1
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Lancaster CL, Yalamanchili PS, Goldy JN, Leung SW, Corbett AH, Moberg KH. The RNA-binding protein Nab2 regulates levels of the RhoGEF Trio to govern axon and dendrite morphology. Mol Biol Cell 2024; 35:ar109. [PMID: 38985523 DOI: 10.1091/mbc.e24-04-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024] Open
Abstract
The Drosophila RNA-binding protein (RBP) Nab2 acts in neurons to regulate neurodevelopment and is orthologous to the human intellectual disability-linked RBP, ZC3H14. Nab2 governs axon projection in mushroom body neurons and limits dendritic arborization of class IV sensory neurons in part by regulating splicing events in ∼150 mRNAs. Analysis of the Sex-lethal (Sxl) mRNA revealed that Nab2 promotes an exon-skipping event and regulates m6A methylation on Sxl pre-mRNA by the Mettl3 methyltransferase. Mettl3 heterozygosity broadly rescues Nab2null phenotypes implying that Nab2 acts through similar mechanisms on other RNAs, including unidentified targets involved in neurodevelopment. Here, we show that Nab2 and Mettl3 regulate the removal of a 5'UTR (untranslated region) intron in the trio pre-mRNA. Trio utilizes two GEF domains to balance Rac and RhoGTPase activity. Intriguingly, an isoform of Trio containing only the RhoGEF domain, GEF2, is depleted in Nab2null nervous tissue. Expression of Trio-GEF2 rescues projection defects in Nab2null axons and dendrites, while the GEF1 Rac1-regulatory domain exacerbates these defects, suggesting Nab2-mediated regulation Trio-GEF activities. Collectively, these data indicate that Nab2-regulated processing of trio is critical for balancing Trio-GEF1 and -GEF2 activity and show that Nab2, Mettl3, and Trio function in a common pathway that shapes axon and dendrite morphology.
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Affiliation(s)
- Carly L Lancaster
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322
| | - Pranav S Yalamanchili
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Jordan N Goldy
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322
| | - Sara W Leung
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
| | - Anita H Corbett
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
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2
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Lester E, Parker R. Tau, RNA, and RNA-Binding Proteins: Complex Interactions in Health and Neurodegenerative Diseases. Neuroscientist 2024; 30:458-472. [PMID: 36892034 DOI: 10.1177/10738584231154551] [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] [Indexed: 03/10/2023]
Abstract
The tau protein is a key contributor to multiple neurodegenerative diseases. The pathology of tau is thought to be related to tau's propensity to form self-templating fibrillar structures that allow tau fibers to propagate in the brain by prion-like mechanisms. Unresolved issues with respect to tau pathology are how the normal function of tau and its misregulation contribute to disease, how cofactors and cellular organelles influence the initiation and propagation of tau fibers, and determining the mechanism of tau toxicity. Herein, we review the connection between tau and degenerative diseases, the basis for tau fibrilization, and how that process interacts with cellular molecules and organelles. One emerging theme is that tau interacts with RNA and RNA-binding proteins, normally and in pathologic aggregates, which may provide insight into alterations in RNA regulation observed in disease.
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Affiliation(s)
- Evan Lester
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
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3
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Mayfield JM, Hitefield NL, Czajewski I, Vanhye L, Holden L, Morava E, van Aalten DMF, Wells L. O-GlcNAc Transferase Congenital Disorder of Glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome. J Biol Chem 2024:107599. [PMID: 39059494 DOI: 10.1016/j.jbc.2024.107599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
O-GlcNAc transferase (OGT) is the sole enzyme responsible for the post-translational modification O-GlcNAc on thousands of target nucleocytoplasmic proteins. To date, nine variants of OGT that segregate with OGT Congenital Disorder of Glycosylation (OGT-CDG) have been reported and characterized. Numerous additional variants have been associated with OGT-CDG, some of which are currently undergoing investigation. This disorder primarily presents with global developmental delay and intellectual disability (ID), alongside other variable neurological features and subtle facial dysmorphisms in patients. Several hypotheses aim to explain the etiology of OGT-CDG, with a prominent hypothesis attributing the pathophysiology of OGT-CDG to mutations segregating with this disorder disrupting the OGT interactome. The OGT interactome consists of thousands of proteins, including substrates as well as interactors that require noncatalytic functions of OGT. A key aim in the field is to identify which interactors and substrates contribute to the primarily neural-specific phenotype of OGT-CDG. In this review, we will discuss the heterogenous phenotypic features of OGT-CDG seen clinically, the variable biochemical effects of mutations associated with OGT-CDG, and the use of animal models to understand this disorder. Furthermore, we will discuss how previously identified OGT interactors causal for ID provide mechanistic targets for investigation that could explain the dysregulated gene expression seen in OGT-CDG models. Identifying shared or unique altered pathways impacted in OGT-CDG patients will provide a better understanding of the disorder as well as potential therapeutic targets.
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Affiliation(s)
- Johnathan M Mayfield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Naomi L Hitefield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Ignacy Czajewski
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Lotte Vanhye
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Laura Holden
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Eva Morava
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Daan M F van Aalten
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, DK.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America.
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4
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Han X, Xing L, Hong Y, Zhang X, Hao B, Lu JY, Huang M, Wang Z, Ma S, Zhan G, Li T, Hao X, Tao Y, Li G, Zhou S, Zheng Z, Shao W, Zeng Y, Ma D, Zhang W, Xie Z, Deng H, Yan J, Deng W, Shen X. Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence. Cell Stem Cell 2024; 31:694-716.e11. [PMID: 38631356 DOI: 10.1016/j.stem.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in a translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that the dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.
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Affiliation(s)
- Xue Han
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Linqing Xing
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xuechun Zhang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Hao
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - J Yuyang Lu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Mengyuan Huang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zuhui Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shaoqian Ma
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ge Zhan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowen Hao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yibing Tao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Guanwen Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuqin Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Zheng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Wen Shao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yitian Zeng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Dacheng Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiangwei Yan
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaohua Shen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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5
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Dawidziuk M, Podwysocka A, Jurek M, Obersztyn E, Bekiesinska-Figatowska M, Goszczanska-Ciuchta A, Bukowska-Olech E, Rygiel AM, Guilbride DL, Wiszniewski W, Gawlinski P. Congenital coenzyme Q5-linked pathology: causal genetic association, core phenotype, and molecular mechanism. J Appl Genet 2023; 64:507-514. [PMID: 37599337 PMCID: PMC10457220 DOI: 10.1007/s13353-023-00773-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 04/29/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023]
Abstract
Coenzyme Q5 (COQ5), a C-methyltransferase, modifies coenzyme Q10 (COQ10) during biosynthesis and interacts with polyA-tail regulating zinc-finger protein ZC3H14 in neural development. Here, we present a fifth patient (a third family) worldwide with neurodevelopmental and physiological symptoms including COQ10 deficiency. Our patient harbors one novel c.681+1G>A and one recurrent p.Gly118Ser variant within COQ5. The patient's mRNA profile reveals multiple COQ5 splice-variants. Subsequently, we comprehensively described patient's clinical features as compared to phenotype and symptoms of other known congenital coenzyme Q5-linked cases. A core spectrum of COQ5-associated symptoms includes reduced COQ10 levels, intellectual disability, encephalopathy, cerebellar ataxia, cerebellar atrophy speech regression/dysarthria, short stature, and developmental delays. Our patient additionally displays dysmorphia, microcephaly, and regressive social faculties. These results formally establish causal association of biallelic COQ5 mutation with pathology, outline a core COQ5-linked phenotype, and identify mRNA mis-splicing as the molecular mechanism underlying all COQ5 variant-linked pathology to date.
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Affiliation(s)
- Mateusz Dawidziuk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Marta Jurek
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | | | | | | | | | - Wojciech Wiszniewski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, USA
| | - Pawel Gawlinski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.
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6
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Jalloh B, Lancaster CL, Rounds JC, Brown BE, Leung SW, Banerjee A, Morton DJ, Bienkowski RS, Fasken MB, Kremsky IJ, Tegowski M, Meyer K, Corbett A, Moberg K. The Drosophila Nab2 RNA binding protein inhibits m 6A methylation and male-specific splicing of Sex lethal transcript in female neuronal tissue. eLife 2023; 12:e64904. [PMID: 37458420 PMCID: PMC10351920 DOI: 10.7554/elife.64904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls adult locomotion, axon projection, dendritic arborization, and memory through a largely undefined set of target RNAs. Here, we show a specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and focus on retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl) that is enriched in female neurons. Previous studies have revealed that this splicing event is regulated in females by N6-methyladenosine (m6A) modification by the Mettl3 complex. At a molecular level, Nab2 associates with Sxl pre-mRNA in neurons and limits Sxl m6A methylation at specific sites. In parallel, reducing expression of the Mettl3, Mettl3 complex components, or the m6A reader Ythdc1 rescues mutant phenotypes in Nab2 flies. Overall, these data identify Nab2 as an inhibitor of m6A methylation and imply significant overlap between Nab2 and Mettl3 regulated RNAs in neuronal tissue.
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Affiliation(s)
- Binta Jalloh
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Carly L Lancaster
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory UniversityAtlantaUnited States
| | - J Christopher Rounds
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Brianna E Brown
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
| | - Sara W Leung
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ayan Banerjee
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Derrick J Morton
- Department of Biology, Emory UniversityAtlantaUnited States
- Emory Institutional Research and Academic Career Development Award (IRACDA), Fellowships in Research and Science Teaching (FIRST) Postdoctoral FellowshipAtlantaUnited States
| | - Rick S Bienkowski
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Milo B Fasken
- Department of Biology, Emory UniversityAtlantaUnited States
| | | | - Matthew Tegowski
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
| | - Kate Meyer
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Anita Corbett
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ken Moberg
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
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7
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Insco ML, Abraham BJ, Dubbury SJ, Kaltheuner IH, Dust S, Wu C, Chen KY, Liu D, Bellaousov S, Cox AM, Martin BJ, Zhang T, Ludwig CG, Fabo T, Modhurima R, Esgdaille DE, Henriques T, Brown KM, Chanock SJ, Geyer M, Adelman K, Sharp PA, Young RA, Boutz PL, Zon LI. Oncogenic CDK13 mutations impede nuclear RNA surveillance. Science 2023; 380:eabn7625. [PMID: 37079685 PMCID: PMC10184553 DOI: 10.1126/science.abn7625] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We found that disrupted nuclear RNA surveillance is oncogenic. Cyclin-dependent kinase 13 (CDK13) is mutated in melanoma, and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance, causing aberrant protein-coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We found recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies, establishing nuclear RNA surveillance as a tumor-suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease.
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Affiliation(s)
- Megan L. Insco
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Sara J. Dubbury
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ines H. Kaltheuner
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Sofia Dust
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Constance Wu
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Kevin Y. Chen
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Stanislav Bellaousov
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Anna M. Cox
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Benjamin J.E. Martin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Calvin G. Ludwig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Tania Fabo
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Rodsy Modhurima
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Dakarai E. Esgdaille
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Phillip A. Sharp
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Richard A. Young
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Paul L. Boutz
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, NY, 14642, USA
- Center for Biomedical Informatics, University of Rochester, Rochester, NY, 14642, USA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
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8
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Corgiat EB, List SM, Rounds JC, Yu D, Chen P, Corbett AH, Moberg KH. The Nab2 RNA-binding protein patterns dendritic and axonal projections through a planar cell polarity-sensitive mechanism. G3 (BETHESDA, MD.) 2022; 12:jkac100. [PMID: 35471546 PMCID: PMC9157165 DOI: 10.1093/g3journal/jkac100] [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] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 11/15/2022]
Abstract
RNA-binding proteins support neurodevelopment by modulating numerous steps in post-transcriptional regulation, including splicing, export, translation, and turnover of mRNAs that can traffic into axons and dendrites. One such RNA-binding protein is ZC3H14, which is lost in an inherited intellectual disability. The Drosophila melanogaster ZC3H14 ortholog, Nab2, localizes to neuronal nuclei and cytoplasmic ribonucleoprotein granules and is required for olfactory memory and proper axon projection into brain mushroom bodies. Nab2 can act as a translational repressor in conjunction with the Fragile-X mental retardation protein homolog Fmr1 and shares target RNAs with the Fmr1-interacting RNA-binding protein Ataxin-2. However, neuronal signaling pathways regulated by Nab2 and their potential roles outside of mushroom body axons remain undefined. Here, we present an analysis of a brain proteomic dataset that indicates that multiple planar cell polarity proteins are affected by Nab2 loss, and couple this with genetic data that demonstrate that Nab2 has a previously unappreciated role in restricting the growth and branching of dendrites that elaborate from larval body-wall sensory neurons. Further analysis confirms that Nab2 loss sensitizes sensory dendrites to the genetic dose of planar cell polarity components and that Nab2-planar cell polarity genetic interactions are also observed during Nab2-dependent control of axon projection in the central nervous system mushroom bodies. Collectively, these data identify the conserved Nab2 RNA-binding protein as a likely component of post-transcriptional mechanisms that limit dendrite growth and branching in Drosophila sensory neurons and genetically link this role to the planar cell polarity pathway. Given that mammalian ZC3H14 localizes to dendritic spines and controls spine density in hippocampal neurons, these Nab2-planar cell polarity genetic data may highlight a conserved path through which Nab2/ZC3H14 loss affects morphogenesis of both axons and dendrites in diverse species.
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Affiliation(s)
- Edwin B Corgiat
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Sara M List
- Neuroscience Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - J Christopher Rounds
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Dehong Yu
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ping Chen
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
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9
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Rounds JC, Corgiat EB, Ye C, Behnke JA, Kelly SM, Corbett AH, Moberg KH. The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology. Genetics 2022; 220:iyab175. [PMID: 34791182 PMCID: PMC8733473 DOI: 10.1093/genetics/iyab175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Nab2 encodes the Drosophila melanogaster member of a conserved family of zinc finger polyadenosine RNA-binding proteins (RBPs) linked to multiple steps in post-transcriptional regulation. Mutation of the Nab2 human ortholog ZC3H14 gives rise to an autosomal recessive intellectual disability but understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part because no comprehensive identification of metazoan Nab2/ZC3H14-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships remain unidentified. Here, we present evidence that Nab2 genetically interacts with Ataxin-2 (Atx2), which encodes a neuronal translational regulator, and that these factors coordinately regulate neuronal morphology, circadian behavior, and adult viability. We then present the first high-throughput identifications of Nab2- and Atx2-associated RNAs in Drosophila brain neurons using RNA immunoprecipitation-sequencing (RIP-Seq). Critically, the RNA interactomes of each RBP overlap, and Nab2 exhibits high specificity in its RNA associations in neurons in vivo, associating with a small fraction of all polyadenylated RNAs. The identities of shared associated transcripts (e.g., drk, me31B, stai) and of transcripts specific to Nab2 or Atx2 (e.g., Arpc2 and tea) promise insight into neuronal functions of, and genetic interactions between, each RBP. Consistent with prior biochemical studies, Nab2-associated neuronal RNAs are overrepresented for internal A-rich motifs, suggesting these sequences may partially mediate Nab2 target selection. These data support a model where Nab2 functionally opposes Atx2 in neurons, demonstrate Nab2 shares associated neuronal RNAs with Atx2, and reveal Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.
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Affiliation(s)
- J Christopher Rounds
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Edwin B Corgiat
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Changtian Ye
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joseph A Behnke
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Seth M Kelly
- Department of Biology, The College of Wooster, Wooster, OH 44691, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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10
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Corgiat EB, List SM, Rounds JC, Corbett AH, Moberg KH. The RNA-binding protein Nab2 regulates the proteome of the developing Drosophila brain. J Biol Chem 2021; 297:100877. [PMID: 34139237 PMCID: PMC8260979 DOI: 10.1016/j.jbc.2021.100877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 12/14/2022] Open
Abstract
The human ZC3H14 gene, which encodes a ubiquitously expressed polyadenosine zinc finger RNA-binding protein, is mutated in an inherited form of autosomal recessive, nonsyndromic intellectual disability. To gain insight into neurological functions of ZC3H14, we previously developed a Drosophila melanogaster model of ZC3H14 loss by deleting the fly ortholog, Nab2. Studies in this invertebrate model revealed that Nab2 controls final patterns of neuron projection within fully developed adult brains, but the role of Nab2 during development of the Drosophila brain is not known. Here, we identify roles for Nab2 in controlling the dynamic growth of axons in the developing brain mushroom bodies, which support olfactory learning and memory, and regulating abundance of a small fraction of the total brain proteome. The group of Nab2-regulated brain proteins, identified by quantitative proteomic analysis, includes the microtubule-binding protein Futsch, the neuronal Ig-family transmembrane protein turtle, the glial:neuron adhesion protein contactin, the Rac GTPase-activating protein tumbleweed, and the planar cell polarity factor Van Gogh, which collectively link Nab2 to the processes of brain morphogenesis, neuroblast proliferation, circadian sleep/wake cycles, and synaptic development. Overall, these data indicate that Nab2 controls the abundance of a subset of brain proteins during the active process of wiring the pupal brain mushroom body and thus provide a window into potentially conserved functions of the Nab2/ZC3H14 RNA-binding proteins in neurodevelopment.
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Affiliation(s)
- Edwin B Corgiat
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA; Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Sara M List
- Graduate Program in Neuroscience, Emory University, Atlanta, Georgia, USA
| | - J Christopher Rounds
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA; Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia, USA.
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA.
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11
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Lee S, Wei L, Zhang B, Goering R, Majumdar S, Wen J, Taliaferro JM, Lai EC. ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing. PLoS Genet 2021; 17:e1009439. [PMID: 33826609 PMCID: PMC8055025 DOI: 10.1371/journal.pgen.1009439] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/19/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
ELAV/Hu factors are conserved RNA binding proteins (RBPs) that play diverse roles in mRNA processing and regulation. The founding member, Drosophila Elav, was recognized as a vital neural factor 35 years ago. Nevertheless, little was known about its impacts on the transcriptome, and potential functional overlap with its paralogs. Building on our recent findings that neural-specific lengthened 3' UTR isoforms are co-determined by ELAV/Hu factors, we address their impacts on splicing. While only a few splicing targets of Drosophila are known, ectopic expression of each of the three family members (Elav, Fne and Rbp9) alters hundreds of cassette exon and alternative last exon (ALE) splicing choices. Reciprocally, double mutants of elav/fne, but not elav alone, exhibit opposite effects on both classes of regulated mRNA processing events in larval CNS. While manipulation of Drosophila ELAV/Hu RBPs induces both exon skipping and inclusion, characteristic ELAV/Hu motifs are enriched only within introns flanking exons that are suppressed by ELAV/Hu factors. Moreover, the roles of ELAV/Hu factors in global promotion of distal ALE splicing are mechanistically linked to terminal 3' UTR extensions in neurons, since both processes involve bypass of proximal polyadenylation signals linked to ELAV/Hu motifs downstream of cleavage sites. We corroborate the direct action of Elav in diverse modes of mRNA processing using RRM-dependent Elav-CLIP data from S2 cells. Finally, we provide evidence for conservation in mammalian neurons, which undergo broad programs of distal ALE and APA lengthening, linked to ELAV/Hu motifs downstream of regulated polyadenylation sites. Overall, ELAV/Hu RBPs orchestrate multiple broad programs of neuronal mRNA processing and isoform diversification in Drosophila and mammalian neurons.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Lu Wei
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Binglong Zhang
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- RNA Bioscience Initiative University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Sonali Majumdar
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
| | - Jiayu Wen
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - J. Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- RNA Bioscience Initiative University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York City, New York, United States of America
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12
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Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland. Hum Genet 2021; 140:1011-1029. [PMID: 33710394 PMCID: PMC8197721 DOI: 10.1007/s00439-021-02268-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022]
Abstract
The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.
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13
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Alqawlaq S, Livne-Bar I, Williams D, D'Ercole J, Leung SW, Chan D, Tuccitto A, Datti A, Wrana JL, Corbett AH, Schmitt-Ulms G, Sivak JM. An endogenous PI3K interactome promoting astrocyte-mediated neuroprotection identifies a novel association with RNA-binding protein ZC3H14. J Biol Chem 2021; 296:100118. [PMID: 33234594 PMCID: PMC7948738 DOI: 10.1074/jbc.ra120.015389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 11/06/2022] Open
Abstract
Astrocytes can support neuronal survival through a range of secreted signals that protect against neurotoxicity, oxidative stress, and apoptotic cascades. Thus, analyzing the effects of the astrocyte secretome may provide valuable insight into these neuroprotective mechanisms. Previously, we characterized a potent neuroprotective activity mediated by retinal astrocyte conditioned media (ACM) on retinal and cortical neurons in metabolic stress models. However, the molecular mechanism underlying this complex activity in neuronal cells has remained unclear. Here, a chemical genetics screen of kinase inhibitors revealed phosphoinositide 3-kinase (PI3K) as a central player transducing ACM-mediated neuroprotection. To identify additional proteins contributing to the protective cascade, endogenous PI3K was immunoprecipitated from neuronal cells exposed to ACM or control media, followed by MS/MS proteomic analyses. These data pointed toward a relatively small number of proteins that coimmunoprecipitated with PI3K, and surprisingly only five were regulated by the ACM signal. These hits included expected PI3K interactors, such as the platelet-derived growth factor receptor A (PDGFRA), as well as novel RNA-binding protein interactors ZC3H14 (zinc finger CCCH-type containing 14) and THOC1 (THO complex protein 1). In particular, ZC3H14 has recently emerged as an important RNA-binding protein with multiple roles in posttranscriptional regulation. In validation studies, we show that PI3K recruitment of ZC3H14 is necessary for PDGF-induced neuroprotection and that this interaction is present in primary retinal ganglion cells. Thus, we identified a novel non-cell autonomous neuroprotective signaling cascade mediated through PI3K that requires recruitment of ZC3H14 and may present a promising strategy to promote astrocyte-secreted prosurvival signals.
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Affiliation(s)
- Samih Alqawlaq
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Izhar Livne-Bar
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Joseph D'Ercole
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Darren Chan
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Alessandra Tuccitto
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Alessandro Datti
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jeffrey L Wrana
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Jeremy M Sivak
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada.
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14
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Su J, Miao X, Archambault D, Mager J, Cui W. ZC3H4-a novel Cys-Cys-Cys-His-type zinc finger protein-is essential for early embryogenesis in mice†. Biol Reprod 2020; 104:325-335. [PMID: 33246328 DOI: 10.1093/biolre/ioaa215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/10/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Zinc finger domains of the Cys-Cys-Cys-His (CCCH) class are evolutionarily conserved proteins that bind nucleic acids and are involved in various biological processes. Nearly 60 CCCH-type zinc finger proteins have been identified in humans and mice, most have not been functionally characterized. Here, we provide the first in vivo functional characterization of ZC3H4-a novel CCCH-type zinc finger protein. Our results show that although Zc3h4 mutant embryos exhibit normal morphology at E3.5 blastocyst stage, they cannot be recovered at E7.5 early post-gastrulation stage, suggesting implantation failure. Outgrowth assays reveal that mutant blastocysts either fail to hatch from the zona pellucida, or can hatch but do not form a typical inner cell mass colony, the source of embryonic stem cells (ESCs). Although there is no change in levels of reactive oxygen species, Zc3h4 mutants display severe DNA breaks and reduced cell proliferation. Analysis of lineage specification reveals that both epiblast and primitive endoderm lineages are compromised with severe reductions in cell number and/or specification in the mutant blastocysts. In summary, these findings demonstrate the essential role of ZC3H4 during early mammalian embryogenesis.
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Affiliation(s)
- Jianmin Su
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA.,Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xiaosu Miao
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Danielle Archambault
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA.,Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA
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15
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Aguilar LC, Paul B, Reiter T, Gendron L, Arul Nambi Rajan A, Montpetit R, Trahan C, Pechmann S, Oeffinger M, Montpetit B. Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2. Nucleic Acids Res 2020; 48:11675-11694. [PMID: 33137177 PMCID: PMC7672433 DOI: 10.1093/nar/gkaa964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are key mediators of RNA metabolism. Whereas some RBPs exhibit narrow transcript specificity, others function broadly across both coding and non-coding RNAs. Here, in Saccharomyces cerevisiae, we demonstrate that changes in RBP availability caused by disruptions to distinct cellular processes promote a common global breakdown in RNA metabolism and nuclear RNA homeostasis. Our data shows that stabilization of aberrant ribosomal RNA (rRNA) precursors in an enp1-1 mutant causes phenotypes similar to RNA exosome mutants due to nucleolar sequestration of the poly(A)-binding protein (PABP) Nab2. Decreased nuclear PABP availability is accompanied by genome-wide changes in RNA metabolism, including increased pervasive transcripts levels and snoRNA processing defects. These phenotypes are mitigated by overexpression of PABPs, inhibition of rDNA transcription, or alterations in TRAMP activity. Our results highlight the need for cells to maintain poly(A)-RNA levels in balance with PABPs and other RBPs with mutable substrate specificity across nucleoplasmic and nucleolar RNA processes.
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Affiliation(s)
- Lisbeth-Carolina Aguilar
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Biplab Paul
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, CA, USA
| | - Louis Gendron
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Christian Trahan
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Sebastian Pechmann
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada
- Food Science Graduate Group, University of California Davis, Davis, CA, USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
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16
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A Genetic Screen Links the Disease-Associated Nab2 RNA-Binding Protein to the Planar Cell Polarity Pathway in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2020; 10:3575-3583. [PMID: 32817074 PMCID: PMC7534439 DOI: 10.1534/g3.120.401637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mutations in the gene encoding the ubiquitously expressed RNA-binding protein ZC3H14 result in a non-syndromic form of autosomal recessive intellectual disability in humans. Studies in Drosophila have defined roles for the ZC3H14 ortholog, Nab2 (aka Drosophila Nab2 or dNab2), in axon guidance and memory due in part to interaction with a second RNA-binding protein, the fly Fragile X homolog Fmr1, and coregulation of shared Nab2-Fmr1 target mRNAs. Despite these advances, neurodevelopmental mechanisms that underlie defective axonogenesis in Nab2 mutants remain undefined. Nab2 null phenotypes in the brain mushroom bodies (MBs) resemble defects caused by alleles that disrupt the planar cell polarity (PCP) pathway, which regulates planar orientation of static and motile cells via a non-canonical arm of the Wnt/Wg pathway. A kinked bristle phenotype in surviving Nab2 mutant adults additionally suggests a defect in F-actin polymerization and bundling, a PCP-regulated processes. To test for Nab2-PCP genetic interactions, a collection of PCP mutant alleles was screened for modification of a rough-eye phenotype produced by Nab2 overexpression in the eye (GMR> Nab2) and, subsequently, for modification of a viability defect among Nab2 nulls. Multiple PCP alleles dominantly modify GMR> Nab2 eye roughening and a subset rescue low survival and thoracic bristle kinking in Nab2 zygotic nulls. Collectively, these genetic interactions identify the PCP pathway as a potential target of the Nab2 RNA-binding protein in developing eye and wing tissues and suggest that altered PCP signaling could contribute to neurological defects that result from loss of Drosophila Nab2 or its vertebrate ortholog ZC3H14.
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17
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Alpert T, Straube K, Carrillo Oesterreich F, Herzel L, Neugebauer KM. Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns. Cell Rep 2020; 33:108324. [PMID: 33113357 DOI: 10.1016/j.celrep.2020.108324] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 01/26/2023] Open
Abstract
Nascent RNA sequencing has revealed that pre-mRNA splicing can occur shortly after introns emerge from RNA polymerase II (RNA Pol II). Differences in co-transcriptional splicing profiles suggest regulation by cis- and/or trans-acting factors. Here, we use single-molecule intron tracking (SMIT) to identify a cohort of regulators by machine learning in budding yeast. Of these, Nab2 displays reduced co-transcriptional splicing when depleted. Unexpectedly, these splicing defects are attributable to aberrant "intrusive" transcriptional readthrough from upstream genes, as revealed by long-read sequencing. Transcripts that originate from the intron-containing gene's own transcription start site (TSS) are efficiently spliced, indicating no direct role of Nab2 in splicing per se. This work highlights the coupling between transcription, splicing, and 3' end formation in the context of gene organization along chromosomes. We conclude that Nab2 is required for proper 3' end processing, which ensures gene-specific control of co-transcriptional RNA processing.
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Affiliation(s)
- Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Korinna Straube
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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18
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Morton DJ, Jalloh B, Kim L, Kremsky I, Nair RJ, Nguyen KB, Rounds JC, Sterrett MC, Brown B, Le T, Karkare MC, McGaughey KD, Sheng S, Leung SW, Fasken MB, Moberg KH, Corbett AH. A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons. PLoS Genet 2020; 16:e1008901. [PMID: 32645003 PMCID: PMC7373318 DOI: 10.1371/journal.pgen.1008901] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 07/21/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022] Open
Abstract
The RNA exosome is an evolutionarily-conserved ribonuclease complex critically important for precise processing and/or complete degradation of a variety of cellular RNAs. The recent discovery that mutations in genes encoding structural RNA exosome subunits cause tissue-specific diseases makes defining the role of this complex within specific tissues critically important. Mutations in the RNA exosome component 3 (EXOSC3) gene cause Pontocerebellar Hypoplasia Type 1b (PCH1b), an autosomal recessive neurologic disorder. The majority of disease-linked mutations are missense mutations that alter evolutionarily-conserved regions of EXOSC3. The tissue-specific defects caused by these amino acid changes in EXOSC3 are challenging to understand based on current models of RNA exosome function with only limited analysis of the complex in any multicellular model in vivo. The goal of this study is to provide insight into how mutations in EXOSC3 impact the function of the RNA exosome. To assess the tissue-specific roles and requirements for the Drosophila ortholog of EXOSC3 termed Rrp40, we utilized tissue-specific RNAi drivers. Depletion of Rrp40 in different tissues reveals a general requirement for Rrp40 in the development of many tissues including the brain, but also highlight an age-dependent requirement for Rrp40 in neurons. To assess the functional consequences of the specific amino acid substitutions in EXOSC3 that cause PCH1b, we used CRISPR/Cas9 gene editing technology to generate flies that model this RNA exosome-linked disease. These flies show reduced viability; however, the surviving animals exhibit a spectrum of behavioral and morphological phenotypes. RNA-seq analysis of these Drosophila Rrp40 mutants reveals increases in the steady-state levels of specific mRNAs and ncRNAs, some of which are central to neuronal function. In particular, Arc1 mRNA, which encodes a key regulator of synaptic plasticity, is increased in the Drosophila Rrp40 mutants. Taken together, this study defines a requirement for the RNA exosome in specific tissues/cell types and provides insight into how defects in RNA exosome function caused by specific amino acid substitutions that occur in PCH1b can contribute to neuronal dysfunction.
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Affiliation(s)
- Derrick J. Morton
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Binta Jalloh
- Genetics and Molecular Biology Graduate Program, Emory University, NE, Atlanta, Georgia, United States of America
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Lily Kim
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Isaac Kremsky
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Rishi J. Nair
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Khuong B. Nguyen
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - J. Christopher Rounds
- Genetics and Molecular Biology Graduate Program, Emory University, NE, Atlanta, Georgia, United States of America
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Maria C. Sterrett
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, NE, Atlanta, Georgia, United States of America
| | - Brianna Brown
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Thalia Le
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Maya C. Karkare
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Kathryn D. McGaughey
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Shaoyi Sheng
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Sara W. Leung
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Milo B. Fasken
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
| | - Kenneth H. Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Anita H. Corbett
- Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
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19
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Zhang C, Cao P, Yang A, Xia X, Li Y, Shi M, Yang Y, Wei X, Yang C, Zhou G. Downregulation of ZC3H14 driven by chromosome 14q31 deletion promotes hepatocellular carcinoma progression by activating integrin signaling. Carcinogenesis 2020; 40:474-486. [PMID: 30371740 DOI: 10.1093/carcin/bgy146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 09/14/2018] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. Genomic copy number deletion at chromosome 14q31.1-32.13 was frequently observed in HCC; however, the relevant functional target(s) at that locus is not well determined. Here, we performed integrative genomic analyses and identified zinc finger CCCH-type containing 14 (ZC3H14) as a promising candidate at 14q31.1-32.13. We observed frequent copy number deletion (17.1%) and downregulation of ZC3H14 in primary HCC tissues. Downregulation of ZC3H14 was significantly associated with poor outcomes of patients with HCC. Overexpression of ZC3H14 in HCC cell lines significantly suppressed HCC cells growth in vitro and metastasis in vivo. In contrast, RNA interference silencing of ZC3H14 inhibited its tumor-suppressive function. Mechanismly, through combing bioinformatics analyses and experimental investigation, we demonstrated that loss of ZC3H14 promotes HCC progression through enhancing integrin pathway. This study suggests that ZC3H14 functions as a novel tumor suppressor and is a candidate prognostic biomarker for HCC patients.
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Affiliation(s)
- Chuxiao Zhang
- Affiliated Tumor Hospital of Guangxi Medical University, Nanning, P. R. China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Pengbo Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Aiqing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Xia Xia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Mengting Shi
- Guangxi Medical University, Nanning, P. R. China
| | - Ying Yang
- Department of Radiation and Oncology, Navy General Hospital, Beijing, P. R. China
| | - Xiaojun Wei
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, Beijing, P. R. China
| | - Chun Yang
- Affiliated Tumor Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China.,Guangxi Medical University, Nanning, P. R. China
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20
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Fattahi Z, Beheshtian M, Mohseni M, Poustchi H, Sellars E, Nezhadi SH, Amini A, Arzhangi S, Jalalvand K, Jamali P, Mohammadi Z, Davarnia B, Nikuei P, Oladnabi M, Mohammadzadeh A, Zohrehvand E, Nejatizadeh A, Shekari M, Bagherzadeh M, Shamsi-Gooshki E, Börno S, Timmermann B, Haghdoost A, Najafipour R, Khorram Khorshid HR, Kahrizi K, Malekzadeh R, Akbari MR, Najmabadi H. Iranome: A catalog of genomic variations in the Iranian population. Hum Mutat 2019; 40:1968-1984. [PMID: 31343797 DOI: 10.1002/humu.23880] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 11/12/2022]
Abstract
Considering the application of human genome variation databases in precision medicine, population-specific genome projects are continuously being developed. However, the Middle Eastern population is underrepresented in current databases. Accordingly, we established Iranome database (www.iranome.com) by performing whole exome sequencing on 800 individuals from eight major Iranian ethnic groups representing the second largest population of Middle East. We identified 1,575,702 variants of which 308,311 were novel (19.6%). Also, by presenting higher frequency for 37,384 novel or known rare variants, Iranome database can improve the power of molecular diagnosis. Moreover, attainable clinical information makes this database a good resource for classifying pathogenicity of rare variants. Principal components analysis indicated that, apart from Iranian-Baluchs, Iranian-Turkmen, and Iranian-Persian Gulf Islanders, who form their own clusters, rest of the population were genetically linked, forming a super-population. Furthermore, only 0.6% of novel variants showed counterparts in "Greater Middle East Variome Project", emphasizing the value of Iranome at national level by releasing a comprehensive catalog of Iranian genomic variations and also filling another gap in the catalog of human genome variations at international level. We introduce Iranome as a resource which may also be applicable in other countries located in neighboring regions historically called Greater Iran (Persia).
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Affiliation(s)
- Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hossein Poustchi
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Erin Sellars
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | | | - Amir Amini
- Information Technology Office, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Peyman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, Iran
| | - Zahra Mohammadi
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Akbar Mohammadzadeh
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Elham Zohrehvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Azim Nejatizadeh
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammad Shekari
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Maryam Bagherzadeh
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Ehsan Shamsi-Gooshki
- Medical Ethics and History of Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Ethics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Aliakbar Haghdoost
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran.,Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Najafipour
- Cellular and Molecular Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad R Akbari
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
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21
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Morris KJ, Corbett AH. The polyadenosine RNA-binding protein ZC3H14 interacts with the THO complex and coordinately regulates the processing of neuronal transcripts. Nucleic Acids Res 2019; 46:6561-6575. [PMID: 29912477 PMCID: PMC6061872 DOI: 10.1093/nar/gky446] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 06/13/2018] [Indexed: 12/14/2022] Open
Abstract
The polyadenosine RNA-binding protein ZC3H14 is important in RNA processing. Although ZC3H14 is ubiquitously expressed, mutation of the ZC3H14 gene causes a non-syndromic form of intellectual disability. Here, we examine the function of ZC3H14 in the brain by identifying ZC3H14-interacting proteins using unbiased mass spectrometry. Through this analysis, we identified physical interactions between ZC3H14 and multiple RNA processing factors. Notably, proteins that comprise the THO complex were amongst the most enriched proteins. We demonstrate that ZC3H14 physically interacts with THO components and that these proteins are required for proper RNA processing, as loss of ZC3H14 or THO components leads to extended bulk poly(A) tail length. Furthermore, we identified the transcripts Atp5g1 and Psd95 as shared RNA targets of ZC3H14 and the THO complex. Our data suggest that ZC3H14 and the THO complex are important for proper processing of Atp5g1 and Psd95 RNA, as depletion of ZC3H14 or THO components leads to decreased steady-state levels of each mature transcript accompanied by accumulation of Atp5g1 and Psd95 pre-mRNA in the cytoplasm. Taken together, this work provides the first unbiased identification of nuclear ZC3H14-interacting proteins from the brain and links the functions of ZC3H14 and the THO complex in the processing of RNA.
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Affiliation(s)
- Kevin J Morris
- Department of Biology, Emory University, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell and Developmental Biology, James T. Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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22
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Bodaleo F, Tapia-Monsalves C, Cea-Del Rio C, Gonzalez-Billault C, Nunez-Parra A. Structural and Functional Abnormalities in the Olfactory System of Fragile X Syndrome Models. Front Mol Neurosci 2019; 12:135. [PMID: 31191246 PMCID: PMC6548058 DOI: 10.3389/fnmol.2019.00135] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/09/2019] [Indexed: 12/18/2022] Open
Abstract
Fragile X Syndrome (FXS) is the most common inherited form of intellectual disability. It is produced by mutation of the Fmr1 gene that encodes for the Fragile Mental Retardation Protein (FMRP), an important RNA-binding protein that regulates the expression of multiple proteins located in neuronal synapses. Individuals with FXS exhibit abnormal sensory information processing frequently leading to hypersensitivity across sensory modalities and consequently a wide array of behavioral symptoms. Insects and mammals engage primarily their sense of smell to create proper representations of the external world and guide adequate decision-making processes. This feature in combination with the exquisitely organized neuronal circuits found throughout the olfactory system (OS) and the wide expression of FMRP in brain regions that process olfactory information makes it an ideal model to study sensory alterations in FXS models. In the last decade several groups have taken advantage of these features and have used the OS of fruit fly and rodents to understand neuronal alteration giving rise to sensory perception issues. In this review article, we will discuss molecular, morphological and physiological aspects of the olfactory information processing in FXS models. We will highlight the decreased inhibitory/excitatory synaptic balance and the diminished synaptic plasticity found in this system resulting in behavioral alteration of individuals in the presence of odorant stimuli.
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Affiliation(s)
- Felipe Bodaleo
- Laboratory of Cellular and Neuronal Dynamics, Department of Biology, Faculty of Science, Universidad de Chile, Santiago, Chile.,Geroscience Center for Brain Health and Metabolism (GERO), Santiago, Chile
| | | | - Christian Cea-Del Rio
- Laboratory of Neurophysiopathology, Centro de Investigacion Biomedica y Aplicada (CIBAP), School of Medicine, Universidad de Santiago de Chile, Santiago, Chile
| | - Christian Gonzalez-Billault
- Laboratory of Cellular and Neuronal Dynamics, Department of Biology, Faculty of Science, Universidad de Chile, Santiago, Chile.,Geroscience Center for Brain Health and Metabolism (GERO), Santiago, Chile.,The Buck Institute for Research on Aging, Novato, CA, United States
| | - Alexia Nunez-Parra
- Department of Biology, Faculty of Science, Universidad de Chile, Santiago, Chile.,Cell Physiology Center, Universidad de Chile, Santiago, Chile
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23
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Costain G, Walker S, Argiropoulos B, Baribeau DA, Bassett AS, Boot E, Devriendt K, Kellam B, Marshall CR, Prasad A, Serrano MA, Stavropoulos DJ, Twede H, Vermeesch JR, Vorstman JAS, Scherer SW. Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders. J Neurodev Disord 2019; 11:3. [PMID: 30732576 PMCID: PMC6366120 DOI: 10.1186/s11689-019-9263-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/23/2019] [Indexed: 01/07/2023] Open
Abstract
Background Ultra-rare genetic variants, including non-recurrent copy number variations (CNVs) affecting important dosage-sensitive genes, are important contributors to the etiology of neurodevelopmental disorders (NDDs). Pairing family-based whole-genome sequencing (WGS) with detailed phenotype data can enable novel gene associations in NDDs. Methods We performed WGS of six members from a three-generation family, where three individuals each had a spectrum of features suggestive of a NDD. CNVs and sequence-level variants were identified and further investigated in disease and control databases. Results We identified a novel 252-kb deletion at 15q21 that overlaps the synaptic gene DMXL2 and the gene GLDN. The microdeletion segregated in NDD-affected individuals. Additional rare inherited and de novo sequence-level variants were found that may also be involved, including a missense change in GRIK5. Multiple CNVs and loss-of-function sequence variants affecting DMXL2 were discovered in additional unrelated individuals with a range of NDDs. Conclusions Disruption of DMXL2 may predispose to NDDs including autism spectrum disorder. The robust interpretation of private variants requires a multifaceted approach that incorporates multigenerational pedigrees and genome-wide and population-scale data.
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Affiliation(s)
- Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.,Medical Genetics Residency Training Program, University of Toronto, Toronto, ON, Canada
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bob Argiropoulos
- Department of Medical Genetics, University of Calgary Cumming School of Medicine, Calgary, AB, Canada
| | | | - Anne S Bassett
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,The Dalglish Family 22q Clinic, Toronto General Hospital, Toronto, ON, Canada
| | - Erik Boot
- The Dalglish Family 22q Clinic, Toronto General Hospital, Toronto, ON, Canada
| | - Koen Devriendt
- Department of Human Genetics, KU Leuven, Leuven, Flanders, Belgium
| | - Barbara Kellam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Aparna Prasad
- Lineagen, Inc, 2677 East Parleys Way, Salt Lake City, UT, 84109, USA
| | - Moises A Serrano
- Lineagen, Inc, 2677 East Parleys Way, Salt Lake City, UT, 84109, USA
| | - D James Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Hope Twede
- Lineagen, Inc, 2677 East Parleys Way, Salt Lake City, UT, 84109, USA
| | | | - Jacob A S Vorstman
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON, Canada.
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24
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Fasken MB, Corbett AH, Stewart M. Structure-function relationships in the Nab2 polyadenosine-RNA binding Zn finger protein family. Protein Sci 2019; 28:513-523. [PMID: 30578643 PMCID: PMC6371209 DOI: 10.1002/pro.3565] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
Abstract
The poly(A) RNA binding Zn finger ribonucleoprotein Nab2 functions to control the length of 3' poly(A) tails in Saccharomyces cerevisiae as well as contributing to the integration of the nuclear export of mature mRNA with preceding steps in the nuclear phase of the gene expression pathway. Nab2 is constructed from an N-terminal PWI-fold domain, followed by QQQP and RGG motifs and then seven CCCH Zn fingers. The nuclear pore-associated proteins Gfd1 and Mlp1 bind to opposite sides of the Nab2 N-terminal domain and function in the nuclear export of mRNA, whereas the Zn fingers, especially fingers 5-7, bind to A-rich regions of mature transcripts and function to regulate poly(A) tail length as well as mRNA compaction prior to nuclear export. Nab2 Zn fingers 5-7 have a defined spatial arrangement, with fingers 5 and 7 arranged on one side of the cluster and finger 6 on the other side. This spatial arrangement facilitates the dimerization of Nab2 when bound to adenine-rich RNAs and regulates both the termination of 3' polyadenylation and transcript compaction. Nab2 also functions to coordinate steps in the nuclear phase of the gene expression pathway, such as splicing and polyadenylation, with the generation of mature mRNA and its nuclear export. Nab2 orthologues in higher Eukaryotes have similar domain structures and play roles associated with the regulation of splicing and polyadenylation. Importantly, mutations in the gene encoding the human Nab2 orthologue ZC3H14 and cause intellectual disability.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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25
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Kazeminasab S, Taskiran II, Fattahi Z, Bazazzadegan N, Hosseini M, Rahimi M, Oladnabi M, Haddadi M, Celik A, Ropers HH, Najmabadi H, Kahrizi K. CNKSR1 gene defect can cause syndromic autosomal recessive intellectual disability. Am J Med Genet B Neuropsychiatr Genet 2018; 177:691-699. [PMID: 30450701 DOI: 10.1002/ajmg.b.32648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The advent of high-throughput sequencing technologies has led to an exponential increase in the identification of novel disease-causing genes in highly heterogeneous diseases. A novel frameshift mutation in CNKSR1 gene was detected by Next-Generation Sequencing (NGS) in an Iranian family with syndromic autosomal recessive intellectual disability (ARID). CNKSR1 encodes a connector enhancer of kinase suppressor of Ras 1, which acts as a scaffold component for receptor tyrosine kinase in mitogen-activated protein kinase (MAPK) cascades. CNKSR1 interacts with proteins which have already been shown to be associated with intellectual disability (ID) in the MAPK signaling pathway and promotes cell migration through RhoA-mediated c-Jun N-terminal kinase (JNK) activation. Lack of CNKSR1 transcripts and protein was observed in lymphoblastoid cells derived from affected patients using qRT-PCR and western blot analysis, respectively. Furthermore, RNAi-mediated knockdown of cnk, the CNKSR1 orthologue in Drosophila melanogaster brain, led to defects in eye and mushroom body (MB) structures. In conclusion, our findings support the possible role of CNKSR1 in brain development which can lead to cognitive impairment.
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Affiliation(s)
- Somayeh Kazeminasab
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Rahimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Haddadi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
| | - Arzu Celik
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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26
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Al-Nabhani M, Al-Rashdi S, Al-Murshedi F, Al-Kindi A, Al-Thihli K, Al-Saegh A, Al-Futaisi A, Al-Mamari W, Zadjali F, Al-Maawali A. Reanalysis of exome sequencing data of intellectual disability samples: Yields and benefits. Clin Genet 2018; 94:495-501. [PMID: 30125339 DOI: 10.1111/cge.13438] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/08/2018] [Accepted: 08/15/2018] [Indexed: 01/07/2023]
Abstract
Recently, with the advancement in next generation sequencing (NGS) along with the improvement of bioinformatics tools, whole exome sequencing (WES) has become the most efficient diagnostic test for patients with intellectual disability (ID). This study aims to estimate the yield of a reanalysis of ID negative exome cases after data reannotation. Total of 50 data files of exome sequencing, representing 50 samples were collected. The inclusion criteria include ID phenotype, and previous analysis indicated a negative result (no abnormality detected). These files were pre-processed and reannotated using ANNOVAR tool. Prioritized variants in the 50 cases studied were classified into three groups, (1) disease-causative variants (2) possible disease-causing variants and (3) variants in novel genes. Reanalysis resulted in the identification of pathogenic/likely pathogenic variants in six cases (12%). Thirteen cases (26%) were classified as having possible disease-causing variants. Candidate genes requiring future functional studies were detected in seven cases (14%). Improvement in bioinformatics tools, update in the genetic databases and literature, and patients' clinical phenotype update were the main reasons for identification of these variants in this study.
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Affiliation(s)
- Maryam Al-Nabhani
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Samiya Al-Rashdi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fathiya Al-Murshedi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Adila Al-Kindi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalid Al-Thihli
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Abeer Al-Saegh
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Amna Al-Futaisi
- Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Watfa Al-Mamari
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman.,Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fahad Zadjali
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
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27
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28
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Bienkowski RS, Banerjee A, Rounds JC, Rha J, Omotade OF, Gross C, Morris KJ, Leung SW, Pak C, Jones SK, Santoro MR, Warren ST, Zheng JQ, Bassell GJ, Corbett AH, Moberg KH. The Conserved, Disease-Associated RNA Binding Protein dNab2 Interacts with the Fragile X Protein Ortholog in Drosophila Neurons. Cell Rep 2018; 20:1372-1384. [PMID: 28793261 DOI: 10.1016/j.celrep.2017.07.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/28/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022] Open
Abstract
The Drosophila dNab2 protein is an ortholog of human ZC3H14, a poly(A) RNA binding protein required for intellectual function. dNab2 supports memory and axon projection, but its molecular role in neurons is undefined. Here, we present a network of interactions that links dNab2 to cytoplasmic control of neuronal mRNAs in conjunction with the fragile X protein ortholog dFMRP. dNab2 and dfmr1 interact genetically in control of neurodevelopment and olfactory memory, and their encoded proteins co-localize in puncta within neuronal processes. dNab2 regulates CaMKII, but not futsch, implying a selective role in control of dFMRP-bound transcripts. Reciprocally, dFMRP and vertebrate FMRP restrict mRNA poly(A) tail length, similar to dNab2/ZC3H14. Parallel studies of murine hippocampal neurons indicate that ZC3H14 is also a cytoplasmic regulator of neuronal mRNAs. Altogether, these findings suggest that dNab2 represses expression of a subset of dFMRP-target mRNAs, which could underlie brain-specific defects in patients lacking ZC3H14.
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Affiliation(s)
- Rick S Bienkowski
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ayan Banerjee
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - J Christopher Rounds
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jennifer Rha
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Omotola F Omotade
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christina Gross
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Kevin J Morris
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sara W Leung
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - ChangHui Pak
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephanie K Jones
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael R Santoro
- Department of Human Genetics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Human Genetics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pediatrics, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James Q Zheng
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University and Emory University School of Medicine, Atlanta, GA 30322, USA.
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29
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Banerjee A, Ifrim MF, Valdez AN, Raj N, Bassell GJ. Aberrant RNA translation in fragile X syndrome: From FMRP mechanisms to emerging therapeutic strategies. Brain Res 2018; 1693:24-36. [PMID: 29653083 PMCID: PMC7377270 DOI: 10.1016/j.brainres.2018.04.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/30/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023]
Abstract
Research in the past decades has unfolded the multifaceted role of Fragile X mental retardation protein (FMRP) and how its absence contributes to the pathophysiology of Fragile X syndrome (FXS). Excess signaling through group 1 metabotropic glutamate receptors is commonly observed in mouse models of FXS, which in part is attributed to dysregulated translation and downstream signaling. Considering the wide spectrum of cellular and physiologic functions that loss of FMRP can affect in general, it may be advantageous to pursue disease mechanism based treatments that directly target translational components or signaling factors that regulate protein synthesis. Various FMRP targets upstream and downstream of the translational machinery are therefore being investigated to further our understanding of the molecular mechanism of RNA and protein synthesis dysregulation in FXS as well as test their potential role as therapeutic interventions to alleviate FXS associated symptoms. In this review, we will broadly discuss recent advancements made towards understanding the role of FMRP in translation regulation, new pre-clinical animal models with FMRP targets located at different levels of the translational and signal transduction pathways for therapeutic intervention as well as future use of stem cells to model FXS associated phenotypes.
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Affiliation(s)
- Anwesha Banerjee
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Marius F Ifrim
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Arielle N Valdez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nisha Raj
- Department of Cell Biology, 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; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA.
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30
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Nishioka K, Wang XF, Miyazaki H, Soejima H, Hirose S. Mbf1 ensures Polycomb silencing by protecting E(z) mRNA from degradation by Pacman. Development 2018. [PMID: 29523653 PMCID: PMC5868998 DOI: 10.1242/dev.162461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Under stress conditions, the coactivator Multiprotein bridging factor 1 (Mbf1) translocates from the cytoplasm into the nucleus to induce stress-response genes. However, its role in the cytoplasm, where it is mainly located, has remained elusive. Here, we show that Drosophila Mbf1 associates with E(z) mRNA and protects it from degradation by the exoribonuclease Pacman (Pcm), thereby ensuring Polycomb silencing. In genetic studies, loss of mbf1 function enhanced a Polycomb phenotype in Polycomb group mutants, and was accompanied by a significant reduction in E(z) mRNA expression. Furthermore, a pcm mutation suppressed the Polycomb phenotype and restored the expression level of E(z) mRNA, while pcm overexpression exhibited the Polycomb phenotype in the mbf1 mutant but not in the wild-type background. In vitro, Mbf1 protected E(z) RNA from Pcm activity. Our results suggest that Mbf1 buffers fluctuations in Pcm activity to maintain an E(z) mRNA expression level sufficient for Polycomb silencing. Highlighted Article: In addition to its role as a nuclear coactivator, a cytoplasmic mRNA-stabilizing function of Multiprotein bridging factor 1 may contribute to various types of stress defense, metabolic processes and neurogenesis in Drosophila.
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Affiliation(s)
- Kenichi Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga 849-8501, Japan
| | - Xian-Feng Wang
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka 411-8540, Japan
| | - Hitomi Miyazaki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga 849-8501, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga 849-8501, Japan
| | - Susumu Hirose
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka 411-8540, Japan
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31
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Rha J, Jones SK, Fidler J, Banerjee A, Leung SW, Morris KJ, Wong JC, Inglis GAS, Shapiro L, Deng Q, Cutler AA, Hanif AM, Pardue MT, Schaffer A, Seyfried NT, Moberg KH, Bassell GJ, Escayg A, García PS, Corbett AH. The RNA-binding protein, ZC3H14, is required for proper poly(A) tail length control, expression of synaptic proteins, and brain function in mice. Hum Mol Genet 2018; 26:3663-3681. [PMID: 28666327 DOI: 10.1093/hmg/ddx248] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
A number of mutations in genes that encode ubiquitously expressed RNA-binding proteins cause tissue specific disease. Many of these diseases are neurological in nature revealing critical roles for this class of proteins in the brain. We recently identified mutations in a gene that encodes a ubiquitously expressed polyadenosine RNA-binding protein, ZC3H14 (Zinc finger CysCysCysHis domain-containing protein 14), that cause a nonsyndromic, autosomal recessive form of intellectual disability. This finding reveals the molecular basis for disease and provides evidence that ZC3H14 is essential for proper brain function. To investigate the role of ZC3H14 in the mammalian brain, we generated a mouse in which the first common exon of the ZC3H14 gene, exon 13 is removed (Zc3h14Δex13/Δex13) leading to a truncated ZC3H14 protein. We report here that, as in the patients, Zc3h14 is not essential in mice. Utilizing these Zc3h14Δex13/Δex13mice, we provide the first in vivo functional characterization of ZC3H14 as a regulator of RNA poly(A) tail length. The Zc3h14Δex13/Δex13 mice show enlarged lateral ventricles in the brain as well as impaired working memory. Proteomic analysis comparing the hippocampi of Zc3h14+/+ and Zc3h14Δex13/Δex13 mice reveals dysregulation of several pathways that are important for proper brain function and thus sheds light onto which pathways are most affected by the loss of ZC3H14. Among the proteins increased in the hippocampi of Zc3h14Δex13/Δex13 mice compared to control are key synaptic proteins including CaMK2a. This newly generated mouse serves as a tool to study the function of ZC3H14 in vivo.
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Affiliation(s)
- Jennifer Rha
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA
| | - Stephanie K Jones
- Department of Biology.,Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Jonathan Fidler
- Department of Anesthesiology, Emory University School of Medicine & Research Division, Atlanta VA Medical Center, Atlanta, GA 30322, USA
| | | | | | - Kevin J Morris
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA.,Department of Biology
| | - Jennifer C Wong
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Andrew S Inglis
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lindsey Shapiro
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA.,Graduate Program in Neuroscience, Emory University, Atlanta, GA 30322, USA
| | - Qiudong Deng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alicia A Cutler
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA.,Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Adam M Hanif
- Department of Opthamology, Emory University School of Medicine & Research Division, & Atlanta VA Medical Center, Atlanta, GA 30322, USA
| | - Machelle T Pardue
- Department of Opthamology, Emory University School of Medicine & Research Division, & Atlanta VA Medical Center, Atlanta, GA 30322, USA
| | - Ashleigh Schaffer
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4955, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kenneth H Moberg
- Department of Cell Biology, 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
| | - Andrew Escayg
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA
| | - Paul S García
- Department of Anesthesiology, Emory University School of Medicine & Research Division, Atlanta VA Medical Center, Atlanta, GA 30322, USA
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32
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Costa CJ, Willis DE. To the end of the line: Axonal mRNA transport and local translation in health and neurodegenerative disease. Dev Neurobiol 2017; 78:209-220. [PMID: 29115051 DOI: 10.1002/dneu.22555] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/20/2017] [Accepted: 11/01/2017] [Indexed: 12/14/2022]
Abstract
Axons and growth cones, by their very nature far removed from the cell body, encounter unique environments and require distinct populations of proteins. It seems only natural, then, that they have developed mechanisms to locally synthesize a host of proteins required to perform their specialized functions. Acceptance of this ability has taken decades; however, there is now consensus that axons do indeed have the capacity for local translation, and that this capacity is even retained into adulthood. Accumulating evidence supports the role of locally synthesized proteins in the proper development, maintenance, and function of neurons, and newly emerging studies also suggest that disruption in this process has implications in a number of neurodevelopmental and neurodegenerative diseases. Here, we briefly review the long history of axonal mRNA localization and local translation, and the role that these locally synthesized proteins play in normal neuronal function. Additionally, we highlight the emerging evidence that dysregulation in these processes contributes to a wide range of pathophysiology, including neuropsychiatric disorders, Alzheimer's, and motor neuron diseases such as spinal muscular atrophy and Amyotrophic Lateral Sclerosis. © 2017 Wiley Periodicals, Inc. Develop. Neurobiol 78: 209-220, 2018.
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Affiliation(s)
| | - Dianna E Willis
- Burke Medical Research Institute, White Plains, New York, 10605.,Brain & Mind Research Institute, Weill Cornell Medicine, New York, New York
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33
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Banerjee A, Vest KE, Pavlath GK, Corbett AH. Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing. Nucleic Acids Res 2017; 45:10706-10725. [PMID: 28977530 PMCID: PMC5737383 DOI: 10.1093/nar/gkx786] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/27/2017] [Indexed: 01/01/2023] Open
Abstract
The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of muscular dystrophy termed oculopharyngeal muscular dystrophy (OPMD). Despite the tissue-specific pathology that occurs in this disease, only recently have studies of PABPN1 begun to explore the role of this protein in skeletal muscle. We have used co-immunoprecipitation and mass spectrometry to identify proteins that interact with PABPN1 in mouse skeletal muscles. Among the interacting proteins we identified Matrin 3 (MATR3) as a novel protein interactor of PABPN1. The MATR3 gene is mutated in a form of distal myopathy and amyotrophic lateral sclerosis (ALS). We demonstrate, that like PABPN1, MATR3 is critical for myogenesis. Furthermore, MATR3 controls critical aspects of RNA processing including alternative polyadenylation and intron retention. We provide evidence that MATR3 also binds and regulates the levels of long non-coding RNA (lncRNA) Neat1 and together with PABPN1 is required for normal paraspeckle function. We demonstrate that PABPN1 and MATR3 are required for paraspeckles, as well as for adenosine to inosine (A to I) RNA editing of Ctn RNA in muscle cells. We provide a functional link between PABPN1 and MATR3 through regulation of a common lncRNA target with downstream impact on paraspeckle morphology and function. We extend our analysis to a mouse model of OPMD and demonstrate altered paraspeckle morphology in the presence of endogenous levels of alanine-expanded PABPN1. In this study, we report protein-binding partners of PABPN1, which could provide insight into novel functions of PABPN1 in skeletal muscle and identify proteins that could be sequestered with alanine-expanded PABPN1 in the nuclear aggregates found in OPMD.
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Affiliation(s)
- Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Katherine E Vest
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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34
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Kelly SM, Elchert A, Kahl M. Dissection and Immunofluorescent Staining of Mushroom Body and Photoreceptor Neurons in Adult Drosophila melanogaster Brains. J Vis Exp 2017. [PMID: 29155751 PMCID: PMC5755316 DOI: 10.3791/56174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nervous system development involves a sequential series of events that are coordinated by several signaling pathways and regulatory networks. Many of the proteins involved in these pathways are evolutionarily conserved between mammals and other eukaryotes, such as the fruit fly Drosophila melanogaster, suggesting that similar organizing principles exist during the development of these organisms. Importantly, Drosophila has been used extensively to identify cellular and molecular mechanisms regulating processes that are required in mammals including neurogenesis, differentiation, axonal guidance, and synaptogenesis. Flies have also been used successfully to model a variety of human neurodevelopmental diseases. Here we describe a protocol for the step-by-step microdissection, fixation, and immunofluorescent localization of proteins within the adult Drosophila brain. This protocol focuses on two example neuronal populations, mushroom body neurons and retinal photoreceptors, and includes optional steps to trace individual mushroom body neurons using Mosaic Analysis with a Repressible Cell Marker (MARCM) technique. Example data from both wild-type and mutant brains are shown along with a brief description of a scoring criteria for axonal guidance defects. While this protocol highlights two well-established antibodies for investigating the morphology of mushroom body and photoreceptor neurons, other Drosophila brain regions and the localization of proteins within other brain regions can also be investigated using this protocol.
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Affiliation(s)
- Seth M Kelly
- Program in Neuroscience, The College of Wooster; Department of Biology, The College of Wooster;
| | - Alexandra Elchert
- Program in Biochemistry, Cellular, and Molecular Biology, The College of Wooster
| | - Michael Kahl
- Department of Biology, The College of Wooster; Program in Biochemistry, Cellular, and Molecular Biology, The College of Wooster
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35
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Gale JR, Aschrafi A, Gioio AE, Kaplan BB. Nuclear-Encoded Mitochondrial mRNAs: A Powerful Force in Axonal Growth and Development. Neuroscientist 2017; 24:142-155. [PMID: 28614981 DOI: 10.1177/1073858417714225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Axons, their growth cones, and synaptic nerve terminals are neuronal subcompartments that have high energetic needs. As such, they are enriched in mitochondria, which supply the ATP necessary to meet these demands. To date, a heterogeneous population of nuclear-encoded mitochondrial mRNAs has been identified in distal axons and growth cones. Accumulating evidence suggests that the local translation of these mRNAs is required for mitochondrial maintenance and axonal viability. Here, we review evidence that suggests a critical role for axonal translation of nuclear-encoded mitochondrial mRNAs in axonal growth and development. Additionally, we explore the role that site-specific translation at the mitochondria itself may play in this process. Finally, we briefly review the clinical implications of dysregulation of local translation of mitochondrial-related mRNAs in neurodevelopmental disorders.
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Affiliation(s)
- Jenna R Gale
- 1 Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Armaz Aschrafi
- 1 Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Anthony E Gioio
- 1 Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Barry B Kaplan
- 1 Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
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36
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Fasken MB, Corbett AH. Links between mRNA splicing, mRNA quality control, and intellectual disability. RNA & DISEASE 2016; 3:e1448. [PMID: 27868086 PMCID: PMC5113822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
In recent years, the impairment of RNA binding proteins that play key roles in the post-transcriptional regulation of gene expression has been linked to numerous neurological diseases. These RNA binding proteins perform critical mRNA processing steps in the nucleus, including splicing, polyadenylation, and export. In many cases, these RNA binding proteins are ubiquitously expressed raising key questions about why only brain function is impaired. Recently, mutations in the ZC3H14 gene, encoding an evolutionarily conserved, polyadenosine RNA binding protein, have been linked to a nonsyndromic form of autosomal recessive intellectual disability. Thus far, research on ZC3H14 and its Nab2 orthologs in budding yeast and Drosophila reveals that ZC3H14/Nab2 is important for mRNA processing and neuronal patterning. Two recent studies now provide evidence that ZC3H14/Nab2 may function in the quality control of mRNA splicing and export and could help to explain the molecular defects that cause neuronal dysfunction and lead to an inherited form of intellectual disability. These studies on ZC3H14/Nab2 reveal new clues to the puzzle of why loss of the ubiquitously expressed ZC3H14 protein specifically affects neurons.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, Emory University, 1510 Clifton Rd., NE RRC 1021, Atlanta, GA 30322, U.S.A
| | - Anita H Corbett
- Department of Biology, Emory University, 1510 Clifton Rd., NE RRC 1021, Atlanta, GA 30322, U.S.A
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37
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Wigington CP, Morris KJ, Newman LE, Corbett AH. The Polyadenosine RNA-binding Protein, Zinc Finger Cys3His Protein 14 (ZC3H14), Regulates the Pre-mRNA Processing of a Key ATP Synthase Subunit mRNA. J Biol Chem 2016; 291:22442-22459. [PMID: 27563065 DOI: 10.1074/jbc.m116.754069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
Polyadenosine RNA-binding proteins (Pabs) regulate multiple steps in gene expression. This protein family includes the well studied Pabs, PABPN1 and PABPC1, as well as the newly characterized Pab, zinc finger CCCH-type containing protein 14 (ZC3H14). Mutations in ZC3H14 are linked to a form of intellectual disability. To probe the function of ZC3H14, we performed a transcriptome-wide analysis of cells depleted of either ZC3H14 or the control Pab, PABPN1. Depletion of PABPN1 affected ∼17% of expressed transcripts, whereas ZC3H14 affected only ∼1% of expressed transcripts. To assess the function of ZC3H14 in modulating target mRNAs, we selected the gene encoding the ATP synthase F0 subunit C (ATP5G1) transcript. Knockdown of ZC3H14 significantly reduced ATP5G1 steady-state mRNA levels. Consistent with results suggesting that ATP5G1 turnover increases upon depletion of ZC3H14, double knockdown of ZC3H14 and the nonsense-mediated decay factor, UPF1, rescues ATP5G1 transcript levels. Furthermore, fractionation reveals an increase in the amount of ATP5G1 pre-mRNA that reaches the cytoplasm when ZC3H14 is depleted and that ZC3H14 binds to ATP5G1 pre-mRNA in the nucleus. These data support a role for ZC3H14 in ensuring proper nuclear processing and retention of ATP5G1 pre-mRNA. Consistent with the observation that ATP5G1 is a rate-limiting component for ATP synthase activity, knockdown of ZC3H14 decreases cellular ATP levels and causes mitochondrial fragmentation. These data suggest that ZC3H14 modulates pre-mRNA processing of select mRNA transcripts and plays a critical role in regulating cellular energy levels, observations that have broad implications for proper neuronal function.
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Affiliation(s)
- Callie P Wigington
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Kevin J Morris
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Laura E Newman
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Anita H Corbett
- From the Department of Biochemistry and .,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
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38
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The Evolutionarily-conserved Polyadenosine RNA Binding Protein, Nab2, Cooperates with Splicing Machinery to Regulate the Fate of pre-mRNA. Mol Cell Biol 2016; 36:2697-2714. [PMID: 27528618 PMCID: PMC5064217 DOI: 10.1128/mcb.00402-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Numerous RNA binding proteins are deposited onto an mRNA transcript to modulate post-transcriptional processing events ensuring proper mRNA maturation. Defining the interplay between RNA binding proteins that couple mRNA biogenesis events is crucial for understanding how gene expression is regulated. To explore how RNA binding proteins control mRNA processing, we investigated a role for the evolutionarily conserved polyadenosine RNA binding protein, Nab2, in mRNA maturation within the nucleus. This work reveals that nab2 mutant cells accumulate intron-containing pre-mRNA in vivo We extend this analysis to identify genetic interactions between mutant alleles of nab2 and genes encoding the splicing factor, MUD2, and the RNA exosome, RRP6, with in vivo consequences of altered pre-mRNA splicing and poly(A) tail length control. As further evidence linking Nab2 proteins to splicing, an unbiased proteomic analysis of vertebrate Nab2, ZC3H14, identifies physical interactions with numerous components of the spliceosome. We validated the interaction between ZC3H14 and U2AF2/U2AF65 Taking all the findings into consideration, we present a model where Nab2/ZC3H14 interacts with spliceosome components to allow proper coupling of splicing with subsequent mRNA processing steps contributing to a kinetic proofreading step that allows properly processed mRNA to exit the nucleus and escape Rrp6-dependent degradation.
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39
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Reuter LM, Sträßer K. Falling for the dark side of transcription: Nab2 fosters RNA polymerase III transcription. Transcription 2016; 7:69-74. [PMID: 27049816 PMCID: PMC4984684 DOI: 10.1080/21541264.2016.1170252] [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] [Indexed: 11/16/2022] Open
Abstract
RNA polymerase III (RNAPIII) synthesizes diverse, small, non-coding RNAs with many important roles in the cellular metabolism. One of the open questions of RNAPIII transcription is whether and how additional factors are involved. Recently, Nab2 was identified as the first messenger ribonucleoprotein particle (mRNP) biogenesis factor with a function in RNAPIII transcription.
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Affiliation(s)
- L Maximilian Reuter
- a Institute of Biochemistry, Justus Liebig University Giessen , Giessen , Germany
| | - Katja Sträßer
- a Institute of Biochemistry, Justus Liebig University Giessen , Giessen , Germany
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40
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Dash S, Siddam AD, Barnum CE, Janga SC, Lachke SA. RNA-binding proteins in eye development and disease: implication of conserved RNA granule components. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:527-57. [PMID: 27133484 DOI: 10.1002/wrna.1355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/21/2016] [Indexed: 01/16/2023]
Abstract
The molecular biology of metazoan eye development is an area of intense investigation. These efforts have led to the surprising recognition that although insect and vertebrate eyes have dramatically different structures, the orthologs or family members of several conserved transcription and signaling regulators such as Pax6, Six3, Prox1, and Bmp4 are commonly required for their development. In contrast, our understanding of posttranscriptional regulation in eye development and disease, particularly regarding the function of RNA-binding proteins (RBPs), is limited. We examine the present knowledge of RBPs in eye development in the insect model Drosophila as well as several vertebrate models such as fish, frog, chicken, and mouse. Interestingly, of the 42 RBPs that have been investigated for their expression or function in vertebrate eye development, 24 (~60%) are recognized in eukaryotic cells as components of RNA granules such as processing bodies, stress granules, or other specialized ribonucleoprotein (RNP) complexes. We discuss the distinct developmental and cellular events that may necessitate potential RBP/RNA granule-associated RNA regulon models to facilitate posttranscriptional control of gene expression in eye morphogenesis. In support of these hypotheses, three RBPs and RNP/RNA granule components Tdrd7, Caprin2, and Stau2 are linked to ocular developmental defects such as congenital cataract, Peters anomaly, and microphthalmia in human patients or animal models. We conclude by discussing the utility of interdisciplinary approaches such as the bioinformatics tool iSyTE (integrated Systems Tool for Eye gene discovery) to prioritize RBPs for deriving posttranscriptional regulatory networks in eye development and disease. WIREs RNA 2016, 7:527-557. doi: 10.1002/wrna.1355 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University & Purdue University Indianapolis, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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41
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Esmaeeli-Nieh S, Fenckova M, Porter IM, Motazacker MM, Nijhof B, Castells-Nobau A, Asztalos Z, Weißmann R, Behjati F, Tzschach A, Felbor U, Scherthan H, Sayfati SM, Ropers HH, Kahrizi K, Najmabadi H, Swedlow JR, Schenck A, Kuss AW. BOD1 Is Required for Cognitive Function in Humans and Drosophila. PLoS Genet 2016; 12:e1006022. [PMID: 27166630 PMCID: PMC4864283 DOI: 10.1371/journal.pgen.1006022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 04/08/2016] [Indexed: 11/19/2022] Open
Abstract
Here we report a stop-mutation in the BOD1 (Biorientation Defective 1) gene, which co-segregates with intellectual disability in a large consanguineous family, where individuals that are homozygous for the mutation have no detectable BOD1 mRNA or protein. The BOD1 protein is required for proper chromosome segregation, regulating phosphorylation of PLK1 substrates by modulating Protein Phosphatase 2A (PP2A) activity during mitosis. We report that fibroblast cell lines derived from homozygous BOD1 mutation carriers show aberrant localisation of the cell cycle kinase PLK1 and its phosphatase PP2A at mitotic kinetochores. However, in contrast to the mitotic arrest observed in BOD1-siRNA treated HeLa cells, patient-derived cells progressed through mitosis with no apparent segregation defects but at an accelerated rate compared to controls. The relatively normal cell cycle progression observed in cultured cells is in line with the absence of gross structural brain abnormalities in the affected individuals. Moreover, we found that in normal adult brain tissues BOD1 expression is maintained at considerable levels, in contrast to PLK1 expression, and provide evidence for synaptic localization of Bod1 in murine neurons. These observations suggest that BOD1 plays a cell cycle-independent role in the nervous system. To address this possibility, we established two Drosophila models, where neuron-specific knockdown of BOD1 caused pronounced learning deficits and significant abnormalities in synapse morphology. Together our results reveal novel postmitotic functions of BOD1 as well as pathogenic mechanisms that strongly support a causative role of BOD1 deficiency in the aetiology of intellectual disability. Moreover, by demonstrating its requirement for cognitive function in humans and Drosophila we provide evidence for a conserved role of BOD1 in the development and maintenance of cognitive features.
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Affiliation(s)
- Sahar Esmaeeli-Nieh
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michaela Fenckova
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Iain M. Porter
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - M. Mahdi Motazacker
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bonnie Nijhof
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Anna Castells-Nobau
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Zoltan Asztalos
- Department Genetics, Aktogen Limited, University of Cambridge, Cambridge, United Kingdom
- Aktogen Hungary Ltd., Bay Zoltán Nonprofit Ltd., Institute for Biotechnology, Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Robert Weißmann
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Andreas Tzschach
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ute Felbor
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Harry Scherthan
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institut für Radiobiologie der Bundeswehr in Verbindung mit der Universität Ulm, München, Germany
| | - Seyed Morteza Sayfati
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H. Hilger. Ropers
- Department for Human Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, Netherlands
| | - Andreas W. Kuss
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
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42
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Abstract
Reuter et al. show that Nab2, a poly(A)-binding protein important for correct poly(A) tail length and nuclear mRNA export, is present at all RNA polymerase III (RNAPIII) transcribed genes. Nab2 is required for the occupancy of RNAPIII and TFIIIB at target genes. RNA polymerase III (RNAPIII) synthesizes most small RNAs, the most prominent being tRNAs. Although the basic mechanism of RNAPIII transcription is well understood, recent evidence suggests that additional proteins play a role in RNAPIII transcription. Here, we discovered by a genome-wide approach that Nab2, a poly(A)-binding protein important for correct poly(A) tail length and nuclear mRNA export, is present at all RNAPIII transcribed genes. The occupancy of Nab2 at RNAPIII transcribed genes is dependent on transcription. Using a novel temperature-sensitive allele of NAB2, nab2-34, we show that Nab2 is required for the occupancy of RNAPIII and TFIIIB at target genes. Furthermore, Nab2 interacts with RNAPIII, TFIIIB, and RNAPIII transcripts. Importantly, impairment of Nab2 function causes an RNAPIII transcription defect in vivo and in vitro. Taken together, we establish Nab2, an important mRNA biogenesis factor, as a novel player required for RNAPIII transcription by stabilizing TFIIIB and RNAPIII at promoters.
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Affiliation(s)
- L Maximilian Reuter
- Institute of Biochemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Dominik M Meinel
- Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Katja Sträßer
- Institute of Biochemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-University Munich, 81377 Munich, Germany
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43
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Goldstein JH, Tim-aroon T, Shieh J, Merrill M, Deeb KK, Zhang S, Bass NE, Bedoyan JK. Novel SMC1A frameshift mutations in children with developmental delay and epilepsy. Eur J Med Genet 2015; 58:562-8. [DOI: 10.1016/j.ejmg.2015.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 09/10/2015] [Accepted: 09/15/2015] [Indexed: 11/26/2022]
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44
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Harrison PF, Powell DR, Clancy JL, Preiss T, Boag PR, Traven A, Seemann T, Beilharz TH. PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA (NEW YORK, N.Y.) 2015; 21:1502-10. [PMID: 26092945 PMCID: PMC4509939 DOI: 10.1261/rna.048355.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/20/2015] [Indexed: 05/21/2023]
Abstract
A major objective of systems biology is to quantitatively integrate multiple parameters from genome-wide measurements. To integrate gene expression with dynamics in poly(A) tail length and adenylation site, we developed a targeted next-generation sequencing approach, Poly(A)-Test RNA-sequencing. PAT-seq returns (i) digital gene expression, (ii) polyadenylation site/s, and (iii) the polyadenylation-state within and between eukaryotic transcriptomes. PAT-seq differs from previous 3' focused RNA-seq methods in that it depends strictly on 3' adenylation within total RNA samples and that the full-native poly(A) tail is included in the sequencing libraries. Here, total RNA samples from budding yeast cells were analyzed to identify the intersect between adenylation state and gene expression in response to loss of the major cytoplasmic deadenylase Ccr4. Furthermore, concordant changes to gene expression and adenylation-state were demonstrated in the classic Crabtree-Warburg metabolic shift. Because all polyadenylated RNA is interrogated by the approach, alternative adenylation sites, noncoding RNA and RNA-decay intermediates were also identified. Most important, the PAT-seq approach uses standard sequencing procedures, supports significant multiplexing, and thus replication and rigorous statistical analyses can for the first time be brought to the measure of 3'-UTR dynamics genome wide.
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Affiliation(s)
- Paul F Harrison
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia Monash Bioinformatics Platform, Monash University, Clayton 3800, Australia
| | - David R Powell
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia Monash Bioinformatics Platform, Monash University, Clayton 3800, Australia
| | - Jennifer L Clancy
- EMBL-Australia Collaborating Laboratory, Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) 2601, Australian Capital Territory, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Laboratory, Genome Biology Department, The John Curtin School of Medical Research (JCSMR), The Australian National University, Acton (Canberra) 2601, Australian Capital Territory, Australia Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
| | - Peter R Boag
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Torsten Seemann
- Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton 3053, Australia
| | - Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
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45
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Hu H, Wienker TF, Musante L, Kalscheuer VM, Kahrizi K, Najmabadi H, Ropers HH. Integrated sequence analysis pipeline provides one-stop solution for identifying disease-causing mutations. Hum Mutat 2015; 35:1427-35. [PMID: 25219469 DOI: 10.1002/humu.22695] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 08/28/2014] [Indexed: 12/23/2022]
Abstract
Next-generation sequencing has greatly accelerated the search for disease-causing defects, but even for experts the data analysis can be a major challenge. To facilitate the data processing in a clinical setting, we have developed a novel medical resequencing analysis pipeline (MERAP). MERAP assesses the quality of sequencing, and has optimized capacity for calling variants, including single-nucleotide variants, insertions and deletions, copy-number variation, and other structural variants. MERAP identifies polymorphic and known causal variants by filtering against public domain databases, and flags nonsynonymous and splice-site changes. MERAP uses a logistic model to estimate the causal likelihood of a given missense variant. MERAP considers the relevant information such as phenotype and interaction with known disease-causing genes. MERAP compares favorably with GATK, one of the widely used tools, because of its higher sensitivity for detecting indels, its easy installation, and its economical use of computational resources. Upon testing more than 1,200 individuals with mutations in known and novel disease genes, MERAP proved highly reliable, as illustrated here for five families with disease-causing variants. We believe that the clinical implementation of MERAP will expedite the diagnostic process of many disease-causing defects.
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Affiliation(s)
- Hao Hu
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
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46
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Kelly SM, Bienkowski R, Banerjee A, Melicharek DJ, Brewer ZA, Marenda DR, Corbett AH, Moberg KH. The Drosophila ortholog of the Zc3h14 RNA binding protein acts within neurons to pattern axon projection in the developing brain. Dev Neurobiol 2015; 76:93-106. [PMID: 25980665 DOI: 10.1002/dneu.22301] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 12/18/2022]
Abstract
The dNab2 polyadenosine RNA binding protein is the D. melanogaster ortholog of the vertebrate ZC3H14 protein, which is lost in a form of inherited intellectual disability (ID). Human ZC3H14 can rescue D. melanogaster dNab2 mutant phenotypes when expressed in all neurons of the developing nervous system, suggesting that dNab2/ZC3H14 performs well-conserved roles in neurons. However, the cellular and molecular requirements for dNab2/ZC3H14 in the developing nervous system have not been defined in any organism. Here we show that dNab2 is autonomously required within neurons to pattern axon projection from Kenyon neurons into the mushroom bodies, which are required for associative olfactory learning and memory in insects. Mushroom body axons lacking dNab2 project aberrantly across the brain midline and also show evidence of defective branching. Coupled with the prior finding that ZC3H14 is highly expressed in rodent hippocampal neurons, this requirement for dNab2 in mushroom body neurons suggests that dNab2/ZC3H14 has a conserved role in supporting axon projection and branching. Consistent with this idea, loss of dNab2 impairs short-term memory in a courtship conditioning assay. Taken together these results reveal a cell-autonomous requirement for the dNab2 RNA binding protein in mushroom body development and provide a window into potential neurodevelopmental functions of the human ZC3H14 protein.
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Affiliation(s)
- Seth M Kelly
- Department of Biology, College of Wooster, Wooster, Ohio, 44691
| | - Rick Bienkowski
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, 30322.,Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322.,Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, 30322
| | - Ayan Banerjee
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322
| | - David J Melicharek
- Department of Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, 19104
| | | | - Daniel R Marenda
- Department of Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, 19104.,Departments of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, Pennsylvania, 19104
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, 30322
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47
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Tran EJ, King MC, Corbett AH. Macromolecular transport between the nucleus and the cytoplasm: Advances in mechanism and emerging links to disease. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2784-2795. [PMID: 25116306 PMCID: PMC4161953 DOI: 10.1016/j.bbamcr.2014.08.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 01/08/2023]
Abstract
Transport of macromolecules between the cytoplasm and the nucleus is critical for the function of all eukaryotic cells. Large macromolecular channels termed nuclear pore complexes that span the nuclear envelope mediate the bidirectional transport of cargoes between the nucleus and cytoplasm. However, the influence of macromolecular trafficking extends past the nuclear pore complex to transcription and RNA processing within the nucleus and signaling pathways that reach into the cytoplasm and beyond. At the Mechanisms of Nuclear Transport biennial meeting held from October 18 to 23, 2013 in Woods Hole, MA, researchers in the field met to report on their recent findings. The work presented highlighted significant advances in understanding nucleocytoplasmic trafficking including how transport receptors and cargoes pass through the nuclear pore complex, the many signaling pathways that impinge on transport pathways, interplay between the nuclear envelope, nuclear pore complexes, and transport pathways, and numerous links between transport pathways and human disease. The goal of this review is to highlight newly emerging themes in nuclear transport and underscore the major questions that are likely to be the focus of future research in the field.
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Affiliation(s)
- Elizabeth J Tran
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907, USA.
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, 4117 Rollins Research Center, 1510 Clifton Road, NE, Atlanta, GA 30322, USA.
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48
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Wigington CP, Williams KR, Meers MP, Bassell GJ, Corbett AH. Poly(A) RNA-binding proteins and polyadenosine RNA: new members and novel functions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:601-22. [PMID: 24789627 PMCID: PMC4332543 DOI: 10.1002/wrna.1233] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/07/2014] [Accepted: 03/06/2014] [Indexed: 02/05/2023]
Abstract
Poly(A) RNA-binding proteins (Pabs) bind with high affinity and specificity to polyadenosine RNA. Textbook models show a nuclear Pab, PABPN1, and a cytoplasmic Pab, PABPC, where the nuclear PABPN1 modulates poly(A) tail length and the cytoplasmic PABPC stabilizes poly(A) RNA in the cytoplasm and also enhances translation. While these conventional roles are critically important, the Pab family has expanded recently both in number and in function. A number of novel roles have emerged for both PAPBPN1 and PABPC that contribute to the fine-tuning of gene expression. Furthermore, as the characterization of the nucleic acid binding properties of RNA-binding proteins advances, additional proteins that show high affinity and specificity for polyadenosine RNA are being discovered. With this expansion of the Pab family comes a concomitant increase in the potential for Pabs to modulate gene expression. Further complication comes from an expansion of the potential binding sites for Pab proteins as revealed by an analysis of templated polyadenosine stretches present within the transcriptome. Thus, Pabs could influence mRNA fate and function not only by binding to the nontemplated poly(A) tail but also to internal stretches of adenosine. Understanding the diverse functions of Pab proteins is not only critical to understand how gene expression is regulated but also to understand the molecular basis for tissue-specific diseases that occur when Pab proteins are altered. Here we describe both conventional and recently emerged functions for PABPN1 and PABPC and then introduce and discuss three new Pab family members, ZC3H14, hnRNP-Q1, and LARP4.
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Affiliation(s)
- Callie P. Wigington
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Kathryn R. Williams
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P. Meers
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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49
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Kambouris M, Maroun RC, Ben-Omran T, Al-Sarraj Y, Errafii K, Ali R, Boulos H, Curmi PA, El-Shanti H. Mutations in zinc finger 407 [ZNF407] cause a unique autosomal recessive cognitive impairment syndrome. Orphanet J Rare Dis 2014; 9:80. [PMID: 24907849 PMCID: PMC4070100 DOI: 10.1186/1750-1172-9-80] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 05/29/2014] [Indexed: 01/14/2023] Open
Abstract
Background A consanguineous Arab family is affected by an apparently novel autosomal recessive disorder characterized by cognitive impairment, failure-to-thrive, hypotonia and dysmorphic features including bilateral ptosis and epicanthic folds, synophrys, midface hypoplasia, downturned mouth corners, thin upper vermillion border and prominent ears, bilateral 5th finger camptodactyly, bilateral short 4th metatarsal bones, and limited knee mobility bilaterally. Methods The family was studied by homozygosity mapping, candidate gene mutation screening and whole Exome Next Generation Sequencing of a single affected member to identify the offending gene and mutation. The mutated gene product was studied by structural bioinformatics methods. Results A damaging c.C5054G mutation affecting an evolutionary highly conserved amino acid p.S1685W was identified in the ZNF407 gene at 18q23. The Serine to Tryptophane mutation affects two of the three ZNF407 isoforms and is located in the last third of the protein, in a linker peptide adjoining two zinc-finger domains. Structural analyses of this mutation shows disruption of an H-bond that locks the relative spatial position of the two fingers, leading to a higher flexibility of the linker and thus to a decreased probability of binding to the target DNA sequence essentially eliminating the functionality of downstream domains and interfering with the expression of various genes under ZNF407 control during fetal brain development. Conclusions ZNF407 is a transcription factor with an essential role in brain development. When specific and limited in number homozygosity intervals exist that harbor the offending gene in consanguineous families, Whole Exome Sequencing of a single affected individual is an efficient approach to gene mapping and mutation identification.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hatem El-Shanti
- Qatar Biomedical Research Institute, Medical Genetics Center, 69 Lusail Street, West Bay Area, P,O, Box: 33123, Doha, Qatar.
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50
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Kelly SM, Leung SW, Pak C, Banerjee A, Moberg KH, Corbett AH. A conserved role for the zinc finger polyadenosine RNA binding protein, ZC3H14, in control of poly(A) tail length. RNA (NEW YORK, N.Y.) 2014; 20:681-688. [PMID: 24671764 PMCID: PMC3988569 DOI: 10.1261/rna.043984.113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
The ZC3H14 gene, which encodes a ubiquitously expressed, evolutionarily conserved, nuclear, zinc finger polyadenosine RNA-binding protein, was recently linked to autosomal recessive, nonsyndromic intellectual disability. Although studies have been carried out to examine the function of putative orthologs of ZC3H14 in Saccharomyces cerevisiae, where the protein is termed Nab2, and Drosophila, where the protein has been designated dNab2, little is known about the function of mammalian ZC3H14. Work from both budding yeast and flies implicates Nab2/dNab2 in poly(A) tail length control, while a role in poly(A) RNA export from the nucleus has been reported only for budding yeast. Here we provide the first functional characterization of ZC3H14. Analysis of ZC3H14 function in a neuronal cell line as well as in vivo complementation studies in a Drosophila model identify a role for ZC3H14 in proper control of poly(A) tail length in neuronal cells. Furthermore, we show here that human ZC3H14 can functionally substitute for dNab2 in fly neurons and can rescue defects in development and locomotion that are present in dNab2 null flies. These rescue experiments provide evidence that this zinc finger-containing class of nuclear polyadenosine RNA-binding proteins plays an evolutionarily conserved role in controlling the length of the poly(A) tail in neurons.
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Affiliation(s)
- Seth M. Kelly
- Department of Biology, College of Wooster, Wooster, Ohio 44691, USA
| | - Sara W. Leung
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - ChangHui Pak
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Ayan Banerjee
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Kenneth H. Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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