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Buchholz S, Zempel H. The six brain-specific TAU isoforms and their role in Alzheimer's disease and related neurodegenerative dementia syndromes. Alzheimers Dement 2024; 20:3606-3628. [PMID: 38556838 PMCID: PMC11095451 DOI: 10.1002/alz.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 04/02/2024]
Abstract
INTRODUCTION Alternative splicing of the human MAPT gene generates six brain-specific TAU isoforms. Imbalances in the TAU isoform ratio can lead to neurodegenerative diseases, underscoring the need for precise control over TAU isoform balance. Tauopathies, characterized by intracellular aggregates of hyperphosphorylated TAU, exhibit extensive neurodegeneration and can be classified by the TAU isoforms present in pathological accumulations. METHODS A comprehensive review of TAU and related dementia syndromes literature was conducted using PubMed, Google Scholar, and preprint server. RESULTS While TAU is recognized as key driver of neurodegeneration in specific tauopathies, the contribution of the isoforms to neuronal function and disease development remains largely elusive. DISCUSSION In this review we describe the role of TAU isoforms in health and disease, and stress the importance of comprehending and studying TAU isoforms in both, physiological and pathological context, in order to develop targeted therapeutic interventions for TAU-associated diseases. HIGHLIGHTS MAPT splicing is tightly regulated during neuronal maturation and throughout life. TAU isoform expression is development-, cell-type and brain region specific. The contribution of TAU to neurodegeneration might be isoform-specific. Ineffective TAU-based therapies highlight the need for specific targeting strategies.
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Affiliation(s)
- Sarah Buchholz
- Institute of Human GeneticsFaculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
- Present address:
Department Schaefer, Neurobiology of AgeingMax Planck Institute for Biology of AgeingCologneGermany
| | - Hans Zempel
- Institute of Human GeneticsFaculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
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2
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Bowles KR, Pugh DA, Pedicone C, Oja L, Weitzman SA, Liu Y, Chen JL, Disney MD, Goate AM. Development of MAPT S305 mutation models exhibiting elevated 4R tau expression, resulting in altered neuronal and astrocytic function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543224. [PMID: 37333200 PMCID: PMC10274740 DOI: 10.1101/2023.06.02.543224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Due to the importance of 4R tau in the pathogenicity of primary tauopathies, it has been challenging to model these diseases in iPSC-derived neurons, which express very low levels of 4R tau. To address this problem we have developed a panel of isogenic iPSC lines carrying the MAPT splice-site mutations S305S, S305I or S305N, derived from four different donors. All three mutations significantly increased the proportion of 4R tau expression in iPSC-neurons and astrocytes, with up to 80% 4R transcripts in S305N neurons from as early as 4 weeks of differentiation. Transcriptomic and functional analyses of S305 mutant neurons revealed shared disruption in glutamate signaling and synaptic maturity, but divergent effects on mitochondrial bioenergetics. In iPSC-astrocytes, S305 mutations induced lysosomal disruption and inflammation and exacerbated internalization of exogenous tau that may be a precursor to the glial pathologies observed in many tauopathies. In conclusion, we present a novel panel of human iPSC lines that express unprecedented levels of 4R tau in neurons and astrocytes. These lines recapitulate previously characterized tauopathy-relevant phenotypes, but also highlight functional differences between the wild type 4R and mutant 4R proteins. We also highlight the functional importance of MAPT expression in astrocytes. These lines will be highly beneficial to tauopathy researchers enabling a more complete understanding of the pathogenic mechanisms underlying 4R tauopathies across different cell types.
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Affiliation(s)
- KR Bowles
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - DA Pugh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - C Pedicone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - L Oja
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - SA Weitzman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Y Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - JL Chen
- Department of Chemistry, Scripps Research Institute, Jupiter, FL, United States of America
| | - MD Disney
- Department of Chemistry, Scripps Research Institute, Jupiter, FL, United States of America
| | - AM Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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3
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How does precursor RNA structure influence RNA processing and gene expression? Biosci Rep 2023; 43:232489. [PMID: 36689327 PMCID: PMC9977717 DOI: 10.1042/bsr20220149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/24/2023] Open
Abstract
RNA is a fundamental biomolecule that has many purposes within cells. Due to its single-stranded and flexible nature, RNA naturally folds into complex and dynamic structures. Recent technological and computational advances have produced an explosion of RNA structural data. Many RNA structures have regulatory and functional properties. Studying the structure of nascent RNAs is particularly challenging due to their low abundance and long length, but their structures are important because they can influence RNA processing. Precursor RNA processing is a nexus of pathways that determines mature isoform composition and that controls gene expression. In this review, we examine what is known about human nascent RNA structure and the influence of RNA structure on processing of precursor RNAs. These known structures provide examples of how other nascent RNAs may be structured and show how novel RNA structures may influence RNA processing including splicing and polyadenylation. RNA structures can be targeted therapeutically to treat disease.
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4
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Childs-Disney JL, Yang X, Gibaut QMR, Tong Y, Batey RT, Disney MD. Targeting RNA structures with small molecules. Nat Rev Drug Discov 2022; 21:736-762. [PMID: 35941229 PMCID: PMC9360655 DOI: 10.1038/s41573-022-00521-4] [Citation(s) in RCA: 141] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
RNA adopts 3D structures that confer varied functional roles in human biology and dysfunction in disease. Approaches to therapeutically target RNA structures with small molecules are being actively pursued, aided by key advances in the field including the development of computational tools that predict evolutionarily conserved RNA structures, as well as strategies that expand mode of action and facilitate interactions with cellular machinery. Existing RNA-targeted small molecules use a range of mechanisms including directing splicing - by acting as molecular glues with cellular proteins (such as branaplam and the FDA-approved risdiplam), inhibition of translation of undruggable proteins and deactivation of functional structures in noncoding RNAs. Here, we describe strategies to identify, validate and optimize small molecules that target the functional transcriptome, laying out a roadmap to advance these agents into the next decade.
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Affiliation(s)
| | - Xueyi Yang
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | | | - Yuquan Tong
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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5
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G R, Mitra A, Pk V. Predicting functional riboSNitches in the context of alternative splicing. Gene X 2022; 837:146694. [PMID: 35738445 DOI: 10.1016/j.gene.2022.146694] [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: 12/09/2021] [Revised: 05/11/2022] [Accepted: 06/17/2022] [Indexed: 11/19/2022] Open
Abstract
RNAs are the major regulators of gene expression, and their secondary structures play crucial roles at different levels. RiboSNitches are disease-associated SNPs that cause changes in the pre-mRNA secondary structural ensemble. Several riboSNitches have been detected in the 5' and 3' untranslated regions and lncRNA. Although cases of secondary structural elements playing a regulatory role in alternative splicing are known, regions specific to splicing events, such as splice junctions have not received much attention. We tested splice-site mutations for their efficiency in disrupting the secondary structure and hypothesized that these could play a crucial role in alternative splicing. Multiple riboSNitch prediction methods were applied to obtain overlapping results that are potentially more reliable. Putative riboSNitches were identified from aberrant 5' and 3' splice site mutations, cancer-causing somatic mutations, and genes that harbor the regulatory RNA secondary structural elements. Our workflow for predicting riboSNitches associated with alternative splicing is novel and paves the way for subsequent experimental validation.
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Affiliation(s)
- Ramya G
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India.
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India.
| | - Vinod Pk
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India.
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6
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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7
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Lee BP, Mulvey L, Barr G, Garratt J, Goodman E, Selman C, Harries LW. Dietary restriction in ILSXISS mice is associated with widespread changes in splicing regulatory factor expression levels. Exp Gerontol 2019; 128:110736. [DOI: 10.1016/j.exger.2019.110736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022]
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8
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Ong AAL, Tan J, Bhadra M, Dezanet C, Patil KM, Chong MS, Kierzek R, Decout JL, Roca X, Chen G. RNA Secondary Structure-Based Design of Antisense Peptide Nucleic Acids for Modulating Disease-Associated Aberrant Tau Pre-mRNA Alternative Splicing. Molecules 2019; 24:molecules24163020. [PMID: 31434312 PMCID: PMC6720520 DOI: 10.3390/molecules24163020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing of tau pre-mRNA is regulated by a 5' splice site (5'ss) hairpin present at the exon 10-intron 10 junction. Single mutations within the hairpin sequence alter hairpin structural stability and/or the binding of splicing factors, resulting in disease-causing aberrant splicing of exon 10. The hairpin structure contains about seven stably formed base pairs and thus may be suitable for targeting through antisense strands. Here, we used antisense peptide nucleic acids (asPNAs) to probe and target the tau pre-mRNA exon 10 5'ss hairpin structure through strand invasion. We characterized by electrophoretic mobility shift assay the binding of the designed asPNAs to model tau splice site hairpins. The relatively short (10-15 mer) asPNAs showed nanomolar binding to wild-type hairpins as well as a disease-causing mutant hairpin C+19G, albeit with reduced binding strength. Thus, the structural stabilizing effect of C+19G mutation could be revealed by asPNA binding. In addition, our cell culture minigene splicing assay data revealed that application of an asPNA targeting the 3' arm of the hairpin resulted in an increased exon 10 inclusion level for the disease-associated mutant C+19G, probably by exposing the 5'ss as well as inhibiting the binding of protein factors to the intronic spicing silencer. On the contrary, the application of asPNAs targeting the 5' arm of the hairpin caused an increased exon 10 exclusion for a disease-associated mutant C+14U, mainly by blocking the 5'ss. PNAs could enter cells through conjugation with amino sugar neamine or by cotransfection with minigene plasmids using a commercially available transfection reagent.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jiazi Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Malini Bhadra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Clément Dezanet
- University Grenoble Alpes/CNRS, Département de Pharmacochimie Moléculaire, ICMG FR 2607, UMR 5063, 470 Rue de la Chimie, F-38041 Grenoble, France
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Mei Sian Chong
- Geriatic Education & Research Institute, 2 Yishun Central 2, Singapore 768024, Singapore
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jean-Luc Decout
- University Grenoble Alpes/CNRS, Département de Pharmacochimie Moléculaire, ICMG FR 2607, UMR 5063, 470 Rue de la Chimie, F-38041 Grenoble, France
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
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9
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Bartys N, Kierzek R, Lisowiec-Wachnicka J. The regulation properties of RNA secondary structure in alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194401. [PMID: 31323437 DOI: 10.1016/j.bbagrm.2019.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
Abstract
The RNA secondary structure is important for many functional processes in the cell. The secondary and tertiary structures of cellular RNAs are essential for the activity of these molecules in processes such as transcription, splicing, translation, and localization. New high-throughput analytical methods, including next generation sequencing, have allowed for the in-depth characterization of the 'RNA structurome': a new term describing how the RNA structure controls the activity of RNA by itself and how it regulates the expression of genes. In this review, we present many examples of the influence of structural motifs of RNA, long range interactions and global RNA structure on the alternative splicing processes. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Natalia Bartys
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
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10
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Chen JL, Moss WN, Spencer A, Zhang P, Childs-Disney JL, Disney MD. The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology. PLoS One 2019; 14:e0219210. [PMID: 31291322 PMCID: PMC6619747 DOI: 10.1371/journal.pone.0219210] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 12/31/2022] Open
Abstract
Tauopathies are neurodegenerative diseases that affect millions of people worldwide including those with Alzheimer’s disease. While many efforts have focused on understanding the role of tau protein in neurodegeneration, there has been little done to systematically analyze and study the structures within tau’s encoding RNA and their connection to disease pathology. Knowledge of RNA structure can provide insights into disease mechanisms and how to affect protein production for therapeutic benefit. Using computational methods based on thermodynamic stability and evolutionary conservation, we identified structures throughout the tau pre-mRNA, especially at exon-intron junctions and within the 5′ and 3′ untranslated regions (UTRs). In particular, structures were identified at twenty exon-intron junctions. The 5′ UTR contains one structured region, which lies within a known internal ribosome entry site. The 3′ UTR contains eight structured regions, including one that contains a polyadenylation signal. A series of functional experiments were carried out to assess the effects of mutations associated with mis-regulation of alternative splicing of exon 10 and to identify regions of the 3′ UTR that contain cis-regulatory elements. These studies defined novel structural regions within the mRNA that affect stability and pre-mRNA splicing and may lead to new therapeutic targets for treating tau-associated diseases.
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Affiliation(s)
- Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Adam Spencer
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Peiyuan Zhang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Jessica L. Childs-Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, United States of America
- * E-mail:
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11
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Busan S, Weidmann CA, Sengupta A, Weeks KM. Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies. Biochemistry 2019; 58:2655-2664. [PMID: 31117385 DOI: 10.1021/acs.biochem.8b01218] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical probing is an important tool for characterizing the complex folded structures of RNA molecules, many of which play key cellular roles. Electrophilic SHAPE reagents create adducts at the 2'-hydroxyl position on the RNA backbone of flexible ribonucleotides with relatively little dependence on nucleotide identity. Strategies for adduct detection such as mutational profiling (MaP) allow accurate, automated calculation of relative adduct frequencies for each nucleotide in a given RNA or group of RNAs. A number of alternative reagents and adduct detection strategies have been proposed, especially for use in living cells. Here we evaluate five SHAPE reagents: three previously well-validated reagents 1M7 (1-methyl-7-nitroisatoic anhydride), 1M6 (1-methyl-6-nitroisatoic anhydride), and NMIA ( N-methylisatoic anhydride), one more recently proposed NAI (2-methylnicotinic acid imidazolide), and one novel reagent 5NIA (5-nitroisatoic anhydride). We clarify the importance of carefully designed software in reading out SHAPE experiments using massively parallel sequencing approaches. We examine SHAPE modification in living cells in diverse cell lines, compare MaP and reverse transcription-truncation as SHAPE adduct detection strategies, make recommendations for SHAPE reagent choice, and outline areas for future development.
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Affiliation(s)
- Steven Busan
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Chase A Weidmann
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Arnab Sengupta
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
| | - Kevin M Weeks
- Department of Chemistry , University of North Carolina , Chapel Hill , North Carolina 27599-3290 , United States
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12
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Tan J, Yang L, Ong AAL, Shi J, Zhong Z, Lye ML, Liu S, Lisowiec-Wachnicka J, Kierzek R, Roca X, Chen G. A Disease-Causing Intronic Point Mutation C19G Alters Tau Exon 10 Splicing via RNA Secondary Structure Rearrangement. Biochemistry 2019; 58:1565-1578. [DOI: 10.1021/acs.biochem.9b00001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiazi Tan
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Lixia Yang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Alan Ann Lerk Ong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Jiahao Shi
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Zhensheng Zhong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Mun Leng Lye
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Shiyi Liu
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Gang Chen
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
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13
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Montes M, Sanford BL, Comiskey DF, Chandler DS. RNA Splicing and Disease: Animal Models to Therapies. Trends Genet 2019; 35:68-87. [PMID: 30466729 PMCID: PMC6339821 DOI: 10.1016/j.tig.2018.10.002] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023]
Abstract
Alternative splicing of pre-mRNA increases genetic diversity, and recent studies estimate that most human multiexon genes are alternatively spliced. If this process is not highly regulated and accurate, it leads to mis-splicing events, which may result in proteins with altered function. A growing body of work has implicated mis-splicing events in a range of diseases, including cancer, neurodegenerative diseases, and muscular dystrophies. Understanding the mechanisms that cause aberrant splicing events and how this leads to disease is vital for designing effective therapeutic strategies. In this review, we focus on advances in therapies targeting splicing, and highlight the animal models developed to recapitulate disease phenotypes as a model for testing these therapies.
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Affiliation(s)
- Matías Montes
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Brianne L Sanford
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel F Comiskey
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Dawn S Chandler
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
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Influence of mismatched and bulged nucleotides on SNP-preferential RNase H cleavage of RNA-antisense gapmer heteroduplexes. Sci Rep 2017; 7:12532. [PMID: 28970564 PMCID: PMC5624880 DOI: 10.1038/s41598-017-12844-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/11/2017] [Indexed: 12/15/2022] Open
Abstract
This study focused on determining design rules for gapmer-type antisense oligonucleotides (ASOs), that can differentiate cleavability of two SNP variants of RNA in the presence of ribonuclease H based on the mismatch type and position in the heteroduplex. We describe the influence of structural motifs formed by several arrangements of multiple mismatches (various types of mismatches and their position within the ASO/target RNA duplex) on RNase H cleavage selectivity of five different SNP types. The targets were mRNA fragments of APP, SCA3, SNCA and SOD1 genes, carrying C-to-G, G-to-C, G-to-A, A-to-G and C-to-U substitutions. The results show that certain arrangements of mismatches enhance discrimination between wild type and mutant SNP alleles of RNA in vitro as well as in HeLa cells. Among the over 120 gapmers tested, we found two gapmers that caused preferential degradation of the mutant allele APP 692 G and one that led to preferential cleavage of the mutant SNCA 53 A allele, both in vitro and in cells. However, several gapmers promoted selective cleavage of mRNA mutant alleles in in vitro experiments only.
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15
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Lee BP, Pilling LC, Emond F, Flurkey K, Harrison DE, Yuan R, Peters LL, Kuchel GA, Ferrucci L, Melzer D, Harries LW. Changes in the expression of splicing factor transcripts and variations in alternative splicing are associated with lifespan in mice and humans. Aging Cell 2016; 15:903-13. [PMID: 27363602 PMCID: PMC5013025 DOI: 10.1111/acel.12499] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2016] [Indexed: 12/31/2022] Open
Abstract
Dysregulation of splicing factor expression and altered alternative splicing are associated with aging in humans and other species, and also with replicative senescence in cultured cells. Here, we assess whether expression changes of key splicing regulator genes and consequent effects on alternative splicing are also associated with strain longevity in old and young mice, across 6 different mouse strains with varying lifespan (A/J, NOD.B10Sn-H2(b) /J, PWD.Phj, 129S1/SvlmJ, C57BL/6J and WSB/EiJ). Splicing factor expression and changes to alternative splicing were associated with strain lifespan in spleen and to a lesser extent in muscle. These changes mainly involved hnRNP splicing inhibitor transcripts with most changes more marked in spleens of young animals from long-lived strains. Changes in spleen isoform expression were suggestive of reduced cellular senescence and retained cellular proliferative capacity in long-lived strains. Changes in muscle isoform expression were consistent with reduced pro-inflammatory signalling in longer-lived strains. Two splicing regulators, HNRNPA1 and HNRNPA2B1, were also associated with parental longevity in humans, in the InCHIANTI aging study. Splicing factors may represent a driver, mediator or early marker of lifespan in mouse, as expression differences were present in the young animals of long-lived strains. Changes to alternative splicing patterns of key senescence genes in spleen and key remodelling genes in muscle suggest that correct regulation of alternative splicing may enhance lifespan in mice. Expression of some splicing factors in humans was also associated with parental longevity, suggesting that splicing regulation may also influence lifespan in humans.
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Affiliation(s)
| | - Luke C. Pilling
- Epidemiology and Public Health; Institute of Biomedical and Clinical Sciences; University of Exeter Medical School; University of Exeter; Devon UK
| | | | - Kevin Flurkey
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - David E. Harrison
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - Rong Yuan
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - Luanne L. Peters
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - George A. Kuchel
- UConn Centre on Aging; University of Connecticut Health Centre; Farmington CT USA
| | | | - David Melzer
- Epidemiology and Public Health; Institute of Biomedical and Clinical Sciences; University of Exeter Medical School; University of Exeter; Devon UK
- UConn Centre on Aging; University of Connecticut Health Centre; Farmington CT USA
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16
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Prado S, Beltrán M, Coiras M, Bedoya LM, Alcamí J, Gallego J. Bioavailable inhibitors of HIV-1 RNA biogenesis identified through a Rev-based screen. Biochem Pharmacol 2016; 107:14-28. [PMID: 26896646 DOI: 10.1016/j.bcp.2016.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/15/2016] [Indexed: 12/23/2022]
Abstract
New antiretroviral agents with alternative mechanisms are needed to complement the combination therapies used to treat HIV-1 infections. Here we report the identification of bioavailable molecules that interfere with the gene expression processes of HIV-1. The compounds were detected by screening a small library of FDA-approved drugs with an assay based on measuring the displacement of Rev, and essential virus-encoded protein, from its high-affinity RNA binding site. The antiretroviral activity of two hits was based on interference with post-integration steps of the HIV-1 cycle. Both hits inhibited RRE-Rev complex formation in vitro, and blocked LTR-dependent gene expression and viral transcription in cellular assays. The best compound altered the splicing pattern of HIV-1 transcripts in a manner consistent with Rev inhibition. This mechanism of action is different from those used by current antiretroviral agents. The screening hits recognized the Rev binding site in the viral RNA, and the best compound did so with substantial selectivity, allowing the identification of a new RNA-binding scaffold. These results may be used for developing novel antiretroviral drugs.
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Affiliation(s)
- Silvia Prado
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Manuela Beltrán
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain
| | - Mayte Coiras
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain
| | - Luis M Bedoya
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain; Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - José Alcamí
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain.
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain.
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