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Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
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Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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2
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Abbasi DA, Berry-Kravis E, Zhao X, Cologna SM. Proteomics insights into fragile X syndrome: Unraveling molecular mechanisms and therapeutic avenues. Neurobiol Dis 2024; 194:106486. [PMID: 38548140 DOI: 10.1016/j.nbd.2024.106486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/08/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Fragile X Syndrome (FXS) is a neurodevelopment disorder characterized by cognitive impairment, behavioral challenges, and synaptic abnormalities, with a genetic basis linked to a mutation in the FMR1 (Fragile X Messenger Ribonucleoprotein 1) gene that results in a deficiency or absence of its protein product, Fragile X Messenger Ribonucleoprotein (FMRP). In recent years, mass spectrometry (MS) - based proteomics has emerged as a powerful tool to uncover the complex molecular landscape underlying FXS. This review provides a comprehensive overview of the proteomics studies focused on FXS, summarizing key findings with an emphasis on dysregulated proteins associated with FXS. These proteins span a wide range of cellular functions including, but not limited to, synaptic plasticity, RNA translation, and mitochondrial function. The work conducted in these proteomic studies provides a more holistic understanding to the molecular pathways involved in FXS and considerably enhances our knowledge into the synaptic dysfunction seen in FXS.
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Affiliation(s)
- Diana A Abbasi
- Departments of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, United States of America
| | - Elizabeth Berry-Kravis
- Departments of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, United States of America
| | - Xinyu Zhao
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, United States of America
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, United States of America.
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3
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Coulson RL, Frattini V, Moyer CE, Hodges J, Walter P, Mourrain P, Zuo Y, Wang GX. Translational modulator ISRIB alleviates synaptic and behavioral phenotypes in Fragile X syndrome. iScience 2024; 27:109259. [PMID: 38510125 PMCID: PMC10951902 DOI: 10.1016/j.isci.2024.109259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/31/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Fragile X syndrome (FXS) is caused by the loss of fragile X messenger ribonucleoprotein (FMRP), a translational regulator that binds the transcripts of proteins involved in synaptic function and plasticity. Dysregulated protein synthesis is a central effect of FMRP loss, however, direct translational modulation has not been leveraged in the treatment of FXS. Thus, we examined the effect of the translational modulator integrated stress response inhibitor (ISRIB) in treating synaptic and behavioral symptoms of FXS. We show that FMRP loss dysregulates synaptic protein abundance, stabilizing dendritic spines through increased PSD-95 levels while preventing spine maturation through reduced glutamate receptor accumulation, thus leading to the formation of dense, immature dendritic spines, characteristic of FXS patients and Fmr1 knockout (KO) mice. ISRIB rescues these deficits and improves social recognition in Fmr1 KO mice. These findings highlight the therapeutic potential of targeting core translational mechanisms in FXS and neurodevelopmental disorders more broadly.
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Affiliation(s)
- Rochelle L. Coulson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Valentina Frattini
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Caitlin E. Moyer
- National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Hodges
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Peter Walter
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
- INSERM 1024, Ecole Normale Supérieure, Paris, France
| | - Yi Zuo
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gordon X. Wang
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
- Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA 94305, USA
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4
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Samuels TJ, Gui J, Gebert D, Karam Teixeira F. Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation. EMBO J 2024; 43:1591-1617. [PMID: 38480936 PMCID: PMC11021484 DOI: 10.1038/s44318-024-00070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/18/2024] Open
Abstract
The tight control of fate transitions during stem cell differentiation is essential for proper tissue development and maintenance. However, the challenges in studying sparsely distributed adult stem cells in a systematic manner have hindered efforts to identify how the multilayered regulation of gene expression programs orchestrates stem cell differentiation in vivo. Here, we synchronised Drosophila female germline stem cell (GSC) differentiation in vivo to perform in-depth transcriptome and translatome analyses at high temporal resolution. This characterisation revealed widespread and dynamic changes in mRNA level, promoter usage, exon inclusion, and translation efficiency. Transient expression of the master regulator, Bam, drives a first wave of expression changes, primarily modifying the cell cycle program. Surprisingly, as Bam levels recede, differentiating cells return to a remarkably stem cell-like transcription and translation program, with a few crucial changes feeding into a second phase driving terminal differentiation to form the oocyte. Altogether, these findings reveal that rather than a unidirectional accumulation of changes, the in vivo differentiation of stem cells relies on distinctly regulated and developmentally sequential waves.
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Affiliation(s)
- Tamsin J Samuels
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK
| | - Jinghua Gui
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
| | - Daniel Gebert
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK
| | - Felipe Karam Teixeira
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK.
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5
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Rivera-Rincón N, Altindag UH, Amin R, Graze RM, Appel AG, Stevison LS. "A comparison of thermal stress response between Drosophila melanogaster and Drosophila pseudoobscura reveals differences between species and sexes". JOURNAL OF INSECT PHYSIOLOGY 2024; 153:104616. [PMID: 38278288 PMCID: PMC11048572 DOI: 10.1016/j.jinsphys.2024.104616] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
The environment is changing faster than anticipated due to climate change, making species more vulnerable to its impacts. The level of vulnerability of species is influenced by factors such as the degree and duration of exposure, as well as the physiological sensitivity of organisms to changes in their environments, which has been shown to vary among species, populations, and individuals. Here, we compared physiological changes in fecundity, critical thermalmaximum (CTmax), respiratory quotient (RQ), and DNA damage in ovaries in response to temperature stress in two species of fruit fly, Drosophila melanogaster (25 vs. 29.5 °C) and Drosophila pseudoobscura (20.5 vs. 25 °C). The fecundity of D. melanogaster was more affected by high temperatures when exposed during egg through adult development, while D. pseudoobscura was most significantly affected when exposed to high temperatures exclusively during egg through pupal development. Additionally, D. melanogaster males exhibited a decrease of CTmax under high temperatures, while females showed an increase of CTmax when exposed to high temperatures during egg through adult development. while D. pseudoobscura females and males showed an increased CTmax only when reared at high temperatures during egg through pupae development. Moreover, both species showed an acceleration in oogenesis and an increase in apoptosis due to heat stress. These changes can likely be attributed to key differences in the geographic range, thermal range, development time, and other different factors between these two systems. Through this comparison of variation in physiology and developmental response to thermal stress, we found important differences between species and sexes that suggest future work needs to account for these factors separately in understanding the effects of constant increased temperatures.
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Affiliation(s)
- N Rivera-Rincón
- Department of Biological Sciences, Auburn University, Auburn, AL USA
| | - U H Altindag
- Department of Biological Sciences, Auburn University, Auburn, AL USA
| | - R Amin
- Department of Biological Sciences, Auburn University, Auburn, AL USA
| | - R M Graze
- Department of Biological Sciences, Auburn University, Auburn, AL USA
| | - A G Appel
- Department of Biological Sciences, Auburn University, Auburn, AL USA
| | - L S Stevison
- Department of Biological Sciences, Auburn University, Auburn, AL USA.
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6
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Coulson RL, Mourrain P, Wang GX. The intersection of sleep and synaptic translation in synaptic plasticity deficits in neurodevelopmental disorders. J Comp Physiol B 2024:10.1007/s00360-023-01531-3. [PMID: 38396062 DOI: 10.1007/s00360-023-01531-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 02/25/2024]
Abstract
Individuals with neurodevelopmental disorders experience persistent sleep deficits, and there is increasing evidence that sleep dysregulation is an underlying cause, rather than merely an effect, of the synaptic and behavioral defects observed in these disorders. At the molecular level, dysregulation of the synaptic proteome is a common feature of neurodevelopmental disorders, though the mechanism connecting these molecular and behavioral phenotypes is an ongoing area of investigation. A role for eIF2α in shifting the local proteome in response to changes in the conditions at the synapse has emerged. Here, we discuss recent progress in characterizing the intersection of local synaptic translation and sleep and propose a reciprocal mechanism of dysregulation in the development of synaptic plasticity defects in neurodevelopmental disorders.
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Affiliation(s)
- Rochelle L Coulson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- INSERM 1024, Ecole Normale Supérieure, Paris, France
| | - Gordon X Wang
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, USA.
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7
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Subramanian M, Mills WT, Paranjpe MD, Onuchukwu US, Inamdar M, Maytin AR, Li X, Pomerantz JL, Meffert MK. Growth-suppressor microRNAs mediate synaptic overgrowth and behavioral deficits in Fragile X mental retardation protein deficiency. iScience 2024; 27:108676. [PMID: 38235335 PMCID: PMC10792201 DOI: 10.1016/j.isci.2023.108676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/20/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024] Open
Abstract
Abnormal neuronal and synapse growth is a core pathology resulting from deficiency of the Fragile X mental retardation protein (FMRP), but molecular links underlying the excessive synthesis of key synaptic proteins remain incompletely defined. We find that basal brain levels of the growth suppressor let-7 microRNA (miRNA) family are selectively lowered in FMRP-deficient mice and activity-dependent let-7 downregulation is abrogated. Primary let-7 miRNA transcripts are not altered in FMRP-deficiency and posttranscriptional misregulation occurs downstream of MAPK pathway induction and elevation of Lin28a, a let-7 biogenesis inhibitor. Neonatal restoration of brain let-7 miRNAs corrects hallmarks of FMRP-deficiency, including dendritic spine overgrowth and social and cognitive behavioral deficits, in adult mice. Blockade of MAPK hyperactivation normalizes let-7 miRNA levels in both brain and peripheral blood plasma from Fmr1 KO mice. These results implicate dysregulated let-7 miRNA biogenesis in the pathogenesis of FMRP-deficiency, and highlight let-7 miRNA-based strategies for future biomarker and therapeutic development.
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Affiliation(s)
- Megha Subramanian
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William T. Mills
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manish D. Paranjpe
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Uche S. Onuchukwu
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manasi Inamdar
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amanda R. Maytin
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinbei Li
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joel L. Pomerantz
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mollie K. Meffert
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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8
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Zou Z, Wei J, Chen Y, Kang Y, Shi H, Yang F, Shi Z, Chen S, Zhou Y, Sepich-Poore C, Zhuang X, Zhou X, Jiang H, Wen Z, Jin P, Luo C, He C. FMRP phosphorylation modulates neuronal translation through YTHDF1. Mol Cell 2023; 83:4304-4317.e8. [PMID: 37949069 PMCID: PMC10872974 DOI: 10.1016/j.molcel.2023.10.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 09/12/2023] [Accepted: 10/19/2023] [Indexed: 11/12/2023]
Abstract
RNA-binding proteins (RBPs) control messenger RNA fate in neurons. Here, we report a mechanism that the stimuli-induced neuronal translation is mediated by phosphorylation of a YTHDF1-binding protein FMRP. Mechanistically, YTHDF1 can condense with ribosomal proteins to promote the translation of its mRNA targets. FMRP regulates this process by sequestering YTHDF1 away from the ribosome; upon neuronal stimulation, FMRP becomes phosphorylated and releases YTHDF1 for translation upregulation. We show that a new small molecule inhibitor of YTHDF1 can reverse fragile X syndrome (FXS) developmental defects associated with FMRP deficiency in an organoid model. Our study thus reveals that FMRP and its phosphorylation are important regulators of activity-dependent translation during neuronal development and stimulation and identifies YTHDF1 as a potential therapeutic target for FXS in which developmental defects caused by FMRP depletion could be reversed through YTHDF1 inhibition.
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Affiliation(s)
- Zhongyu Zou
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Yantao Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yunhee Kang
- Department of Psychiatry and Behavioral Sciences, Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hailing Shi
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Fan Yang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Zhuoyue Shi
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Shijie Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Ying Zhou
- Department of Psychiatry and Behavioral Sciences, Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Caraline Sepich-Poore
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoxi Zhuang
- Department of Neurobiology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoming Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hualiang Jiang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Psychiatry and Behavioral Sciences, Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
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Yu J, Woo Y, Kim H, An S, Park SK, Jang SK. FMRP Enhances the Translation of 4EBP2 mRNA during Neuronal Differentiation. Int J Mol Sci 2023; 24:16319. [PMID: 38003508 PMCID: PMC10671300 DOI: 10.3390/ijms242216319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
FMRP is a multifunctional protein encoded by the Fragile X Messenger Ribonucleoprotein 1 gene (FMR1). The inactivation of the FMR1 gene results in fragile X syndrome (FXS), a serious neurodevelopmental disorder. FMRP deficiency causes abnormal neurite outgrowth, which is likely to lead to abnormal learning and memory capabilities. However, the mechanism of FMRP in modulating neuronal development remains unknown. We found that FMRP enhances the translation of 4EBP2, a neuron-specific form of 4EBPs that inactivates eIF4E by inhibiting the interaction between eIF4E and eIF4G. Depletion of 4EBP2 results in abnormal neurite outgrowth. Moreover, the impairment of neurite outgrowth upon FMRP depletion was overcome by the ectopic expression of 4EBP2. These results suggest that FMRP controls neuronal development by enhancing 4EBP2 expression at the translational level. In addition, treatment with 4EGI-1, a chemical that blocks eIF4E activity, restored neurite length in FMRP-depleted and 4EBP2-depleted cells. In conclusion, we discovered that 4EBP2 functions as a key downstream regulator of FMRP activity in neuronal development and that FMRP represses eIF4E activity by enhancing 4EBP2 translation.
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Affiliation(s)
| | | | | | | | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Gyeongsangbuk, Republic of Korea; (J.Y.); (Y.W.); (H.K.); (S.A.)
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Gyeongsangbuk, Republic of Korea; (J.Y.); (Y.W.); (H.K.); (S.A.)
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10
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Maltman N, Willer R, Sterling A. An Exploratory Study of Pragmatic Language Use Across Contexts With the Pragmatic Rating Scale-School Age Among Autistic Boys and Boys With Fragile X Syndrome Plus Autism. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2023; 66:4547-4557. [PMID: 37844621 PMCID: PMC10721239 DOI: 10.1044/2023_jslhr-23-00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/21/2023] [Accepted: 08/24/2023] [Indexed: 10/18/2023]
Abstract
PURPOSE Autistic boys and boys with co-occurring fragile X syndrome and autism spectrum disorder (FXS + ASD) demonstrate similar pragmatic language difficulties. The Pragmatic Rating Scale-School Age (PRS-SA) captures ecologically valid metrics of pragmatic language impairments in these populations. It is traditionally scored based on the Autism Diagnostic Observation Schedule (ADOS), which may limit the use of the PRS-SA more broadly in research and clinical contexts. METHOD This study evaluated the feasibility of the PRS-SA based on a shorter, semistructured conversational context compared to the ADOS in school-age autistic boys (n = 16) and boys with FXS + ASD (n = 16), matched on ASD traits. Differences across ADOS and conversational contexts and associations with ASD-related social difficulties were evaluated. RESULTS Findings revealed differences in PRS-SA scores between ADOS and conversational contexts, but only for the FXS + ASD group. Limited associations were observed between PRS-SA scores and ASD traits. CONCLUSIONS Results from this study indicate the feasibility of using the PRS-SA in a shorter conversational context than the ADOS to assess pragmatic language among autistic boys. For boys with FXS + ASD, contextual differences warrant careful consideration in future work.
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Affiliation(s)
| | - Rebecca Willer
- Department of Communication Sciences and Disorders, University of Wisconsin–Madison
| | - Audra Sterling
- Waisman Center, University of Wisconsin–Madison
- Department of Communication Sciences and Disorders, University of Wisconsin–Madison
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11
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Benachenhou S, Laroui A, Dionne O, Rojas D, Toupin A, Çaku A. Cholesterol alterations in fragile X syndrome, autism spectrum disorders and other neurodevelopmental disorders. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2023; 173:115-139. [PMID: 37993175 DOI: 10.1016/bs.irn.2023.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Neurodevelopmental disorders (NDDs) are a group of etiologically diverse diseases primarily associated with abnormal brain development, impaired cognition, and various behavioral problems. The majority of NDDs present a wide range of clinical phenotypes while sharing distinct cellular and biochemical alterations. Low plasma cholesterol levels have been reported in a subset of NNDs including, autism spectrum disorder (ASD) and fragile X syndrome (FXS). The present review focuses on cholesterol metabolism and discusses the current evidence of lipid disruption in ASD, FXS, and other genetically related NDDs. The characterization of these common deficits might provide valuable insights into their underlying physiopathology and help identify potential therapeutic targets.
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Affiliation(s)
- Sérine Benachenhou
- Biochemistry and Functional Genomic Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Asma Laroui
- Biochemistry and Functional Genomic Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Olivier Dionne
- Biochemistry and Functional Genomic Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Daniela Rojas
- Biochemistry and Functional Genomic Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Amanda Toupin
- Biochemistry and Functional Genomic Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Artuela Çaku
- Biochemistry and Functional Genomic Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.
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12
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Gundermann DG, Lymer S, Blau J. A rapid and dynamic role for FMRP in the plasticity of adult neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555985. [PMID: 37693612 PMCID: PMC10491314 DOI: 10.1101/2023.09.01.555985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Fragile X syndrome (FXS) is a neuro-developmental disorder caused by silencing Fmr1, which encodes the RNA-binding protein FMRP. Although Fmr1 is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss of Fmr1 in models of FXS. We have used the precision of Drosophila genetics to test if Fmr1 acutely affects adult neuronal plasticity in vivo, focusing on the s-LNv circadian pacemaker neurons that show 24 hour rhythms in structural plasticity. We found that over-expressing Fmr1 for only 4 hours blocks the activity-dependent expansion of s-LNv projections without altering the circadian clock or activity-regulated gene expression. Conversely, acutely reducing Fmr1 expression prevented s-LNv projections from retracting. One FMRP target that we identified in s-LNvs is sif, which encodes a Rac1 GEF. Our data indicate that FMRP normally reduces sif mRNA translation at dusk to reduce Rac1 activity. Overall, our data reveal a previously unappreciated rapid and direct role for FMRP in acutely regulating neuronal plasticity in adult neurons, and underscore the importance of RNA-binding proteins in this process.
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Affiliation(s)
- Daniel G Gundermann
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Seana Lymer
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
- Current address: Proteintech Genomics, 11588 Sorrento Valley Rd, San Diego, CA 92121
| | - Justin Blau
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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13
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Villalobos-Cantor S, Barrett RM, Condon AF, Arreola-Bustos A, Rodriguez KM, Cohen MS, Martin I. Rapid cell type-specific nascent proteome labeling in Drosophila. eLife 2023; 12:83545. [PMID: 37092974 PMCID: PMC10125018 DOI: 10.7554/elife.83545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/09/2023] [Indexed: 04/25/2023] Open
Abstract
Controlled protein synthesis is required to regulate gene expression and is often carried out in a cell type-specific manner. Protein synthesis is commonly measured by labeling the nascent proteome with amino acid analogs or isotope-containing amino acids. These methods have been difficult to implement in vivo as they require lengthy amino acid replacement procedures. O-propargyl-puromycin (OPP) is a puromycin analog that incorporates into nascent polypeptide chains. Through its terminal alkyne, OPP can be conjugated to a fluorophore-azide for directly visualizing nascent protein synthesis, or to a biotin-azide for capture and identification of newly-synthesized proteins. To achieve cell type-specific OPP incorporation, we developed phenylacetyl-OPP (PhAc-OPP), a puromycin analog harboring an enzyme-labile blocking group that can be removed by penicillin G acylase (PGA). Here, we show that cell type-specific PGA expression in Drosophila can be used to achieve OPP labeling of newly-synthesized proteins in targeted cell populations within the brain. Following a brief 2 hr incubation of intact brains with PhAc-OPP, we observe robust imaging and affinity purification of OPP-labeled nascent proteins in PGA-targeted cell populations. We apply this method to show a pronounced age-related decline in neuronal protein synthesis in the fly brain, demonstrating the capability of PhAc-OPP to quantitatively capture in vivo protein synthesis states. This method, which we call POPPi (PGA-dependent OPP incorporation), should be applicable for rapidly visualizing protein synthesis and identifying nascent proteins synthesized under diverse physiological and pathological conditions with cellular specificity in vivo.
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Affiliation(s)
- Stefanny Villalobos-Cantor
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Ruth M Barrett
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alec F Condon
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alicia Arreola-Bustos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Kelsie M Rodriguez
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
- Parkinson Center of Oregon, Oregon Health and Science University, Portland, United States
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14
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Geng J, Khaket TP, Pan J, Li W, Zhang Y, Ping Y, Cobos Sillero MI, Lu B. Deregulation of ER-mitochondria contact formation and mitochondrial calcium homeostasis mediated by VDAC in fragile X syndrome. Dev Cell 2023; 58:597-615.e10. [PMID: 37040696 PMCID: PMC10113018 DOI: 10.1016/j.devcel.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 07/31/2022] [Accepted: 03/06/2023] [Indexed: 04/13/2023]
Abstract
Loss of fragile X messenger ribonucleoprotein (FMRP) causes fragile X syndrome (FXS), the most prevalent form of inherited intellectual disability. Here, we show that FMRP interacts with the voltage-dependent anion channel (VDAC) to regulate the formation and function of endoplasmic reticulum (ER)-mitochondria contact sites (ERMCSs), structures that are critical for mitochondrial calcium (mito-Ca2+) homeostasis. FMRP-deficient cells feature excessive ERMCS formation and ER-to-mitochondria Ca2+ transfer. Genetic and pharmacological inhibition of VDAC or other ERMCS components restored synaptic structure, function, and plasticity and rescued locomotion and cognitive deficits of the Drosophila dFmr1 mutant. Expressing FMRP C-terminal domain (FMRP-C), which confers FMRP-VDAC interaction, rescued the ERMCS formation and mito-Ca2+ homeostasis defects in FXS patient iPSC-derived neurons and locomotion and cognitive deficits in Fmr1 knockout mice. These results identify altered ERMCS formation and mito-Ca2+ homeostasis as contributors to FXS and offer potential therapeutic targets.
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Affiliation(s)
- Ji Geng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tejinder Pal Khaket
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jie Pan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wen Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yong Ping
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Key Laboratory of Psychotic Disorders (No. 13dz2260500), Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | | | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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15
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Svalina MN, Sullivan R, Restrepo D, Huntsman MM. From circuits to behavior: Amygdala dysfunction in fragile X syndrome. Front Integr Neurosci 2023; 17:1128529. [PMID: 36969493 PMCID: PMC10034113 DOI: 10.3389/fnint.2023.1128529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by a repeat expansion mutation in the promotor region of the FMR1 gene resulting in transcriptional silencing and loss of function of fragile X messenger ribonucleoprotein 1 protein (FMRP). FMRP has a well-defined role in the early development of the brain. Thus, loss of the FMRP has well-known consequences for normal cellular and synaptic development leading to a variety of neuropsychiatric disorders including an increased prevalence of amygdala-based disorders. Despite our detailed understanding of the pathophysiology of FXS, the precise cellular and circuit-level underpinnings of amygdala-based disorders is incompletely understood. In this review, we discuss the development of the amygdala, the role of neuromodulation in the critical period plasticity, and recent advances in our understanding of how synaptic and circuit-level changes in the basolateral amygdala contribute to the behavioral manifestations seen in FXS.
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Affiliation(s)
- Matthew N. Svalina
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Regina Sullivan
- Brain Institute, Nathan Kline Institute, Orangeburg, NY, United States
- Child and Adolescent Psychiatry, Child Study Center, New York University School of Medicine, New York, NY, United States
| | - Diego Restrepo
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Molly M. Huntsman
- Neuroscience Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- *Correspondence: Molly M. Huntsman,
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16
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FMRP activity and control of Csw/SHP2 translation regulate MAPK-dependent synaptic transmission. PLoS Biol 2023; 21:e3001969. [PMID: 36701299 PMCID: PMC9879533 DOI: 10.1371/journal.pbio.3001969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 12/16/2022] [Indexed: 01/27/2023] Open
Abstract
Noonan syndrome (NS) and NS with multiple lentigines (NSML) cognitive dysfunction are linked to SH2 domain-containing protein tyrosine phosphatase-2 (SHP2) gain-of-function (GoF) and loss-of-function (LoF), respectively. In Drosophila disease models, we find both SHP2 mutations from human patients and corkscrew (csw) homolog LoF/GoF elevate glutamatergic transmission. Cell-targeted RNAi and neurotransmitter release analyses reveal a presynaptic requirement. Consistently, all mutants exhibit reduced synaptic depression during high-frequency stimulation. Both LoF and GoF mutants also show impaired synaptic plasticity, including reduced facilitation, augmentation, and post-tetanic potentiation. NS/NSML diseases are characterized by elevated MAPK/ERK signaling, and drugs suppressing this signaling restore normal neurotransmission in mutants. Fragile X syndrome (FXS) is likewise characterized by elevated MAPK/ERK signaling. Fragile X Mental Retardation Protein (FMRP) binds csw mRNA and neuronal Csw protein is elevated in Drosophila fragile X mental retardation 1 (dfmr1) nulls. Moreover, phosphorylated ERK (pERK) is increased in dfmr1 and csw null presynaptic boutons. We find presynaptic pERK activation in response to stimulation is reduced in dfmr1 and csw nulls. Trans-heterozygous csw/+; dfmr1/+ recapitulate elevated presynaptic pERK activation and function, showing FMRP and Csw/SHP2 act within the same signaling pathway. Thus, a FMRP and SHP2 MAPK/ERK regulative mechanism controls basal and activity-dependent neurotransmission strength.
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17
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Kulkarni A, Vidal-Henriquez E, Zwicker D. Effective simulations of interacting active droplets. Sci Rep 2023; 13:733. [PMID: 36639416 PMCID: PMC9839783 DOI: 10.1038/s41598-023-27630-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional approaches, like solving the Cahn-Hilliard equation. To overcome this challenge, we here present an alternative, efficient method. The main idea is to focus on the relevant degrees of freedom, like droplet positions and sizes. We derive dynamical equations for these quantities using approximate analytical solutions obtained from a sharp interface limit and linearized equations in the bulk phases. We verify our method against fully-resolved simulations and show that it can describe interacting droplets under the influence of chemical reactions and external gradients using only a fraction of the computational costs of traditional methods. Our method can be extended to include other processes in the future and will thus serve as a relevant platform for understanding the dynamics of droplets in cells.
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Affiliation(s)
- Ajinkya Kulkarni
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | | | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany.
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18
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Chowdhury MN, Jin H. The RGG motif proteins: Interactions, functions, and regulations. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1748. [PMID: 35661420 PMCID: PMC9718894 DOI: 10.1002/wrna.1748] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 01/31/2023]
Abstract
Proteins with motifs rich in arginines and glycines were discovered decades ago and are functionally involved in a staggering range of essential processes in the cell. Versatile, specific, yet adaptable molecular interactions enabled by the unique combination of arginine and glycine, combined with multiplicity of molecular recognition conferred by repeated di-, tri-, and multiple peptide motifs, allow RGG motif proteins to interact with a broad range of proteins and nucleic acids. Furthermore, posttranslational modifications at the arginines in the motif extend the RGG protein's capacity for a fine-tuned regulation. In this review, we focus on the biochemical properties of the RGG motif, its molecular interactions with RNAs and proteins, and roles of the posttranslational modification in modulating their interactions. We discuss current knowledge of the RGG motif proteins involved in mRNA transport and translation, highlight our merging understanding of their molecular functions in translational regulation and summarize areas of research in the future critical in understanding this important family of proteins. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Mechanisms.
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Affiliation(s)
- Mashiat N. Chowdhury
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801,Corresponding author: Phone: (217)244-9493, Fax: (217)244-5858,
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19
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Zhang Y, Kang JY, Liu M, Huang Y. Diverse roles of biomolecular condensation in eukaryotic translational regulation. RNA Biol 2023; 20:893-907. [PMID: 37906632 PMCID: PMC10730148 DOI: 10.1080/15476286.2023.2275108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/02/2023] Open
Abstract
Biomolecular condensates, forming membrane-less organelles, orchestrate the sub-cellular compartment to execute designated biological processes. An increasing body of evidence demonstrates the involvement of these biomolecular condensates in translational regulation. This review summarizes recent discoveries concerning biomolecular condensates associated with translational regulation, including their composition, assembly, and functions. Furthermore, we discussed the common features among these biomolecular condensates and the critical questions in the translational regulation areas. These emerging discoveries shed light on the enigmatic translational machinery, refine our understanding of translational regulation, and put forth potential therapeutic targets for diseases born out of translation dysregulation.
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Grants
- 32171186 AND 91940302 National Natural Science Foundation of China
- 91940305, 31830109, 31821004, 31961133022, 91640201, 32170815, AND 32101037 TO M.L., AND 32201058 National Natural Science Foundation of China
- 2022YFC2702600 National Key R&D Program of China
- 17JC1420100, 2017SHZDZX01, 19JC1410200, 21ZR1470200, 21PJ1413800, 21YF1452700, AND 21ZR1470500 Science and Technology Commission of Shanghai Municipality
- 2022YFC2702600 National Key R&D Program of China
- 2022T150425 China Postdoctoral Science Foundation
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Affiliation(s)
- Yuhan Zhang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Yan Kang
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mofang Liu
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ying Huang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
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20
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Kurosaki T, Mitsutomi S, Hewko A, Akimitsu N, Maquat LE. Integrative omics indicate FMRP sequesters mRNA from translation and deadenylation in human neuronal cells. Mol Cell 2022; 82:4564-4581.e11. [PMID: 36356584 PMCID: PMC9753132 DOI: 10.1016/j.molcel.2022.10.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/17/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
How fragile X syndrome protein (FMRP) binds mRNAs and regulates mRNA metabolism remains unclear. Our previous work using human neuronal cells focused on mRNAs targeted for nonsense-mediated mRNA decay (NMD), which we showed are generally bound by FMRP and destabilized upon FMRP loss. Here, we identify >400 high-confidence FMRP-bound mRNAs, only ∼35% of which are NMD targets. Integrative transcriptomics together with SILAC-LC-MS/MS reveal that FMRP loss generally results in mRNA destabilization and more protein produced per FMRP target. We use our established RIP-seq technology to show that FMRP footprints are independent of protein-coding potential, target GC-rich and structured sequences, and are densest in 5' UTRs. Regardless of where within an mRNA FMRP binds, we find that FMRP protects mRNAs from deadenylation and directly binds the cytoplasmic poly(A)-binding protein. Our results reveal how FMRP sequesters polyadenylated mRNAs into stabilized and translationally repressed complexes, whose regulation is critical for neurogenesis and synaptic plasticity.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
| | - Shuhei Mitsutomi
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA; Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Alexander Hewko
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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21
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Abstract
Recent advances in genomics have revealed a wide spectrum of genetic variants associated with neurodevelopmental disorders at an unprecedented scale. An increasing number of studies have consistently identified mutations-both inherited and de novo-impacting the function of specific brain circuits. This suggests that, during brain development, alterations in distinct neural circuits, cell types, or broad regulatory pathways ultimately shaping synapses might be a dysfunctional process underlying these disorders. Here, we review findings from human studies and animal model research to provide a comprehensive description of synaptic and circuit mechanisms implicated in neurodevelopmental disorders. We discuss how specific synaptic connections might be commonly disrupted in different disorders and the alterations in cognition and behaviors emerging from imbalances in neuronal circuits. Moreover, we review new approaches that have been shown to restore or mitigate dysfunctional processes during specific critical windows of brain development. Considering the heterogeneity of neurodevelopmental disorders, we also highlight the recent progress in developing improved clinical biomarkers and strategies that will help to identify novel therapeutic compounds and opportunities for early intervention.
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Affiliation(s)
- David Exposito-Alonso
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom;
- Current affiliation: Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA;
| | - Beatriz Rico
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom;
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22
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Pre-conceptional and prenatal exposure to secondhand smoke and autism spectrum disorder: a national multi-center study in China. World J Pediatr 2022:10.1007/s12519-022-00644-z. [PMID: 36355326 DOI: 10.1007/s12519-022-00644-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Despite extensive research evaluating the association between prenatal exposure to secondhand smoke (SHS) and the development of autism spectrum disorders (ASD), no study has investigated the association by considering the pre-conceptional period. This study aimed to investigate the associations of pre-conceptional and prenatal SHS exposure and the development of ASD among toddlers. METHODS In this cross-sectional study, parents of 6049 toddlers aged 16-30 months were recruited from 7 tertiary hospitals, 21 communities, and 7 kindergartens located in seven cities in six provinces from five geographical regions of China. We analyzed the associations of SHS exposure and the odds of ASD among toddlers in different exposure windows (pre-conceptional and/or prenatal periods). Data were analyzed from November 2021 to January 2022. RESULTS Among the 6049 toddlers included in the analysis [22.7 (4.1) months; 44.8% girls], 71 were identified and diagnosed with ASD. Compared with the unexposed toddlers, toddlers with pre-conceptional SHS exposure had higher odds of ASD (OR 2.30, 95% CI 1.36-3.84), while we observed a non-significantly positive association regarding prenatal SHS exposure. When considering both pre-conceptional and prenatal periods, toddlers who were continuously exposed to SHS during these two periods had higher odds than those without SHS exposure (OR 2.32, 95% CI 1.24-4.14). CONCLUSION We reported positive SHS-ASD associations when exposed during the pre-conceptional period and continuously exposed during pre-conceptional and prenatal periods, emphasizing the critical window of pre-conception for targeted intervention on smoking.
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23
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Scarpitti MR, Warrick JE, Yoder EL, Kearse MG. A noncanonical RNA-binding domain of the fragile X protein, FMRP, elicits translational repression independent of mRNA G-quadruplexes. J Biol Chem 2022; 298:102660. [PMID: 36328245 PMCID: PMC9712993 DOI: 10.1016/j.jbc.2022.102660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Loss of functional fragile X mental retardation protein (FMRP) causes fragile X syndrome, the leading form of inherited intellectual disability and the most common monogenic cause of autism spectrum disorders. FMRP is an RNA-binding protein that controls neuronal mRNA localization and translation. FMRP is thought to inhibit translation elongation after being recruited to target transcripts via binding RNA G-quadruplexes (G4s) within the coding sequence. Here, we directly test this model and report that FMRP inhibits translation independent of mRNA G4s. Furthermore, we found that the RGG box motif together with its natural C-terminal domain forms a noncanonical RNA-binding domain (ncRBD) that is essential for translational repression. The ncRBD elicits broad RNA-binding ability and binds to multiple reporter mRNAs and all four homopolymeric RNAs. Serial deletion analysis of the ncRBD identified that the regions required for mRNA binding and translational repression overlap but are not identical. Consistent with FMRP stalling elongating ribosomes and causing the accumulation of slowed 80S ribosomes, transcripts bound by FMRP via the ncRBD cosediment with heavier polysomes and were present in puromycin-resistant ribosome complexes. Together, this work identifies a ncRBD and translational repression domain that shifts our understanding of how FMRP inhibits translation independent of mRNA G4s.
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Affiliation(s)
- MaKenzie R. Scarpitti
- The Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Julia E. Warrick
- The Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Evelyn L. Yoder
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Michael G. Kearse
- The Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA,Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA,For correspondence: Michael G. Kearse
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24
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Subcellular spatial transcriptomics identifies three mechanistically different classes of localizing RNAs. Nat Commun 2022; 13:6355. [PMID: 36289223 PMCID: PMC9606379 DOI: 10.1038/s41467-022-34004-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 10/03/2022] [Indexed: 12/25/2022] Open
Abstract
Intracellular RNA localization is a widespread and dynamic phenomenon that compartmentalizes gene expression and contributes to the functional polarization of cells. Thus far, mechanisms of RNA localization identified in Drosophila have been based on a few RNAs in different tissues, and a comprehensive mechanistic analysis of RNA localization in a single tissue is lacking. Here, by subcellular spatial transcriptomics we identify RNAs localized in the apical and basal domains of the columnar follicular epithelium (FE) and we analyze the mechanisms mediating their localization. Whereas the dynein/BicD/Egl machinery controls apical RNA localization, basally-targeted RNAs require kinesin-1 to overcome a default dynein-mediated transport. Moreover, a non-canonical, translation- and dynein-dependent mechanism mediates apical localization of a subgroup of dynein-activating adaptor-encoding RNAs (BicD, Bsg25D, hook). Altogether, our study identifies at least three mechanisms underlying RNA localization in the FE, and suggests a possible link between RNA localization and dynein/dynactin/adaptor complex formation in vivo.
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25
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Susco SG, Ghosh S, Mazzucato P, Angelini G, Beccard A, Barrera V, Berryer MH, Messana A, Lam D, Hazelbaker DZ, Barrett LE. Molecular convergence between Down syndrome and fragile X syndrome identified using human pluripotent stem cell models. Cell Rep 2022; 40:111312. [PMID: 36070702 PMCID: PMC9465809 DOI: 10.1016/j.celrep.2022.111312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/19/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Down syndrome (DS), driven by an extra copy of chromosome 21 (HSA21), and fragile X syndrome (FXS), driven by loss of the RNA-binding protein FMRP, are two common genetic causes of intellectual disability and autism. Based upon the number of DS-implicated transcripts bound by FMRP, we hypothesize that DS and FXS may share underlying mechanisms. Comparing DS and FXS human pluripotent stem cell (hPSC) and glutamatergic neuron models, we identify increased protein expression of select targets and overlapping transcriptional perturbations. Moreover, acute upregulation of endogenous FMRP in DS patient cells using CRISPRa is sufficient to significantly reduce expression levels of candidate proteins and reverse 40% of global transcriptional perturbations. These results pinpoint specific molecular perturbations shared between DS and FXS that can be leveraged as a strategy for target prioritization; they also provide evidence for the functional relevance of previous associations between FMRP targets and disease-implicated genes. Many neurodevelopmental disorders driven by distinct genetic alterations share phenotypes, but the extent to which they share underlying mechanisms remains an important unanswered question. Using transcript and protein-level analyses in human cellular models, Susco et al. uncover specific areas of molecular convergence between Down syndrome and fragile X syndrome.
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Affiliation(s)
- Sara G Susco
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrizia Mazzucato
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gabriella Angelini
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda Beccard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Victor Barrera
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Martin H Berryer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Angelica Messana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daisy Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dane Z Hazelbaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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26
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Kang JY, Wen Z, Pan D, Zhang Y, Li Q, Zhong A, Yu X, Wu YC, Chen Y, Zhang X, Kou PC, Geng J, Wang YY, Hua MM, Zong R, Li B, Shi HJ, Li D, Fu XD, Li J, Nelson DL, Guo X, Zhou Y, Gou LT, Huang Y, Liu MF. LLPS of FXR1 drives spermiogenesis by activating translation of stored mRNAs. Science 2022; 377:eabj6647. [PMID: 35951695 DOI: 10.1126/science.abj6647] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Postmeiotic spermatids use a unique strategy to coordinate gene expression with morphological transformation, in which transcription and translation take place at separate developmental stages, but how mRNAs stored as translationally inert messenger ribonucleoproteins in developing spermatids become activated remains largely unknown. Here, we report that the RNA binding protein FXR1, a member of the fragile X-related (FXR) family, is highly expressed in late spermatids and undergoes liquid-liquid phase separation (LLPS) to merge messenger ribonucleoprotein granules with the translation machinery to convert stored mRNAs into a translationally activated state. Germline-specific Fxr1 ablation in mice impaired the translation of target mRNAs and caused defective spermatid development and male infertility, and a phase separation-deficient FXR1L351P mutation in Fxr1 knock-in mice produced the same developmental defect. These findings uncover a mechanism for translational reprogramming with LLPS as a key driver in spermiogenesis.
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Affiliation(s)
- Jun-Yan Kang
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ze Wen
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Duo Pan
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuhan Zhang
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ai Zhong
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xinghai Yu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yi-Chen Wu
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiangzheng Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Peng-Cheng Kou
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Junlan Geng
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ying-Yi Wang
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Min-Min Hua
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
| | - Ruiting Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Biao Li
- Department of Nuclear Medicine, Rui Jin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Hui-Juan Shi
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai, China
| | - Dangsheng Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Jinsong Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - David L Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Zhou
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China.,Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Lan-Tao Gou
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ying Huang
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
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27
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Su S, Xue Y, Sharov A, Zhang Y, Lee SK, Martindale J, Li W, Ku WL, Zhao K, De S, Shen W, Sen P, Gorospe M, Xu D, Wang W. A dual-activity topoisomerase complex regulates mRNA translation and turnover. Nucleic Acids Res 2022; 50:7013-7033. [PMID: 35748872 PMCID: PMC9262614 DOI: 10.1093/nar/gkac538] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/06/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
Topoisomerase 3β (TOP3B) and TDRD3 form a dual-activity topoisomerase complex that interacts with FMRP and can change the topology of both DNA and RNA. Here, we investigated the post-transcriptional influence of TOP3B and associated proteins on mRNA translation and turnover. First, we discovered that in human HCT116 colon cancer cells, knock-out (KO) of TOP3B had similar effects on mRNA turnover and translation as did TDRD3-KO, while FMRP-KO resulted in rather distinct effects, indicating that TOP3B had stronger coordination with TDRD3 than FMRP in mRNA regulation. Second, we identified TOP3B-bound mRNAs in HCT116 cells; we found that while TOP3B did not directly influence the stability or translation of most TOP3B target mRNAs, it stabilized a subset of target mRNAs but had a more complex effect on translation-enhancing for some mRNAs whereas reducing for others. Interestingly, a point mutation that specifically disrupted TOP3B catalytic activity only partially recapitulated the effects of TOP3B-KO on mRNA stability and translation, suggesting that the impact of TOP3B on target mRNAs is partly linked to its ability to change topology of mRNAs. Collectively, our data suggest that TOP3B-TDRD3 can regulate mRNA translation and turnover by mechanisms that are dependent and independent of topoisomerase activity.
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Affiliation(s)
- Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alexei Sharov
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Wai Lim Ku
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 1000871, China
| | - Weidong Wang
- To whom correspondence should be addressed. Tel: +1 410 454 8418; Fax: +1 410 558 8331.
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28
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Flanagan K, Baradaran-Heravi A, Yin Q, Dao Duc K, Spradling AC, Greenblatt EJ. FMRP-dependent production of large dosage-sensitive proteins is highly conserved. Genetics 2022; 221:6613139. [PMID: 35731217 PMCID: PMC9339308 DOI: 10.1093/genetics/iyac094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022] Open
Abstract
Mutations in FMR1 are the most common heritable cause of autism spectrum disorder. FMR1 encodes an RNA-binding protein, FMRP, which binds to long, autism-relevant transcripts and is essential for normal neuronal and ovarian development. In contrast to the prevailing model that FMRP acts to block translation elongation, we previously found that FMRP activates the translation initiation of large proteins in Drosophila oocytes. We now provide evidence that FMRP-dependent translation is conserved and occurs in the mammalian brain. Our comparisons of the mammalian cortex and Drosophila oocyte ribosome profiling data show that translation of FMRP-bound mRNAs decreases to a similar magnitude in FMRP-deficient tissues from both species. The steady-state levels of several FMRP targets were reduced in the Fmr1 KO mouse cortex, including a ∼50% reduction of Auts2, a gene implicated in an autosomal dominant autism spectrum disorder. To distinguish between effects on elongation and initiation, we used a novel metric to detect the rate-limiting ribosome stalling. We found no evidence that FMRP target protein production is governed by translation elongation rates. FMRP translational activation of large proteins may be critical for normal human development, as more than 20 FMRP targets including Auts2 are dosage sensitive and are associated with neurodevelopmental disorders caused by haploinsufficiency.
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Affiliation(s)
- Keegan Flanagan
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Qi Yin
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, British Columbia, BC V6T 1Z2
| | - Allan C Spradling
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
| | - Ethan J Greenblatt
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3 Canada.,Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, Maryland 21218 USA
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29
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Peng Y, Gavis ER. The Drosophila hnRNP F/H homolog Glorund recruits dFMRP to inhibit nanos translation elongation. Nucleic Acids Res 2022; 50:7067-7083. [PMID: 35699205 PMCID: PMC9262583 DOI: 10.1093/nar/gkac500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
Translational control of maternal mRNAs generates spatial and temporal patterns of protein expression necessary to begin animal development. Translational repression of unlocalized nanos (nos) mRNA in late-stage Drosophila oocytes by the hnRNP F/H homolog, Glorund (Glo), is important for embryonic body patterning. While previous work has suggested that repression occurs at both the translation initiation and elongation phases, the molecular mechanism by which Glo regulates nos translation remains elusive. Here, we have identified the Drosophila fragile X mental retardation protein, dFMRP, as a Glo interaction partner with links to the translational machinery. Using an oocyte-based in vitro translation system, we confirmed that Glo regulates both initiation and elongation of a nos translational reporter and showed that dFMRP specifically represses translation elongation and promotes ribosome stalling. Furthermore, we combined mutational analysis and in vivo and in vitro binding assays to show that Glo's qRRM2 domain specifically and directly interacts with dFMRP. Our findings suggest that Glo regulates nos translation elongation by recruiting dFMRP and that Glo's RNA-binding domains can also function as protein-protein interaction interfaces critical for its regulatory functions. Additionally, they reveal a mechanism for targeting dFMRP to specific transcripts.
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Affiliation(s)
- Yingshi Peng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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30
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Seo SS, Louros SR, Anstey N, Gonzalez-Lozano MA, Harper CB, Verity NC, Dando O, Thomson SR, Darnell JC, Kind PC, Li KW, Osterweil EK. Excess ribosomal protein production unbalances translation in a model of Fragile X Syndrome. Nat Commun 2022; 13:3236. [PMID: 35688821 PMCID: PMC9187743 DOI: 10.1038/s41467-022-30979-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/23/2022] [Indexed: 12/21/2022] Open
Abstract
Dysregulated protein synthesis is a core pathogenic mechanism in Fragile X Syndrome (FX). The mGluR Theory of FX predicts that pathological synaptic changes arise from the excessive translation of mRNAs downstream of mGlu1/5 activation. Here, we use a combination of CA1 pyramidal neuron-specific TRAP-seq and proteomics to identify the overtranslating mRNAs supporting exaggerated mGlu1/5 -induced long-term synaptic depression (mGluR-LTD) in the FX mouse model (Fmr1−/y). Our results identify a significant increase in the translation of ribosomal proteins (RPs) upon mGlu1/5 stimulation that coincides with a reduced translation of long mRNAs encoding synaptic proteins. These changes are mimicked and occluded in Fmr1−/y neurons. Inhibiting RP translation significantly impairs mGluR-LTD and prevents the length-dependent shift in the translating population. Together, these results suggest that pathological changes in FX result from a length-dependent alteration in the translating population that is supported by excessive RP translation. Dysregulated protein synthesis is key contributor to Fragile X syndrome. Here the authors identify a relationship between ribosome expression and the translation of long mRNAs that contributes to synaptic weakening in a model of Fragile X syndrome.
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Affiliation(s)
- Sang S Seo
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Susana R Louros
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Natasha Anstey
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Miguel A Gonzalez-Lozano
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Callista B Harper
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Nicholas C Verity
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Owen Dando
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Sophie R Thomson
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Jennifer C Darnell
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Peter C Kind
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Emily K Osterweil
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK. .,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK.
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31
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Bülow P, Segal M, Bassell GJ. Mechanisms Driving the Emergence of Neuronal Hyperexcitability in Fragile X Syndrome. Int J Mol Sci 2022; 23:ijms23116315. [PMID: 35682993 PMCID: PMC9181819 DOI: 10.3390/ijms23116315] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
Hyperexcitability is a shared neurophysiological phenotype across various genetic neurodevelopmental disorders, including Fragile X syndrome (FXS). Several patient symptoms are associated with hyperexcitability, but a puzzling feature is that their onset is often delayed until their second and third year of life. It remains unclear how and why hyperexcitability emerges in neurodevelopmental disorders. FXS is caused by the loss of FMRP, an RNA-binding protein which has many critical roles including protein synthesis-dependent and independent regulation of ion channels and receptors, as well as global regulation of protein synthesis. Here, we discussed recent literature uncovering novel mechanisms that may drive the progressive onset of hyperexcitability in the FXS brain. We discussed in detail how recent publications have highlighted defects in homeostatic plasticity, providing new insight on the FXS brain and suggest pharmacotherapeutic strategies in FXS and other neurodevelopmental disorders.
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Affiliation(s)
- Pernille Bülow
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Correspondence: (P.B.); (G.J.B.)
| | - Menahem Segal
- Department of Brain Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Correspondence: (P.B.); (G.J.B.)
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32
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The Use of “Retardation” in FRAXA, FMRP, FMR1 and Other Designations. Cells 2022; 11:cells11061044. [PMID: 35326495 PMCID: PMC8947541 DOI: 10.3390/cells11061044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
The European Fragile X Network met in Wroclaw, Poland, November 2021, and agreed to work towards the eradication of the word “retardation” in regard to the naming of the fragile X gene (FRAXA) and protein (FMRP). There are further genes which have “retardation” or abbreviations for “retardation” in their names or full designations, including FMR1, FMR2, FXR1, FXR2, NUFIP1, AFF1, CYFIP1, etc. “Retardation” was commonly used as a term in years past, but now any reference, even in an abbreviation, is offensive. This article discusses the stigmatisation associated with “retardation”, which leads to discrimination; the inaccuracy of using “retardation” in these designations; and the breadth of fragile X syndrome being beyond that of neurodiversity. A more inclusive terminology is called for, one which ceases to use any reference to “retardation”. Precedents for offensive gene names being altered is set out. The proposal is to approach the HGNC (HUGO [Human Genome Organisation] Gene Nomenclature Committee) for new terminology to be enacted. Ideas from other researchers in the field are welcomed.
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33
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Gandara ACP, Drummond-Barbosa D. Warm and cold temperatures have distinct germline stem cell lineage effects during Drosophila oogenesis. Development 2022; 149:274368. [PMID: 35156684 PMCID: PMC8959152 DOI: 10.1242/dev.200149] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022]
Abstract
Despite their medical and economic relevance, it remains largely unknown how suboptimal temperatures affect adult insect reproduction. Here, we report an in-depth analysis of how chronic adult exposure to suboptimal temperatures affects oogenesis using the model insect Drosophila melanogaster. In adult females maintained at 18°C (cold) or 29°C (warm), relative to females at the 25°C control temperature, egg production was reduced through distinct cellular mechanisms. Chronic 18°C exposure improved germline stem cell maintenance, survival of early germline cysts and oocyte quality, but reduced follicle growth with no obvious effect on vitellogenesis. By contrast, in females at 29°C, germline stem cell numbers and follicle growth were similar to those at 25°C, while early germline cyst death and degeneration of vitellogenic follicles were markedly increased and oocyte quality plummeted over time. Finally, we also show that these effects are largely independent of diet, male factors or canonical temperature sensors. These findings are relevant not only to cold-blooded organisms, which have limited thermoregulation, but also potentially to warm-blooded organisms, which are susceptible to hypothermia, heatstroke and fever.
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Affiliation(s)
- Ana Caroline P Gandara
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Drummond-Barbosa
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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34
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Sears JC, Broadie K. Temporally and Spatially Localized PKA Activity within Learning and Memory Circuitry Regulated by Network Feedback. eNeuro 2022; 9:ENEURO.0450-21.2022. [PMID: 35301221 PMCID: PMC8982635 DOI: 10.1523/eneuro.0450-21.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/18/2022] [Accepted: 03/12/2022] [Indexed: 12/02/2022] Open
Abstract
Dynamic functional connectivity within brain circuits requires coordination of intercellular signaling and intracellular signal transduction. Critical roles for cAMP-dependent protein kinase A (PKA) signaling are well established in the Drosophila mushroom body (MB) learning and memory circuitry, but local PKA activity within this well-mapped neuronal network is uncharacterized. Here, we use an in vivo PKA activity sensor (PKA-SPARK) to test spatiotemporal regulatory requirements in the MB axon lobes. We find immature animals have little detectable PKA activity, whereas postcritical period adults show high field-selective activation primarily in just 3/16 defined output regions. In addition to the age-dependent PKA activity in distinct α'/β' lobe nodes, females show sex-dependent elevation compared with males in these same restricted regions. Loss of neural cell body Fragile X mental retardation protein (FMRP) and Rugose [human Neurobeachin (NBEA)] suppresses localized PKA activity, whereas overexpression (OE) of MB lobe PKA-synergist Meng-Po (human SBK1) promotes PKA activity. Elevated Meng-Po subverts the PKA age-dependence, with elevated activity in immature animals, and spatial-restriction, with striking γ lobe activity. Testing circuit signaling requirements with temperature-sensitive shibire (human Dynamin) blockade, we find broadly expanded PKA activity within the MB lobes. Using transgenic tetanus toxin to block MB synaptic output, we find greatly heightened PKA activity in virtually all MB lobe fields, although the age-dependence is maintained. We conclude spatiotemporally restricted PKA activity signaling within this well-mapped learning/memory circuit is age-dependent and sex-dependent, driven by FMRP-Rugose pathway activation, temporally promoted by Meng-Po kinase function, and restricted by output neurotransmission providing network feedback.
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Affiliation(s)
- James C Sears
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN 37235
- Vanderbilt Brain Institute, Vanderbilt University and Medical Center, Nashville, TN 37235
| | - Kendal Broadie
- Department of Biological Sciences, Vanderbilt University and Medical Center, Nashville, TN 37235
- Vanderbilt Brain Institute, Vanderbilt University and Medical Center, Nashville, TN 37235
- Department of Cell and Developmental Biology, Vanderbilt University and Medical Center, Nashville, TN 37235
- Department of Pharmacology, Vanderbilt University and Medical Center, Nashville, TN 37235
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Dynamic FMR1 granule phase switch instructed by m6A modification contributes to maternal RNA decay. Nat Commun 2022; 13:859. [PMID: 35165263 PMCID: PMC8844045 DOI: 10.1038/s41467-022-28547-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/18/2022] [Indexed: 01/28/2023] Open
Abstract
Maternal RNA degradation is critical for embryogenesis and is tightly controlled by maternal RNA-binding proteins. Fragile X mental-retardation protein (FMR1) binds target mRNAs to form ribonucleoprotein (RNP) complexes/granules that control various biological processes, including early embryogenesis. However, how FMR1 recognizes target mRNAs and how FMR1-RNP granule assembly/disassembly regulates FMR1-associated mRNAs remain elusive. Here we show that Drosophila FMR1 preferentially binds mRNAs containing m6A-marked “AGACU” motif with high affinity to contributes to maternal RNA degradation. The high-affinity binding largely depends on a hydrophobic network within FMR1 KH2 domain. Importantly, this binding greatly induces FMR1 granule condensation to efficiently recruit unmodified mRNAs. The degradation of maternal mRNAs then causes granule de-condensation, allowing normal embryogenesis. Our findings reveal that sequence-specific mRNAs instruct FMR1-RNP granules to undergo a dynamic phase-switch, thus contributes to maternal mRNA decay. This mechanism may represent a general principle that regulated RNP-granules control RNA processing and normal development. Maternal RNA degradation is critical for embryogenesis and is tightly controlled by maternal RNA-binding proteins. Here the authors show that a subset of m6A-modified mRNAs regulates the dynamics of RNA-granules, thus contributes to maternal mRNA decay.
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Roden CA, Gladfelter AS. Design considerations for analyzing protein translation regulation by condensates. RNA (NEW YORK, N.Y.) 2022; 28:88-96. [PMID: 34670845 PMCID: PMC8675288 DOI: 10.1261/rna.079002.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
One proposed role for biomolecular condensates that contain RNA is translation regulation. In several specific contexts, translation has been shown to be modulated by the presence of a phase-separating protein and under conditions which promote phase separation, and likely many more await discovery. A powerful tool for determining the rules for condensate-dependent translation is the use of engineered RNA sequences, which can serve as reporters for translation efficiency. This Perspective will discuss design features to consider in engineering RNA reporters to determine the role of phase separation in translational regulation. Specifically, we will cover (i) how to engineer RNA sequence to recapitulate native protein/RNA interactions, (ii) the advantages and disadvantages for commonly used reporter RNA sequences, and (iii) important control experiments to distinguish between binding- and condensation-dependent translational repression. The goal of this review is to promote the design and application of faithful translation reporters to demonstrate a physiological role of biomolecular condensates in translation.
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Affiliation(s)
- Christine A Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
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Hale CR, Sawicka K, Mora K, Fak JJ, Kang JJ, Cutrim P, Cialowicz K, Carroll TS, Darnell RB. FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons. eLife 2021; 10:71892. [PMID: 34939924 PMCID: PMC8820740 DOI: 10.7554/elife.71892] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Neurons rely on translation of synaptic mRNAs in order to generate activity-dependent changes in plasticity. Here, we develop a strategy combining compartment-specific crosslinking immunoprecipitation (CLIP) and translating ribosome affinity purification (TRAP) in conditionally tagged mice to precisely define the ribosome-bound dendritic transcriptome of CA1 pyramidal neurons. We identify CA1 dendritic transcripts with differentially localized mRNA isoforms generated by alternative polyadenylation and alternative splicing, including many that have altered protein-coding capacity. Among dendritic mRNAs, FMRP targets were found to be overrepresented. Cell-type-specific FMRP-CLIP and TRAP in microdissected CA1 neuropil revealed 383 dendritic FMRP targets and suggests that FMRP differentially regulates functionally distinct modules in CA1 dendrites and cell bodies. FMRP regulates ~15–20% of mRNAs encoding synaptic functions and 10% of chromatin modulators, in the dendrite and cell body, respectively. In the absence of FMRP, dendritic FMRP targets had increased ribosome association, consistent with a function for FMRP in synaptic translational repression. Conversely, downregulation of FMRP targets involved in chromatin regulation in cell bodies suggests a role for FMRP in stabilizing mRNAs containing stalled ribosomes in this compartment. Together, the data support a model in which FMRP regulates the translation and expression of synaptic and nuclear proteins within different compartments of a single neuronal cell type. The brain has over 100 billion neurons that together form vast networks to relay electrical signals. A neuron receives electrical signals from other neurons via branch-like structures known as dendrites. The signals then travel into the cell body of the neuron. If their sum reaches a threshold, they fire a new signal through a single outgoing projection known as the axon, which is connected to the dendrites of other neurons. A single neuron has thousands of dendrites that each receive inputs from different axons, and it is thought that the strengthening and weakening of these dendritic connections enables us to learn and store memories. Dendrites are filled with molecules known as messenger ribonucleic acids (mRNAs) that act as templates to make proteins. Axonal signals reaching the dendrites can trigger these mRNAs to make new proteins that strengthen or weaken the connections between the two neurons, which is believed to be necessary for generating long-term memories. A protein called FMRP is found in both the cell body and dendrites and is able to bind to and regulate the ability of mRNAs to make proteins. A loss of the gene encoding FMRP is the most common cause of inherited intellectual disability and autism in humans, but it remains unclear precisely what role this protein plays in learning and memory. Hale et al. used genetic and bioinformatics approaches to specifically study mRNAs in the dendrites and the cell body of a specific type of neuron involved in memory in mice. The experiments revealed that FMRP played different roles in the dendrites and cell body. In the dendrites, FMRP interacted with mRNAs encoding proteins that can change how the neuron responds to a signal from a neighboring neuron and may alter how strong the connections between the neurons are. On the other hand, FMRP in the cell body modulated the activities of mRNAs encoding proteins that in turn regulate the activities of genes. These findings change the way we think about how memory may work by suggesting that groups of mRNAs encoding proteins with certain activities are found in distinct parts of a single neuron. These observations offer new ways to approach intellectual disabilities and autism spectrum disorder.
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Affiliation(s)
- Caryn R Hale
- Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, United States
| | - Kirsty Sawicka
- Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, United States
| | - Kevin Mora
- Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, United States
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, United States
| | - Jin Joo Kang
- Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, United States
| | - Paula Cutrim
- Laboratory of Molecular Neuro-Oncology, Rockefeller University, New York, United States
| | - Katarzyna Cialowicz
- Bio-Imaging Resource Center, Rockefeller University, New York, United States
| | - Thomas S Carroll
- Bioinformatics Resouce Center, Rockefeller University, New York, United States
| | - Robert B Darnell
- Howard Hughes Medical Institute, Rockefeller University, New York, United States
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Wang J, Zhang T, Yu Z, Tan WT, Wen M, Shen Y, Lambert FRP, Huber RG, Wan Y. Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks. Mol Cell 2021; 81:4942-4953.e8. [PMID: 34655516 DOI: 10.1016/j.molcel.2021.09.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/01/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022]
Abstract
The distribution, dynamics, and function of RNA structures in human development are under-explored. Here, we systematically assayed RNA structural dynamics and their relationship with gene expression, translation, and decay during human neurogenesis. We observed that the human ESC transcriptome is globally more structurally accessible than differentiated cells and undergoes extensive RNA structure changes, particularly in the 3' UTR. Additionally, RNA structure changes during differentiation are associated with translation and decay. We observed that RBP and miRNA binding is associated with RNA structural changes during early neuronal differentiation, and splicing is associated during later neuronal differentiation. Furthermore, our analysis suggests that RBPs are major factors in structure remodeling and co-regulate additional RBPs and miRNAs through structure. We demonstrated an example of this by showing that PUM2-induced structure changes on LIN28A enable miR-30 binding. This study deepens our understanding of the widespread and complex role of RNA-based gene regulation during human development.
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Affiliation(s)
- Jiaxu Wang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Tong Zhang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Zhang Yu
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Wen Ting Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Ming Wen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Yang Shen
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Finnlay R P Lambert
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Roland G Huber
- Bioinformatics Institute, A(∗)STAR, Singapore 138671, Singapore
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore.
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Mercer M, Jang S, Ni C, Buszczak M. The Dynamic Regulation of mRNA Translation and Ribosome Biogenesis During Germ Cell Development and Reproductive Aging. Front Cell Dev Biol 2021; 9:710186. [PMID: 34805139 PMCID: PMC8595405 DOI: 10.3389/fcell.2021.710186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/07/2021] [Indexed: 01/21/2023] Open
Abstract
The regulation of mRNA translation, both globally and at the level of individual transcripts, plays a central role in the development and function of germ cells across species. Genetic studies using flies, worms, zebrafish and mice have highlighted the importance of specific RNA binding proteins in driving various aspects of germ cell formation and function. Many of these mRNA binding proteins, including Pumilio, Nanos, Vasa and Dazl have been conserved through evolution, specifically mark germ cells, and carry out similar functions across species. These proteins typically influence mRNA translation by binding to specific elements within the 3′ untranslated region (UTR) of target messages. Emerging evidence indicates that the global regulation of mRNA translation also plays an important role in germ cell development. For example, ribosome biogenesis is often regulated in a stage specific manner during gametogenesis. Moreover, oocytes need to produce and store a sufficient number of ribosomes to support the development of the early embryo until the initiation of zygotic transcription. Accumulating evidence indicates that disruption of mRNA translation regulatory mechanisms likely contributes to infertility and reproductive aging in humans. These findings highlight the importance of gaining further insights into the mechanisms that control mRNA translation within germ cells. Future work in this area will likely have important impacts beyond germ cell biology.
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Affiliation(s)
- Marianne Mercer
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Seoyeon Jang
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chunyang Ni
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Michael Buszczak
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Jang S, Lee J, Mathews J, Ruess H, Williford AO, Rangan P, Betrán E, Buszczak M. The Drosophila ribosome protein S5 paralog RpS5b promotes germ cell and follicle cell differentiation during oogenesis. Development 2021; 148:272089. [PMID: 34495316 DOI: 10.1242/dev.199511] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/01/2021] [Indexed: 01/15/2023]
Abstract
Emerging evidence suggests that ribosome heterogeneity may have important functional consequences in the translation of specific mRNAs within different cell types and under various conditions. Ribosome heterogeneity comes in many forms, including post-translational modification of ribosome proteins (RPs), absence of specific RPs and inclusion of different RP paralogs. The Drosophila genome encodes two RpS5 paralogs: RpS5a and RpS5b. While RpS5a is ubiquitously expressed, RpS5b exhibits enriched expression in the reproductive system. Deletion of RpS5b results in female sterility marked by developmental arrest of egg chambers at stages 7-8, disruption of vitellogenesis and posterior follicle cell (PFC) hyperplasia. While transgenic rescue experiments suggest functional redundancy between RpS5a and RpS5b, molecular, biochemical and ribo-seq experiments indicate that RpS5b mutants display increased rRNA transcription and RP production, accompanied by increased protein synthesis. Loss of RpS5b results in microtubule-based defects and in mislocalization of Delta and Mindbomb1, leading to failure of Notch pathway activation in PFCs. Together, our results indicate that germ cell-specific expression of RpS5b promotes proper egg chamber development by ensuring the homeostasis of functional ribosomes.
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Affiliation(s)
- Seoyeon Jang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeon Lee
- Lydia Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeremy Mathews
- Lydia Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Holly Ruess
- Lydia Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anna O Williford
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Prashanth Rangan
- RNA Institute, Department of Biological Sciences, University at Albany, SUNY, Albany, NY 12222, USA
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Lombardo MV, Eyler L, Pramparo T, Gazestani VH, Hagler DJ, Chen CH, Dale AM, Seidlitz J, Bethlehem RAI, Bertelsen N, Barnes CC, Lopez L, Campbell K, Lewis NE, Pierce K, Courchesne E. Atypical genomic cortical patterning in autism with poor early language outcome. SCIENCE ADVANCES 2021; 7:eabh1663. [PMID: 34516910 PMCID: PMC8442861 DOI: 10.1126/sciadv.abh1663] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/15/2021] [Indexed: 05/21/2023]
Abstract
Cortical regionalization develops via genomic patterning along anterior-posterior (A-P) and dorsal-ventral (D-V) gradients. Here, we find that normative A-P and D-V genomic patterning of cortical surface area (SA) and thickness (CT), present in typically developing and autistic toddlers with good early language outcome, is absent in autistic toddlers with poor early language outcome. Autistic toddlers with poor early language outcome are instead specifically characterized by a secondary and independent genomic patterning effect on CT. Genes involved in these effects can be traced back to midgestational A-P and D-V gene expression gradients and different prenatal cell types (e.g., progenitor cells and excitatory neurons), are functionally important for vocal learning and human-specific evolution, and are prominent in prenatal coexpression networks enriched for high-penetrance autism risk genes. Autism with poor early language outcome may be explained by atypical genomic cortical patterning starting in prenatal development, which may detrimentally affect later regional functional specialization and circuit formation.
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Affiliation(s)
- Michael V. Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Lisa Eyler
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- VISN 22 Mental Illness Research, Education, and Clinical Center, VA San Diego Healthcare System, San Diego, CA, USA
| | - Tiziano Pramparo
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Vahid H. Gazestani
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Donald J. Hagler
- Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
| | - Chi-Hua Chen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Anders M. Dale
- Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Jakob Seidlitz
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard A. I. Bethlehem
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Natasha Bertelsen
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Cynthia Carter Barnes
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen Campbell
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
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Pinheiro H, Pimentel MR, Sequeira C, Oliveira LM, Pezzarossa A, Roman W, Gomes ER. mRNA distribution in skeletal muscle is associated with mRNA size. J Cell Sci 2021; 134:jcs256388. [PMID: 34297126 PMCID: PMC7611476 DOI: 10.1242/jcs.256388] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Skeletal muscle myofibers are large and elongated cells with multiple and evenly distributed nuclei. Nuclear distribution suggests that each nucleus influences a specific compartment within the myofiber and implies a functional role for nuclear positioning. Compartmentalization of specific mRNAs and proteins has been reported at the neuromuscular and myotendinous junctions, but mRNA distribution in non-specialized regions of the myofibers remains largely unexplored. We report that the bulk of mRNAs are enriched around the nucleus of origin and that this perinuclear accumulation depends on recently transcribed mRNAs. Surprisingly, mRNAs encoding large proteins - giant mRNAs - are spread throughout the cell and do not exhibit perinuclear accumulation. Furthermore, by expressing exogenous transcripts with different sizes we found that size contributes to mRNA spreading independently of mRNA sequence. Both these mRNA distribution patterns depend on microtubules and are independent of nuclear dispersion, mRNA expression level and stability, and the characteristics of the encoded protein. Thus, we propose that mRNA distribution in non-specialized regions of skeletal muscle is size selective to ensure cellular compartmentalization and simultaneous long-range distribution of giant mRNAs.
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Affiliation(s)
- Helena Pinheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Mafalda Ramos Pimentel
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Catarina Sequeira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Luís Manuel Oliveira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Anna Pezzarossa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - William Roman
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Edgar R. Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Instituto de Histologia e Biologia do Desenvolvimento, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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Schieweck R, Riedemann T, Forné I, Harner M, Bauer KE, Rieger D, Ang FY, Hutten S, Demleitner AF, Popper B, Derdak S, Sutor B, Bilban M, Imhof A, Kiebler MA. Pumilio2 and Staufen2 selectively balance the synaptic proteome. Cell Rep 2021; 35:109279. [PMID: 34161769 DOI: 10.1016/j.celrep.2021.109279] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/05/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022] Open
Abstract
Neurons have the capacity to adapt to environmental stimuli, a phenomenon termed cellular plasticity. The underlying processes are controlled by a network of RNA-binding proteins (RBPs). Their precise impact, however, is largely unknown. To address this important question, we chose Pumilio2 (Pum2) and Staufen2 (Stau2), which both regulate synaptic transmission. Surprisingly, even though both RBPs dynamically interact with each other in neurons, their respective impact on the transcriptome and proteome is highly selective. Although Pum2 deficiency leads to reduced translation and protein expression, Stau2 depletion preferentially impacts RNA levels and increases protein abundance. Furthermore, we show that Pum2 activates expression of key GABAergic synaptic components, e.g., the GABAA receptor scaffold protein Gephyrin. Consequently, Pum2 depletion selectively reduced the amplitude of miniature inhibitory postsynaptic currents. Together, our data argue for an important role of RBPs to maintain proteostasis in order to control distinct aspects of synaptic transmission.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Therese Riedemann
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center (BMC), Department for Molecular Biology (Protein Analysis Unit), Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Max Harner
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Karl E Bauer
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Daniela Rieger
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Foong Yee Ang
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Saskia Hutten
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Antonia F Demleitner
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Bastian Popper
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany; Biomedical Center (BMC), Core Facility Animal Models, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Sophia Derdak
- Medical University of Vienna, Core Facilities, Lazarettgasse 14, 1090 Vienna, Austria
| | - Bernd Sutor
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Axel Imhof
- Biomedical Center (BMC), Department for Molecular Biology (Protein Analysis Unit), Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany.
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44
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Bülow P, Zlatic SA, Wenner PA, Bassell GJ, Faundez V. FMRP attenuates activity dependent modifications in the mitochondrial proteome. Mol Brain 2021; 14:75. [PMID: 33931071 PMCID: PMC8086361 DOI: 10.1186/s13041-021-00783-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/21/2021] [Indexed: 12/21/2022] Open
Abstract
Homeostatic plasticity is necessary for the construction and maintenance of functional neuronal networks, but principal molecular mechanisms required for or modified by homeostatic plasticity are not well understood. We recently reported that homeostatic plasticity induced by activity deprivation is dysregulated in cortical neurons from Fragile X Mental Retardation protein (FMRP) knockout mice (Bulow et al. in Cell Rep 26: 1378-1388 e1373, 2019). These findings led us to hypothesize that identifying proteins sensitive to activity deprivation and/or FMRP expression could reveal pathways required for or modified by homeostatic plasticity. Here, we report an unbiased quantitative mass spectrometry used to quantify steady-state proteome changes following chronic activity deprivation in wild type and Fmr1-/y cortical neurons. Proteome hits responsive to both activity deprivation and the Fmr1-/y genotype were significantly annotated to mitochondria. We found an increased number of mitochondria annotated proteins whose expression was sensitive to activity deprivation in Fmr1-/y cortical neurons as compared to wild type neurons. These findings support a novel role of FMRP in attenuating mitochondrial proteome modifications induced by activity deprivation.
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Affiliation(s)
- Pernille Bülow
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Stephanie A Zlatic
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Peter A Wenner
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Victor Faundez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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45
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Allen EG, Charen K, Hipp HS, Shubeck L, Amin A, He W, Nolin SL, Glicksman A, Tortora N, McKinnon B, Shelly KE, Sherman SL. Refining the risk for fragile X-associated primary ovarian insufficiency (FXPOI) by FMR1 CGG repeat size. Genet Med 2021; 23:1648-1655. [PMID: 33927378 PMCID: PMC8460441 DOI: 10.1038/s41436-021-01177-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 01/23/2023] Open
Abstract
Purpose Approximately 20–30% of women with an FMR1 premutation experience fragile X–associated primary ovarian insufficiency (FXPOI); however, current risk estimates based on repeat size only identify women with the midrange of repeats to be at the highest risk. Methods To better understand the risk by repeat size, we collected self-reported reproductive histories on 1,668 women and divided them into high-resolution repeat size bins of ~5 CGG repeats to determine a more accurate risk for FXPOI in relation to CGG repeat length. Results As previously reported, women with 70–100 CGG repeats were at the highest risk for FXPOI using various statistical models to compare average age at menopause and risk of FXPOI, with women with 85–89 repeats being at the highest risk. Importantly, women with <65 repeats or >120 repeats did not have a significantly increased risk for FXPOI compared to women with <45 repeats. Conclusion Using a large cross-section study on 1,668 women, we have provided more personalized risk assessment for FXPOI using high-resolution repeat size bins. Understanding the variability in risk has important implications for family planning and overall health among women with a premutation.
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Affiliation(s)
- Emily Graves Allen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Krista Charen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Heather S Hipp
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lisa Shubeck
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ashima Amin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Weiya He
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah L Nolin
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Anne Glicksman
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Nicole Tortora
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Bonnie McKinnon
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Katharine E Shelly
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephanie L Sherman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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46
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Genetic removal of p70 S6K1 corrects coding sequence length-dependent alterations in mRNA translation in fragile X syndrome mice. Proc Natl Acad Sci U S A 2021; 118:2001681118. [PMID: 33906942 DOI: 10.1073/pnas.2001681118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Loss of the fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS). FMRP is widely thought to repress protein synthesis, but its translational targets and modes of control remain in dispute. We previously showed that genetic removal of p70 S6 kinase 1 (S6K1) corrects altered protein synthesis as well as synaptic and behavioral phenotypes in FXS mice. In this study, we examined the gene specificity of altered messenger RNA (mRNA) translation in FXS and the mechanism of rescue with genetic reduction of S6K1 by carrying out ribosome profiling and RNA sequencing on cortical lysates from wild-type, FXS, S6K1 knockout, and double knockout mice. We observed reduced ribosome footprint (RF) abundance in the majority of differentially translated genes in the cortices of FXS mice. We used molecular assays to discover evidence that the reduction in RF abundance reflects an increased rate of ribosome translocation, which is captured as a decrease in the number of translating ribosomes at steady state and is normalized by inhibition of S6K1. We also found that genetic removal of S6K1 prevented a positive-to-negative gradation of alterations in translation efficiencies (RF/mRNA) with coding sequence length across mRNAs in FXS mouse cortices. Our findings reveal the identities of dysregulated mRNAs and a molecular mechanism by which reduction of S6K1 prevents altered translation in FXS.
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47
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Richter JD, Zhao X. The molecular biology of FMRP: new insights into fragile X syndrome. Nat Rev Neurosci 2021; 22:209-222. [PMID: 33608673 PMCID: PMC8094212 DOI: 10.1038/s41583-021-00432-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 01/31/2023]
Abstract
Fragile X mental retardation protein (FMRP) is the product of the fragile X mental retardation 1 gene (FMR1), a gene that - when epigenetically inactivated by a triplet nucleotide repeat expansion - causes the neurodevelopmental disorder fragile X syndrome (FXS). FMRP is a widely expressed RNA-binding protein with activity that is essential for proper synaptic plasticity and architecture, aspects of neural function that are known to go awry in FXS. Although the neurophysiology of FXS has been described in remarkable detail, research focusing on the molecular biology of FMRP has only scratched the surface. For more than two decades, FMRP has been well established as a translational repressor; however, recent whole transcriptome and translatome analyses in mouse and human models of FXS have shown that FMRP is involved in the regulation of nearly all aspects of gene expression. The emerging mechanistic details of the mechanisms by which FMRP regulates gene expression may offer ways to design new therapies for FXS.
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Affiliation(s)
- Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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48
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Di Marco B, Dell'Albani P, D'Antoni S, Spatuzza M, Bonaccorso CM, Musumeci SA, Drago F, Bardoni B, Catania MV. Fragile X mental retardation protein (FMRP) and metabotropic glutamate receptor subtype 5 (mGlu5) control stress granule formation in astrocytes. Neurobiol Dis 2021; 154:105338. [PMID: 33775821 DOI: 10.1016/j.nbd.2021.105338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/18/2022] Open
Abstract
Fragile X syndrome (FXS) is a common form of intellectual disability and autism caused by the lack of Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein involved in RNA transport and protein synthesis. Upon cellular stress, global protein synthesis is blocked and mRNAs are recruited into stress granules (SGs), together with RNA-binding proteins including FMRP. Activation of group-I metabotropic glutamate (mGlu) receptors stimulates FMRP-mediated mRNA transport and protein synthesis, but their role in SGs formation is unexplored. To this aim, we pre-treated wild type (WT) and Fmr1 knockout (KO) cultured astrocytes with the group-I-mGlu receptor agonist (S)-3,5-Dihydroxyphenylglycine (DHPG) and exposed them to sodium arsenite (NaAsO2), a widely used inducer of SGs formation. In WT cultures the activation of group-I mGlu receptors reduced SGs formation and recruitment of FMRP into SGs, and also attenuated phosphorylation of eIF2α, a key event crucially involved in SGs formation and inhibition of protein synthesis. In contrast, Fmr1 KO astrocytes, which exhibited a lower number of SGs than WT astrocytes, did not respond to agonist stimulation. Interestingly, the mGlu5 receptor negative allosteric modulator (NAM) 2-methyl-6-(phenylethynyl)pyridine (MPEP) antagonized DHPG-mediated SGs reduction in WT and reversed SGs formation in Fmr1 KO cultures. Our findings reveal a novel function of mGlu5 receptor as modulator of SGs formation and open new perspectives for understanding cellular response to stress in FXS pathophysiology.
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Affiliation(s)
- B Di Marco
- Institute for Biomedical Research and Innovation - The National Research Council of Italy (IRIB-CNR), Catania, Italy
| | - P Dell'Albani
- Institute for Biomedical Research and Innovation - The National Research Council of Italy (IRIB-CNR), Catania, Italy
| | - S D'Antoni
- Institute for Biomedical Research and Innovation - The National Research Council of Italy (IRIB-CNR), Catania, Italy
| | - M Spatuzza
- Oasi Research Institute - IRCCS, Troina, Italy
| | | | | | - F Drago
- Department of Biomedical and Biotecnological Sciences, University of Catania, Italy
| | - B Bardoni
- Université Côte d'Azur, Inserm, CNRS UMR7275, Institute of Molecular and Cellular Pharmacology, Valbonne 06560, France
| | - M V Catania
- Institute for Biomedical Research and Innovation - The National Research Council of Italy (IRIB-CNR), Catania, Italy; Oasi Research Institute - IRCCS, Troina, Italy.
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49
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Roden C, Gladfelter AS. RNA contributions to the form and function of biomolecular condensates. Nat Rev Mol Cell Biol 2021; 22:183-195. [PMID: 32632317 PMCID: PMC7785677 DOI: 10.1038/s41580-020-0264-6] [Citation(s) in RCA: 278] [Impact Index Per Article: 92.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 01/08/2023]
Abstract
Biomolecular condensation partitions cellular contents and has important roles in stress responses, maintaining homeostasis, development and disease. Many nuclear and cytoplasmic condensates are rich in RNA and RNA-binding proteins (RBPs), which undergo liquid-liquid phase separation (LLPS). Whereas the role of RBPs in condensates has been well studied, less attention has been paid to the contribution of RNA to LLPS. In this Review, we discuss the role of RNA in biomolecular condensation and highlight considerations for designing condensate reconstitution experiments. We focus on RNA properties such as composition, length, structure, modifications and expression level. These properties can modulate the biophysical features of native condensates, including their size, shape, viscosity, liquidity, surface tension and composition. We also discuss the role of RNA-protein condensates in development, disease and homeostasis, emphasizing how their properties and function can be determined by RNA. Finally, we discuss the multifaceted cellular functions of biomolecular condensates, including cell compartmentalization through RNA transport and localization, supporting catalytic processes, storage and inheritance of specific molecules, and buffering noise and responding to stress.
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Affiliation(s)
- Christine Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Whitman Center, Marine Biology Laboratory, Woods Hole, MA, USA.
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50
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Huang JS, Yang FC, Chien WC, Yeh TC, Chung CH, Tsai CK, Tsai SJ, Yang SS, Tzeng NS, Chen MH, Liang CS. Risk of Substance Use Disorder and Its Associations With Comorbidities and Psychotropic Agents in Patients With Autism. JAMA Pediatr 2021; 175:e205371. [PMID: 33394019 PMCID: PMC7783585 DOI: 10.1001/jamapediatrics.2020.5371] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
IMPORTANCE The risk of substance use disorder (SUD) in patients with autism spectrum disorder (ASD) remains unclear. OBJECTIVE To investigate the risk of SUD in patients with ASD and its associations with comorbidities, psychotropic agents (PAs), and mortality. DESIGN, SETTING, AND PARTICIPANTS This retrospective, population-based, cohort study of 1 936 512 participants used data from the Taiwan National Health Insurance Research Database and was conducted from January 1, 2000, to December 31, 2015. Included participants attended at least 3 outpatient visits within the 1-year study period for symptomatic ASD as determined by the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnostic codes. Individuals diagnosed with ASD before 2000, those diagnosed with SUD before the first visit for ASD, and those with missing data were excluded from the analysis. Patients with ASD and non-ASD controls were matched 1:4 by age, sex, and index date. EXPOSURES Symptomatic ASD evaluated for at least 3 outpatient visits within the 1-year study period. MAIN OUTCOMES AND MEASURES Adjusted hazard ratios (aHRs) with 95% CIs for SUD, including alcohol use disorder (AUD) and drug use disorder (DUD), and the risk of mortality were calculated. Data were analyzed from March 1 to July 13, 2020. RESULTS A total of 6599 individuals with ASD (mean [SD] age, 11.9 [5.1] years; 5094 boys [77.2%]; mean [SD] follow-up period, 8.1 [8.3] years; median follow-up period, 4.3 [interquartile range [IQR], 2.3-5.3] years) and 26 396 controls (mean [SD] age, 12.1 [5.8] years; 20 376 boys [77.2%]; mean [SD] follow-up period, 8.6 [8.9] years; median follow-up period, 4.4 [IQR, 2.4-5.4] years) were enrolled in the study. According to multivariable-adjusted analysis, the aHRs for SUD (2.33; 95% CI, 1.89-2.87), AUD (2.07; 95% CI, 1.60-2.63), and DUD (3.00; 95% CI, 2.15-4.58) were significantly higher in the ASD group than in the non-ASD controls. The aHRs for SUD in the ASD subgroups with 1 PA (0.60; 95% CI, 0.43-0.66) and with multiple PAs (0.37; 95% CI, 0.28-0.49) were significantly lower than those in the ASD subgroup with no PAs. Comparisons between patients with ASD and non-ASD controls with the same comorbidities showed higher aHRs for SUD among patients with ASD (range, 1.17-2.55); moreover, the ASD subgroup not receiving any PAs had an aHR of 6.39 (95% CI, 5.11-7.87) for SUD when they had comorbid tic disorder and aHRs of 5.48 (95% CI, 5.12-5.70) for AUD and 5.42 (95% CI, 5.12-5.80) for DUD when they had comorbid impulse control disorder. The mortality risk was significantly higher in patients with ASD and concomitant SUD than in non-ASD controls without SUD (aHR, 3.17; 95% CI, 2.69-3.89). CONCLUSIONS AND RELEVANCE These findings suggest that patients with ASD are vulnerable to the development of SUD. Comorbid ASD and SUD were associated with an increase in mortality risk.
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Affiliation(s)
- Jing-Syuan Huang
- Department of Psychiatry, Beitou Branch, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Fu-Chi Yang
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wu-Chien Chien
- Department of Medical Research, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan,School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Ta-Chuan Yeh
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chi-Hsiang Chung
- Department of Medical Research, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Kuang Tsai
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Sung-Sen Yang
- Department of Medical Research, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Nian-Shen Tzeng
- Department of Psychiatry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Mu-Hong Chen
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chih-Sung Liang
- Department of Psychiatry, Beitou Branch, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
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