate genes, we were able to distill genetic alterations in several schizophrenia risk genes, including GAD1, PLXNA2, RELN and FEZ1. Four inherited copy number variations (CNVs; including a large deletion at 16p13.11) implicated for schizophrenia were identified in four families, respectively. Most of families carried both missense DNMs and inherited risk variants, which might suggest that DNMs, inherited rare damaging variants and common risk alleles together conferred to schizophrenia susceptibility. Our results support that schizophrenia is caused by a combination of multiple genetic factors, with each DNM/variant showing a relatively small effect size.
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Affiliation(s)
- Jinsong Tang
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
| | - Hong Li
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China; Department of Psychiatry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Qun Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
| | - Zongchang Li
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Ying He
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yanhui Liao
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Ya Wang
- Neuropsychology and Applied Cognitive Neuroscience Laboratory, and CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fan He
- Beijing Key Laboratory of Mental Disorders, Department of Psychiatry, Beijing Anding Hospital, and Center of Schizophrenia, Beijing Institute for Brain Disorders and Laboratory of Brain Disorders of the Ministry of Science and Technology, Capital Medical University, Beijing 100088, China
| | - Fengyu Zhang
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yin Yao Shugart
- Unit on Statistical Genomics, Intramural Research Programs, National Institute of Mental Health, NIH, Bethesda 20892, USA
| | - Chunyu Liu
- Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yanqing Tang
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang 110122, China.
| | - Raymond C K Chan
- Neuropsychology and Applied Cognitive Neuroscience Laboratory, and CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chuan-Yue Wang
- Beijing Key Laboratory of Mental Disorders, Department of Psychiatry, Beijing Anding Hospital, and Center of Schizophrenia, Beijing Institute for Brain Disorders and Laboratory of Brain Disorders of the Ministry of Science and Technology, Capital Medical University, Beijing 100088, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xiaogang Chen
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China.
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330
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Subasic D, Stoeger T, Eisenring S, Matia-González AM, Imig J, Zheng X, Xiong L, Gisler P, Eberhard R, Holtackers R, Gerber AP, Pelkmans L, Hengartner MO. Post-transcriptional control of executioner caspases by RNA-binding proteins. Genes Dev 2017; 30:2213-2225. [PMID: 27798844 PMCID: PMC5088569 DOI: 10.1101/gad.285726.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/16/2016] [Indexed: 12/03/2022]
Abstract
In this study, Subasic et al. investigated the post-transcriptional control of caspases. The authors describe four conserved RNA-binding proteins (RBPs) that sequentially repress the CED-3 caspase in distinct regions of the C. elegans germline and identify seven RBPs that regulate human caspase-3 expression and/or activation, suggesting that translational inhibition of executioner caspases by RBPs might be a general strategy used widely across the animal kingdom to control apoptosis. Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)—PUF-8, MEX-3, GLD-1, and CGH-1—that sequentially repress the CED-3 caspase in distinct regions of the Caenorhabditis elegans germline. We demonstrate that GLD-1 represses ced-3 mRNA translation via two binding sites in its 3′ untranslated region (UTR), thereby ensuring a dual control of unwanted cell death: at the level of p53/CEP-1 and at the executioner caspase level. Moreover, we identified seven RBPs that regulate human caspase-3 expression and/or activation, including human PUF-8, GLD-1, and CGH-1 homologs PUM1, QKI, and DDX6. Given the presence of unusually long executioner caspase 3′ UTRs in many metazoans, translational control of executioner caspases by RBPs might be a strategy used widely across the animal kingdom to control apoptosis.
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Affiliation(s)
- Deni Subasic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Stoeger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Systems Biology PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Seline Eisenring
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ana M Matia-González
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Jochen Imig
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Lei Xiong
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Pascal Gisler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ralf Eberhard
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - René Holtackers
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - André P Gerber
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Lucas Pelkmans
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Michael O Hengartner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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331
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Raab-Graham KF, Niere F. mTOR referees memory and disease through mRNA repression and competition. FEBS Lett 2017; 591:1540-1554. [PMID: 28493559 DOI: 10.1002/1873-3468.12675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/11/2022]
Abstract
Mammalian target of rapamycin (mTOR) activity is required for memory and is dysregulated in disease. Activation of mTOR promotes protein synthesis; however, new studies are demonstrating that mTOR activity also represses the translation of mRNAs. Almost three decades ago, Kandel and colleagues hypothesised that memory was due to the induction of positive regulators and removal of negative constraints. Are these negative constraints repressed mRNAs that code for proteins that block memory formation? Herein, we will discuss the mRNAs coded by putative memory suppressors, how activation/inactivation of mTOR repress protein expression at the synapse, how mTOR activity regulates RNA binding proteins, mRNA stability, and translation, and what the possible implications of mRNA repression are to memory and neurodegenerative disorders.
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Affiliation(s)
- Kimberly F Raab-Graham
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Farr Niere
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston Salem, NC, USA
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332
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Wang X, Mu Y, Sun M, Han J. Bidirectional regulation of fragile X mental retardation protein phosphorylation controls rhodopsin homoeostasis. J Mol Cell Biol 2017; 9:104-116. [PMID: 27702760 DOI: 10.1093/jmcb/mjw041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/29/2016] [Indexed: 01/03/2023] Open
Abstract
Homoeostatic regulation of the light sensor, rhodopsin, is critical for the maintenance of light sensitivity and survival of photoreceptors. The major fly rhodopsin, Rh1, undergoes light-induced endocytosis and degradation, but its protein and mRNA levels remain constant during light/dark cycles. It is not clear how translation of Rh1 is regulated. Here, we show that adult photoreceptors maintain a constant, abundant quantity of ninaE mRNA, which encodes Rh1. We demonstrate that the Fmr1 protein associates with ninaE mRNA and represses its translation. Further, light exposure triggers a calcium-dependent dephosphorylation of Fmr1, which relieves suppression of Rh1 translation. We demonstrate that Mts, the catalytic subunit of protein phosphatase 2A (PP2A), mediates light-induced Fmr1 dephosphorylation in a regulatory B subunit of PP2A (CKa)-dependent manner. Finally, we show that blocking light-induced Rh1 translation results in reduced light sensitivity. Our results reveal the molecular mechanism of Rh1 homoeostasis and physiological consequence of Rh1 dysregulation.
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Affiliation(s)
- Xiao Wang
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Yawen Mu
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Mengshi Sun
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Junhai Han
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
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333
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Gene-set analysis shows association between FMRP targets and autism spectrum disorder. Eur J Hum Genet 2017; 25:863-868. [PMID: 28422133 DOI: 10.1038/ejhg.2017.55] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/14/2017] [Accepted: 03/14/2017] [Indexed: 11/08/2022] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous group of disorders characterized by problems with social interaction, communication, and repetitive and restricted behavior. Despite its high heritability and the substantial progress made in elucidating genetic associations, the corresponding biological mechanisms are largely unknown. Our objective is to investigate the contribution of common genetic variation to biological pathways functionally involved in ASD. We conducted gene-set analyses to identify ASD-associated functional biological pathways using the statistical tools MAGMA and INRICH. Gene-set selection was based on previously reported associations with psychiatric disorders and resulted in testing of specific synaptic and glial sets, a glutamate pathway gene-set, mitochondrial gene-sets and gene-sets consisting of fragile X mental retardation protein (FMRP) targets. In total 32 gene-sets were tested. We used Psychiatric Genomics Consortium genome-wide association studies summary statistics of ASD. The study is based on the largest ASD sample to date (N=5305). We found one significantly associated gene-set consisting of FMRP-targeting transcripts (MAGMA: p corr.=0.014, INRICH: p corr.=0.031; all competitive P-values). The results indicate the involvement of FMRP-targeted transcripts in ASD in common genetic variation. This novel finding is in line with the literature as FMRP has been linked to fragile X syndrome, ASD and cognitive development in whole-exome sequencing and copy number variant studies. This gene-set has also been linked to Schizophrenia suggesting that FMRP-targeted transcripts might be involved in a general mechanism with shared genetic etiology between psychiatric disorders.
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334
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Rosario R, Childs AJ, Anderson RA. RNA-binding proteins in human oogenesis: Balancing differentiation and self-renewal in the female fetal germline. Stem Cell Res 2017; 21:193-201. [PMID: 28434825 PMCID: PMC5446320 DOI: 10.1016/j.scr.2017.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 03/29/2017] [Accepted: 04/13/2017] [Indexed: 12/11/2022] Open
Abstract
Primordial germ cells undergo three significant processes on their path to becoming primary oocytes: the initiation of meiosis, the formation and breakdown of germ cell nests, and the assembly of single oocytes into primordial follicles. However at the onset of meiosis, the germ cell becomes transcriptionally silenced. Consequently translational control of pre-stored mRNAs plays a central role in coordinating gene expression throughout the remainder of oogenesis; RNA binding proteins are key to this regulation. In this review we examine the role of exemplars of such proteins, namely LIN28, DAZL, BOLL and FMRP, and highlight how their roles during germ cell development are critical to oogenesis and the establishment of the primordial follicle pool. RNA-binding proteins (RBPs) are key regulators of gene expression during oogenesis. RBPs LIN28, DAZL, BOLL and FMRP display stage-specific expression in fetal oocytes. LIN28 and DAZL may regulate self-renewal and progression into meiosis respectively. BOLL and FMRP may be involved in the later stages of prophase I and oocyte growth. RBPs may have critical roles in establishing the ovarian reserve during fetal life.
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Affiliation(s)
- Roseanne Rosario
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrew J Childs
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London NW1 0TU, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
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335
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Garzia A, Meyer C, Morozov P, Sajek M, Tuschl T. Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins. Methods 2017; 118-119:24-40. [PMID: 27765618 PMCID: PMC5393971 DOI: 10.1016/j.ymeth.2016.10.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/11/2016] [Accepted: 10/14/2016] [Indexed: 12/21/2022] Open
Abstract
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in combination with next-generation sequencing is a powerful method for identifying endogenous targets of RNA-binding proteins (RBPs). Depending on the characteristics of each RBP, key steps in the PAR-CLIP procedure must be optimized. Here we present a comprehensive step-by-step PAR-CLIP protocol with detailed explanations of the critical steps. Furthermore, we report the application of a new PAR-CLIP data analysis pipeline to three distinct RBPs targeting different annotation categories of cellular RNAs.
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Affiliation(s)
- Aitor Garzia
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Pavel Morozov
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marcin Sajek
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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336
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Pilaz LJ, Silver DL. Moving messages in the developing brain-emerging roles for mRNA transport and local translation in neural stem cells. FEBS Lett 2017; 591:1526-1539. [PMID: 28304078 DOI: 10.1002/1873-3468.12626] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/06/2017] [Accepted: 03/11/2017] [Indexed: 11/10/2022]
Abstract
The mammalian cerebral cortex is a complex brain structure integral to our higher cognition. During embryonic cortical development, radial glial progenitors (RGCs) produce neurons and serve as physical structures for migrating neurons. Recent discoveries highlight new roles for RNA localization and local translation in RGCs, both at the cell body and at distal structures called basal endfeet. By implementing technologies from the field of RNA research to brain development, investigators can manipulate RNA-binding proteins as well as visualize single-molecule RNAs, live movement of mRNAs and their binding proteins, and translation. Going forward, these studies establish a framework for investigating how post-transcriptional RNA regulation helps shape RGC function and triggers neurodevelopmental diseases.
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Affiliation(s)
- Louis-Jan Pilaz
- Department of Molecular Genetics and Microbiology, Regeneration Next, Duke University Medical Center, Durham, NC, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Regeneration Next, 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.,Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
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337
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Ba W, Nadif Kasri N. RhoGTPases at the synapse: An embarrassment of choice. Small GTPases 2017; 8:106-113. [PMID: 27492682 PMCID: PMC5464131 DOI: 10.1080/21541248.2016.1206352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 12/14/2022] Open
Abstract
Activity-dependent modifications in the strength of excitatory synapses are considered to be major cellular mechanisms that contribute to the plasticity of neuronal networks underlying learning and memory. Key mechanisms for the regulation of synaptic efficacy involve the dynamic changes in size and number of dendritic spines, as well as the synaptic incorporation and removal of AMPA-type glutamate receptors (AMPAr). As key regulators of the actin cytoskeleton, the Rho subfamily of GTP-binding proteins play a critical role in synaptic development and plasticity. They shuttle between the active GTP-bound form and the inactive GDP-bound form under the regulation of dedicated guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). More than 80 human GEFs and 70 GAPs have been identified, most of which are expressed in the brain with a specific spatial and temporal expression pattern. However, the function of most GEFs and GAPs in the brain has not been elucidated. In this review, we highlight the novel neuronal function of the synaptic RhoGAP ARHGAP12 and the ID-associated RhoGEF TRIO and further propose 3 possible approaches of neurons utilizing Rho GTPase regulatory proteins to accurately modulate synaptic function.
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Affiliation(s)
- W. Ba
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - N. Nadif Kasri
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
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338
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Patzlaff NE, Nemec KM, Malone SG, Li Y, Zhao X. Fragile X related protein 1 (FXR1P) regulates proliferation of adult neural stem cells. Hum Mol Genet 2017; 26:1340-1352. [PMID: 28204491 PMCID: PMC6075589 DOI: 10.1093/hmg/ddx034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/16/2017] [Accepted: 01/19/2017] [Indexed: 11/14/2022] Open
Abstract
Fragile X related protein 1 (FXR1P) is a member of the fragile X family of RNA-binding proteins, which includes FMRP and FXR2P. Both FMRP and FXR2P regulate neurogenesis, a process affected in a number of neurological and neuropsychiatric disorders, including fragile X syndrome. Although FXR1P has been implicated in various developmental processes and neuropsychiatric diseases, its role in neurodevelopment is not well understood. The goal of the present study was to elucidate the function of FXR1P in adult neurogenesis. We used an inducible mouse model that allows us to investigate how FXR1P deficiency in adult neural stem cells (aNSCs) affects proliferation and neuronal differentiation. Deletion of FXR1 in aNSCs resulted in fewer adult-born cells in the dentate gyrus (DG) overall, reducing populations across different stages of neurogenesis, including radial glia-like cells, intermediate progenitors, neuroblasts, immature neurons and neurons. We hypothesized that this reduction in new cell numbers resulted from impaired proliferation, which we confirmed both in vivo and in vitro. We discovered that FXR1P-deficient aNSCs have altered expression of a select number of cell-cycle genes, and we identified the mRNA of cyclin-dependent kinase inhibitor 1A (Cdkn1a, p21) as a direct target of FXR1P. Restoration of p21 mRNA to wild-type levels rescued the proliferation deficit in cells lacking FXR1P, demonstrating that p21 is a mediator of FXR1P in aNSCs. These results indicate that FXR1P plays an important role in regulating aNSC self-renewal and maintenance in the adult brain, which may have implications for a number of neurodevelopmental and psychiatric disorders.
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Affiliation(s)
- Natalie E. Patzlaff
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kelsey M. Nemec
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sydney G. Malone
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yue Li
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Molecular and Cellular Pharmacology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
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339
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Bonasera SJ, Chaudoin TR, Goulding EH, Mittek M, Dunaevsky A. Decreased home cage movement and oromotor impairments in adult Fmr1-KO mice. GENES BRAIN AND BEHAVIOR 2017; 16:564-573. [PMID: 28218824 DOI: 10.1111/gbb.12374] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 01/16/2017] [Accepted: 02/15/2017] [Indexed: 01/15/2023]
Abstract
Fragile X syndrome (FXS) is a common inherited disorder that significantly impacts family and patient day-to-day living across the entire life span. The childhood and adolescent behavioral consequences of FXS are well appreciated. However, there are significantly fewer studies (except those examining psychiatric comorbidities) assessing behavioral phenotypes seen in adults with FXS. Mice engineered with a genetic lesion of fragile X mental retardation 1 (Fmr1) recapitulate important molecular and neuroanatomical characteristics of FXS, and provide a means to evaluate adult behavioral phenotypes associated with FXS. We give the first description of baseline behaviors including feeding, drinking, movement and their circadian rhythms; all observed over 16 consecutive days following extensive environmental habituation in adult Fmr1-KO mutant mice. We find no genotypic changes in mouse food ingestion, feeding patterns, metabolism or circadian patterns of movement, feeding and drinking. After habituation, Fmr1-KO mice show significantly less daily movement during their active phase (the dark cycle). However, Fmr1-KO mice have more bouts of activity during the light cycle compared with wild types. In addition, Fmr1-KO mice show significantly less daily water ingestion during the circadian dark cycle, and this reduction in water intake is accompanied by a decrease in the amount of water ingested per lick. The observed water ingestion and circadian phenotypes noted in Fmr1-KO mice recapitulate known clinical aspects previously described in FXS. The finding of decreased movement in Fmr1-KO mice is novel, and suggests a dissociation between baseline and novelty-evoked activity for Fmr1-KO mice.
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Affiliation(s)
- S J Bonasera
- Division of Geriatrics, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE
| | - T R Chaudoin
- Division of Geriatrics, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE
| | - E H Goulding
- Department of Psychiatry and Behavioral Sciences, Northwestern University, Chicago, IL
| | - M Mittek
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE
| | - A Dunaevsky
- Department of Developmental Neuroscience, Monroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
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340
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Chen R, Davis LK, Guter S, Wei Q, Jacob S, Potter MH, Cox NJ, Cook EH, Sutcliffe JS, Li B. Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism. Mol Autism 2017; 8:14. [PMID: 28344757 PMCID: PMC5361831 DOI: 10.1186/s13229-017-0130-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/10/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is one of the most highly heritable neuropsychiatric disorders, but underlying molecular mechanisms are still unresolved due to extreme locus heterogeneity. Leveraging meaningful endophenotypes or biomarkers may be an effective strategy to reduce heterogeneity to identify novel ASD genes. Numerous lines of evidence suggest a link between hyperserotonemia, i.e., elevated serotonin (5-hydroxytryptamine or 5-HT) in whole blood, and ASD. However, the genetic determinants of blood 5-HT level and their relationship to ASD are largely unknown. METHODS In this study, pursuing the hypothesis that de novo variants (DNVs) and rare risk alleles acting in a recessive mode may play an important role in predisposition of hyperserotonemia in people with ASD, we carried out whole exome sequencing (WES) in 116 ASD parent-proband trios with most (107) probands having 5-HT measurements. RESULTS Combined with published ASD DNVs, we identified USP15 as having recurrent de novo loss of function mutations and discovered evidence supporting two other known genes with recurrent DNVs (FOXP1 and KDM5B). Genes harboring functional DNVs significantly overlap with functional/disease gene sets known to be involved in ASD etiology, including FMRP targets and synaptic formation and transcriptional regulation genes. We grouped the probands into High-5HT and Normal-5HT groups based on normalized serotonin levels, and used network-based gene set enrichment analysis (NGSEA) to identify novel hyperserotonemia-related ASD genes based on LoF and missense DNVs. We found enrichment in the High-5HT group for a gene network module (DAWN-1) previously implicated in ASD, and this points to the TGF-β pathway and cell junction processes. Through analysis of rare recessively acting variants (RAVs), we also found that rare compound heterozygotes (CHs) in the High-5HT group were enriched for loci in an ASD-associated gene set. Finally, we carried out rare variant group-wise transmission disequilibrium tests (gTDT) and observed significant association of rare variants in genes encoding a subset of the serotonin pathway with ASD. CONCLUSIONS Our study identified USP15 as a novel gene implicated in ASD based on recurrent DNVs. It also demonstrates the potential value of 5-HT as an effective endophenotype for gene discovery in ASD, and the effectiveness of this strategy needs to be further explored in studies of larger sample sizes.
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Affiliation(s)
- Rui Chen
- Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA
| | - Lea K Davis
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.,Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN USA
| | - Stephen Guter
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL USA
| | - Qiang Wei
- Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA
| | - Suma Jacob
- Department of Psychiatry, University of Minnesota, Minneapolis, MN USA
| | - Melissa H Potter
- Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA.,Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN USA
| | - Edwin H Cook
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL USA
| | - James S Sutcliffe
- Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA
| | - Bingshan Li
- Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA
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341
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Duy PQ, Budimirovic DB. Fragile X Syndrome: Lessons Learned from the Most Translated Neurodevelopmental Disorder in Clinical Trials. Transl Neurosci 2017; 8:7-8. [PMID: 28400977 PMCID: PMC5382936 DOI: 10.1515/tnsci-2017-0002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 11/25/2022] Open
Abstract
Fragile X syndrome (FXS) is the leading genetic cause of autism spectrum disorder (ASD) and inherited intellectual disability (ID) worldwide. Preclinical successes in understanding the biology of FXS have led to numerous translational attempts in human clinical trials of therapeutics that target the excitatory/inhibitory neural signaling imbalances thought to underlie FXS. Despite the preclinical success story, the negative results of the human clinical trials have been deemed to be at least in part disappointing by the field. In this commentary, we contend that such negative studies results in clinical trials may actually propel the FXS field forward by serving as important lessons for designing and implementing improved future clinical trials such that can objectively assess the full range of responses to new therapeutics.
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Affiliation(s)
- Phan Q. Duy
- Department of Biology Johns Hopkins University Baltimore, MD 21218, USA
- E-mail:
| | - Dejan B. Budimirovic
- Clinical Research Center, Clinical Trials Unit & Fragile X Clinic, Kennedy Krieger Institute, Johns Hopkins Medical Institutions Baltimore, MD 21205, USA
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342
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Polishchuk M, Paz I, Kohen R, Mesika R, Yakhini Z, Mandel-Gutfreund Y. A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data. Methods 2017; 118-119:73-81. [PMID: 28274760 DOI: 10.1016/j.ymeth.2017.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 01/08/2023] Open
Abstract
RNA binding proteins (RBPs) play an important role in regulating many processes in the cell. RBPs often recognize their RNA targets in a specific manner. In addition to the RNA primary sequence, the structure of the RNA has been shown to play a central role in RNA recognition by RBPs. In recent years, many experimental approaches, both in vitro and in vivo, were developed and employed to identify and characterize RBP targets and extract their binding specificities. In vivo binding techniques, such as CrossLinking and ImmunoPrecipitation (CLIP)-based methods, enable the characterization of protein binding sites on RNA targets. However, these methods do not provide information regarding the structural preferences of the protein. While methods to obtain the structure of RNA are available, inferring both the sequence and the structure preferences of RBPs remains a challenge. Here we present SMARTIV, a novel computational tool for discovering combined sequence and structure binding motifs from in vivo RNA binding data relying on the sequences of the target sites, the ranking of their binding scores and their predicted secondary structure. The combined motifs are provided in a unified representation that is informative and easy for visual perception. We tested the method on CLIP-seq data from different platforms for a variety of RBPs. Overall, we show that our results are highly consistent with known binding motifs of RBPs, offering additional information on their structural preferences.
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Affiliation(s)
- Maya Polishchuk
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Vavilov Institute of General Genetics, Russian Academy of Science, Moscow 11933, Russia
| | - Inbal Paz
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Refael Kohen
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Rona Mesika
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Zohar Yakhini
- Faculty of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel; School of Computer Science, Herzliya Interdisciplinary Center, Herzliya 46150, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Faculty of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel.
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343
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Zhou LT, Ye SH, Yang HX, Zhou YT, Zhao QH, Sun WW, Gao MM, Yi YH, Long YS. A novel role of fragile X mental retardation protein in pre-mRNA alternative splicing through RNA-binding protein 14. Neuroscience 2017; 349:64-75. [PMID: 28257890 DOI: 10.1016/j.neuroscience.2017.02.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/16/2017] [Accepted: 02/20/2017] [Indexed: 02/08/2023]
Abstract
Fragile X mental retardation protein (FMRP), an important RNA-binding protein responsible for fragile X syndrome, is involved in posttranscriptional control of gene expression that links with brain development and synaptic functions. Here, we reveal a novel role of FMRP in pre-mRNA alternative splicing, a general event of posttranscriptional regulation. Using co-immunoprecipitation and immunofluorescence assays, we identified that FMRP interacts with an alternative-splicing-associated protein RNA-binding protein 14 (RBM14) in a RNA-dependent fashion, and the two proteins partially colocalize in the nuclei of hippocampal neurons. We show that the relative skipping/inclusion ratio of the micro-exon L in the Protrudin gene and exon 10 in the Tau gene decreased in the hippocampus of Fmr1 knockout (KO) mice. Knockdown of either FMRP or RBM14 alters the relative skipping/inclusion ratio of Protrudin and Tau in cultured Neuro-2a cells, similar to that in the Fmr1 KO mice. Furthermore, overexpression of FMRP leads to an opposite pattern of the splicing, which can be offset by RBM14 knockdown. RNA immunoprecipitation assays indicate that FMRP promotes RBM14's binding to the mRNA targets. In addition, overexpression of the long form of Protrudin or the short form of Tau promotes protrusion growth of the retinoic acid-treated, neuronal-differentiated Neuro-2a cells. Together, these data suggest a novel function of FMRP in the regulation of pre-mRNA alternative splicing through RBM14 that may be associated with normal brain function and FMRP-related neurological disorders.
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Affiliation(s)
- Lin-Tao Zhou
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Shun-Hua Ye
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Hai-Xuan Yang
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Yong-Ting Zhou
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Qi-Hua Zhao
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Wei-Wen Sun
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Mei-Mei Gao
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Yong-Hong Yi
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China; Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Yue-Sheng Long
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China.
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344
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Namjoshi SV, Raab-Graham KF. Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. Front Mol Neurosci 2017; 10:45. [PMID: 28286470 PMCID: PMC5323403 DOI: 10.3389/fnmol.2017.00045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.
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Affiliation(s)
- Sanjeev V Namjoshi
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA
| | - Kimberly F Raab-Graham
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA; Department of Physiology and Pharmacology, Wake Forest Health Sciences, Medical Center Boulevard, Winston-SalemNC, USA
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345
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Sethna F, Feng W, Ding Q, Robison AJ, Feng Y, Wang H. Enhanced expression of ADCY1 underlies aberrant neuronal signalling and behaviour in a syndromic autism model. Nat Commun 2017; 8:14359. [PMID: 28218269 PMCID: PMC5321753 DOI: 10.1038/ncomms14359] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/20/2016] [Indexed: 12/14/2022] Open
Abstract
Fragile X syndrome (FXS), caused by the loss of functional FMRP, is a leading cause of autism. Neurons lacking FMRP show aberrant mRNA translation and intracellular signalling. Here, we identify that, in Fmr1 knockout neurons, type 1 adenylyl cyclase (Adcy1) mRNA translation is enhanced, leading to excessive production of ADCY1 protein and insensitivity to neuronal stimulation. Genetic reduction of Adcy1 normalizes the aberrant ERK1/2- and PI3K-mediated signalling, attenuates excessive protein synthesis and corrects dendritic spine abnormality in Fmr1 knockout mice. Genetic reduction of Adcy1 also ameliorates autism-related symptoms including repetitive behaviour, defective social interaction and audiogenic seizures. Moreover, peripheral administration of NB001, an experimental compound that preferentially suppresses ADCY1 activity over other ADCY subtypes, attenuates the behavioural abnormalities in Fmr1 knockout mice. These results demonstrate a connection between the elevated Adcy1 translation and abnormal ERK1/2 signalling and behavioural symptoms in FXS. Fragile X syndrome (FXS) is a leading cause of autism and neurons lacking FMRP show aberrant mRNA translation and intracellular signalling. Here, the authors show that neurons from Fmr1 knockout mice have increased levels of ADCY1 protein, producing abnormal ERK1/2 signalling, dysregulated protein synthesis and behavioural symptoms associated with FXS.
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Affiliation(s)
- Ferzin Sethna
- Genetics Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Wei Feng
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Qi Ding
- Department of Physiology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Alfred J Robison
- Department of Physiology, Michigan State University, East Lansing, Michigan 48824, USA.,Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Yue Feng
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Hongbing Wang
- Department of Physiology, Michigan State University, East Lansing, Michigan 48824, USA.,Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA
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346
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Loss-of-function of PTPR γ and ζ, observed in sporadic schizophrenia, causes brain region-specific deregulation of monoamine levels and altered behavior in mice. Psychopharmacology (Berl) 2017; 234:575-587. [PMID: 28025742 DOI: 10.1007/s00213-016-4490-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 11/17/2016] [Indexed: 12/12/2022]
Abstract
RATIONALE The receptor protein tyrosine phosphatase PTPRG has been genetically associated with psychiatric disorders and is a ligand for members of the contactin family, which are themselves linked to autism spectrum disorders. OBJECTIVE Based on our finding of a phosphatase-null de novo mutation in PTPRG associated with a case of sporadic schizophrenia, we used PTPRG knockout (KO) mice to model the effect of a loss-of-function mutation. We compared the results with loss-of-function in its close paralogue PTPRZ, previously associated with schizophrenia. We tested PTPRG -/- , PTPRZ -/- , and wild-type male mice for effects on social behavior, forced swim test, and anxiety, as well as on regional brain neurochemistry. RESULTS The most notable behavioral consequences of PTPRG gene inactivation were reduced immobilization in the forced swim test, suggestive of some negative symptoms of schizophrenia. By contrast, PTPRZ -/- mice demonstrated marked social alteration with increased aggressivity, reminiscent of some positive symptoms of schizophrenia. Both knockouts showed elevated dopamine levels in prefrontal cortex, hippocampus, and most particularly amygdala, but not striatum, accompanied by reduced dopamine beta hydroxylase activity only in amygdala. In addition, PTPRG KO elicited a distinct increase in hippocampal serotonin level not observed in PTPRZ KO. CONCLUSION PTPRG and PTPRZ gene loss therefore induces distinct patterns of behavioral change and region-specific alterations in neurotransmitters, highlighting their usefulness as models for neuropsychiatric disorder mechanisms and making these receptors attractive targets for therapy.
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347
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Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental conditions characterized by deficits in social communication and by repetitive and stereotypic patterns of behaviors, with no pharmacological treatments available to treat these core symptoms. Oxytocin is a neuropeptide that powerfully regulates mammalian social behavior and has been shown to exert pro-social effects when administered intranasally to healthy human subjects. In the last decade, there has been a significant interest in using oxytocin to treat social behavior deficits in ASD. However, little attention has been paid to whether the oxytocin system is perturbed in subgroups of individuals with ASD and whether these individuals are likely to benefit more from an oxytocin treatment. This oversight may in part be due to the enormous heterogeneity of ASD and the lack of methods to carefully probe the OXT system in human subjects. Animal models for ASD are valuable tools to clarify the implication of the oxytocin system in ASD and can help determine whether perturbation in this system should be considered in future clinical studies as stratifying biomarkers to inform targeted treatments in subgroups of individuals with ASD. In this chapter, we review the literature on genetic- and environmental-based animal models for ASD, in which perturbations in the oxytocin system and/or the effect of oxytocin administration on the ASD-associated phenotype have been investigated.
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348
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Multiplex CRISPR/Cas9-based genome engineering enhanced by Drosha-mediated sgRNA-shRNA structure. Sci Rep 2016; 6:38970. [PMID: 27941919 PMCID: PMC5150520 DOI: 10.1038/srep38970] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system has recently been developed into a powerful genome-editing technology, as it requires only two key components (Cas9 protein and sgRNA) to function and further enables multiplex genome targeting and homology-directed repair (HDR) based precise genome editing in a wide variety of organisms. Here, we report a novel and interesting strategy by using the Drosha-mediated sgRNA-shRNA structure to direct Cas9 for multiplex genome targeting and precise genome editing. For multiplex genome targeting assay, we achieved more than 9% simultaneous mutant efficiency for 3 genomic loci among the puromycin-selected cell clones. By introducing the shRNA against DNA ligase IV gene (LIG4) into the sgRNA-shRNA construct, the HDR-based precise genome editing efficiency was improved as more than 2-fold. Our works provide a useful tool for multiplex and precise genome modifying in mammalian cells.
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349
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McCoy M, Poliquin-Duchesneau D, Corbin F. Molecular dynamics of FMRP and other RNA-binding proteins in MEG-01 differentiation: the role of mRNP complexes in non-neuronal development. Biochem Cell Biol 2016; 94:597-608. [DOI: 10.1139/bcb-2015-0131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Asymmetrically differentiating cells are formed with the aid of RNA-binding proteins (RBPs), which can bind, stabilize, regulate, and transport target mRNAs. The loss of RBPs in neurons may lead to severe neurodevelopmental diseases such as the Fragile X Syndrome with the absence of the Fragile X Mental Retardation Protein (FMRP). Because the latter is ubiquitous and shares many similarities with other RBPs involved in the development of peripheral cells, we suggest that FMRP would have a role in the differentiation of all tissues where it is expressed. A MEG-01 differentiation model was, therefore, established to study the global developmental functions of FMRP. PMA induction of MEG-01 cells causes important morphological changes driven by cytoskeletal dynamics. Cytoskeleton change and colocalization analyses were performed by confocal microscopy and sucrose gradient fractionation. Total cellular protein content and de novo synthesis were also analyzed. Microtubular transport mediates the displacement of FMRP and other RBP-containing mRNP complexes towards regions of the cell in development. De novo protein synthesis decreases significantly upon differentiation and total protein content composition is altered. Because those results are comparable with those obtained in neurons, the absence of FMRP would have significant consequences in cells everywhere in the body. The latter should be further investigated to give a better understanding of the systemic implications of imbalances of FMRP and other functionally similar RBPs.
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Affiliation(s)
- M. McCoy
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - D. Poliquin-Duchesneau
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - F. Corbin
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
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350
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Dynamic mRNA Transport and Local Translation in Radial Glial Progenitors of the Developing Brain. Curr Biol 2016; 26:3383-3392. [PMID: 27916527 DOI: 10.1016/j.cub.2016.10.040] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/22/2016] [Accepted: 10/19/2016] [Indexed: 11/23/2022]
Abstract
In the developing brain, neurons are produced from neural stem cells termed radial glia [1, 2]. Radial glial progenitors span the neuroepithelium, extending long basal processes to form endfeet hundreds of micrometers away from the soma. Basal structures influence neuronal migration, tissue integrity, and proliferation [3-7]. Yet, despite the significance of these distal structures, their cell biology remains poorly characterized, impeding our understanding of how basal processes and endfeet influence neurogenesis. Here we use live imaging of embryonic brain tissue to visualize, for the first time, rapid mRNA transport in radial glia, revealing that the basal process is a highway for directed molecular transport. RNA- and mRNA-binding proteins, including the syndromic autism protein FMRP, move in basal processes at velocities consistent with microtubule-based transport, accumulating in endfeet. We develop an ex vivo tissue preparation to mechanically isolate radial glia endfeet from the soma, and we use photoconvertible proteins to demonstrate that mRNA is locally translated. Using RNA immunoprecipitation and microarray analyses of endfeet, we discover FMRP-bound transcripts, which encode signaling and cytoskeletal regulators, including many implicated in autism and neurogenesis. We show FMRP controls transport and localization of one target, Kif26a. These discoveries reveal a rich, regulated local transcriptome in radial glia, far from the soma, and establish a tractable mammalian model for studying mRNA transport and local translation in vivo. We conclude that cytoskeletal and signaling events at endfeet may be controlled through translation of specific mRNAs transported from the soma, exposing new mechanistic layers within stem cells of the developing brain.
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