1
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Choquet K, Patop IL, Churchman LS. The regulation and function of post-transcriptional RNA splicing. Nat Rev Genet 2025; 26:378-394. [PMID: 40217094 DOI: 10.1038/s41576-025-00836-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2025] [Indexed: 05/23/2025]
Abstract
Eukaryotic RNA transcripts undergo extensive processing before becoming functional messenger RNAs, with splicing being a critical and highly regulated step that occurs both co-transcriptionally and post-transcriptionally. Recent analyses have revealed, with unprecedented spatial and temporal resolution, that up to 40% of mammalian introns are retained after transcription termination and are subsequently removed largely while transcripts remain chromatin-associated. Post-transcriptional splicing has emerged as a key layer of gene expression regulation during development, stress response and disease progression. The control of post-transcriptional splicing regulates protein production through delayed splicing and nuclear export, or nuclear retention and degradation of specific transcript isoforms. Here, we review current methodologies for detecting post-transcriptional splicing, discuss the mechanisms controlling the timing of splicing and examine how this temporal regulation affects gene expression programmes in healthy cells and in disease states.
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Affiliation(s)
- Karine Choquet
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ines L Patop
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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2
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Munneke MJ, Yuan Y, Preisner EC, Shelton CD, Carroll DT, Kirchoff NS, Dickson KP, Cantu JO, Douglass MV, Calcutt MW, Gibson-Corley KN, Nicholson MR, Byndloss MX, Britton RA, de Crécy-Lagard V, Skaar EP. A thiouracil desulfurase protects Clostridioides difficile RNA from 4-thiouracil incorporation, providing a competitive advantage in the gut. Cell Host Microbe 2025; 33:573-588.e7. [PMID: 40139192 PMCID: PMC11985272 DOI: 10.1016/j.chom.2025.03.001] [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: 08/19/2024] [Revised: 02/03/2025] [Accepted: 03/03/2025] [Indexed: 03/29/2025]
Abstract
Nucleotides are essential building blocks for major cellular macromolecules and are critical for life. Consequently, bacterial pathogens must acquire or synthesize nucleotides during infection. Clostridioides difficile is the most common hospital-acquired gastrointestinal infection, and nutrient acquisition is critical for pathogenesis. However, the impact of nucleotide metabolism on C. difficile infection remains unclear. Here, we discover that 4-thiouracil (4-TU), a pyrimidine analog present in the human gut, is toxic to commensal bacteria. 4-TU hijacks the uracil salvage pathway for incorporation into RNA through the uracil phosphoribosyltransferase activity encoded by PyrR and Upp. C. difficile can salvage 4-TU as a pyrimidine source through the enzymatic action of a thiouracil desulfurase (TudS), thereby contributing to C. difficile fitness in mice fed 4-TU or MiniBioreactor models of infection containing exogenous 4-TU. Collectively, these results reveal a molecular mechanism for C. difficile to utilize a poisonous pyrimidine analog in the vertebrate gut to outcompete commensal microbes.
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Affiliation(s)
- Matthew J Munneke
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Eva C Preisner
- Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Catherine D Shelton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA
| | - Darian T Carroll
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA
| | - Nicole S Kirchoff
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA
| | - Ken P Dickson
- Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jose O Cantu
- Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin V Douglass
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA
| | - Maribeth R Nicholson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA; Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert A Britton
- Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232-7917, USA.
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3
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Hayes LR, Zaepfel B, Duan L, Starner AC, Bartels MD, Rothacher RL, Martin S, French R, Zhang Z, Sinha IR, Ling JP, Sun S, Ayala YM, Coller J, Van Nostrand EL, Florea L, Kalab P. 5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.02.646885. [PMID: 40236187 PMCID: PMC11996483 DOI: 10.1101/2025.04.02.646885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
TDP-43, an essential nucleic acid binding protein and splicing regulator, is broadly disrupted in neurodegeneration. TDP-43 nuclear localization and function depend on the abundance of its nuclear RNA targets and its recruitment into large ribonucleoprotein complexes, which restricts TDP-43 nuclear efflux. To further investigate the interplay between TDP-43 and nascent RNAs, we aimed to employ 5-ethynyluridine (5EU), a widely used uridine analog for 'click chemistry' labeling of newly transcribed RNAs. Surprisingly, 5EU induced the nuclear accumulation of TDP-43 and other RNA-binding proteins and attenuated TDP-43 mislocalization caused by disruption of the nuclear transport apparatus. RNA FISH demonstrated 5EU-induced nuclear accumulation of polyadenylated and GU-repeat-rich RNAs, suggesting increased retention of both processed and intronic RNAs. TDP-43 eCLIP confirmed that 5EU preserved TDP-43 binding at predominantly GU-rich intronic sites. RNAseq revealed significant 5EU-induced changes in alternative splicing, accompanied by an overall reduction in splicing diversity, without any major changes in RNA stability or TDP-43 splicing regulatory function. These data suggest that 5EU may impede RNA splicing efficiency and subsequent nuclear RNA processing and export. Our findings have important implications for studies utilizing 5EU and offer unexpected confirmation that the accumulation of endogenous nuclear RNAs promotes TDP-43 nuclear localization.
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4
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Rosa-Mercado NA, Buskirk AR, Green R. Translation elongation inhibitors stabilize select short-lived transcripts. RNA (NEW YORK, N.Y.) 2024; 30:1572-1585. [PMID: 39293933 PMCID: PMC11571809 DOI: 10.1261/rna.080138.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024]
Abstract
Translation elongation inhibitors are commonly used to study different cellular processes. Yet, their specific impact on transcription and mRNA decay has not been thoroughly assessed. Here, we use TimeLapse sequencing to investigate how translational stress impacts mRNA dynamics in human cells. Our results reveal that a distinct group of transcripts is stabilized in response to the translation elongation inhibitor emetine. These stabilized mRNAs are short-lived at steady state, and many of them encode C2H2 zinc finger proteins. The codon usage of these stabilized transcripts is suboptimal compared to other expressed transcripts, including other short-lived mRNAs that are not stabilized after emetine treatment. Finally, we show that stabilization of these transcripts is independent of ribosome quality control factors and signaling pathways activated by ribosome collisions. Our data describe a group of short-lived transcripts whose degradation is particularly sensitive to the inhibition of translation elongation.
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Affiliation(s)
- Nicolle A Rosa-Mercado
- Johns Hopkins University School of Medicine, Department of Molecular Biology & Genetics, Baltimore, Maryland 21205, USA
| | - Allen R Buskirk
- Johns Hopkins University School of Medicine, Department of Molecular Biology & Genetics, Baltimore, Maryland 21205, USA
| | - Rachel Green
- Johns Hopkins University School of Medicine, Department of Molecular Biology & Genetics, Baltimore, Maryland 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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5
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Pfeiffer P, Nilsson J, Gallud A, Baladi T, Le HN, Bood M, Lemurell M, Dahlén A, Grøtli M, Esbjörner E, Wilhelmsson L. Metabolic RNA labeling in non-engineered cells following spontaneous uptake of fluorescent nucleoside phosphate analogues. Nucleic Acids Res 2024; 52:10102-10118. [PMID: 39162218 PMCID: PMC11417403 DOI: 10.1093/nar/gkae722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/04/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
RNA and its building blocks play central roles in biology and have become increasingly important as therapeutic agents and targets. Hence, probing and understanding their dynamics in cells is important. Fluorescence microscopy offers live-cell spatiotemporal monitoring but requires labels. We present two fluorescent adenine analogue nucleoside phosphates which show spontaneous uptake and accumulation in cultured human cells, likely via nucleoside transporters, and show their potential utilization as cellular RNA labels. Upon uptake, one nucleotide analogue, 2CNqAXP, localizes to the cytosol and the nucleus. We show that it could then be incorporated into de novo synthesized cellular RNA, i.e. it was possible to achieve metabolic fluorescence RNA labeling without using genetic engineering to enhance incorporation, uptake-promoting strategies, or post-labeling through bio-orthogonal chemistries. By contrast, another nucleotide analogue, pAXP, only accumulated outside of the nucleus and was rapidly excreted. Consequently, this analogue did not incorporate into RNA. This difference in subcellular accumulation and retention results from a minor change in nucleobase chemical structure. This demonstrates the importance of careful design of nucleoside-based drugs, e.g. antivirals to direct their subcellular localization, and shows the potential of fine-tuning fluorescent base analogue structures to enhance the understanding of the function of such drugs.
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Affiliation(s)
- Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- LanteRNA (Stealth Labels Biotech AB), c/o Chalmers Ventures AB, Vera Sandbergs allé 8, SE-41296 Gothenburg, Sweden
| | - Audrey Gallud
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43181 Gothenburg, Sweden
| | - Tom Baladi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Hoang-Ngoan Le
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mattias Bood
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
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6
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Ietswaart R, Smalec BM, Xu A, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN, Churchman LS. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. Mol Cell 2024; 84:2765-2784.e16. [PMID: 38964322 PMCID: PMC11315470 DOI: 10.1016/j.molcel.2024.06.008] [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: 09/23/2022] [Revised: 05/15/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024]
Abstract
Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ziad Mohamoud Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chantal K Guegler
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Luke Gilbert
- Arc Institute, Palo Alto, CA 94305, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94518, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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7
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Müller JM, Moos K, Baar T, Maier KC, Zumer K, Tresch A. Nuclear export is a limiting factor in eukaryotic mRNA metabolism. PLoS Comput Biol 2024; 20:e1012059. [PMID: 38753883 PMCID: PMC11135743 DOI: 10.1371/journal.pcbi.1012059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/29/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
The eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by sequencing of RNA (SLAM-seq) in the nuclear and cytosolic compartments of human cancer cells. We develop a model that reliably quantifies mRNA-specific synthesis, nuclear export, and nuclear and cytosolic degradation rates on a genome-wide scale. We find that nuclear degradation of polyadenylated mRNA is negligible and nuclear mRNA export is slow, while cytosolic mRNA degradation is comparatively fast. Consequently, an mRNA molecule generally spends most of its life in the nucleus. We also observe large differences in the nuclear export rates of different 3'UTR transcript isoforms. Furthermore, we identify genes whose expression is abruptly induced upon metabolic labeling. These transcripts are exported substantially faster than average mRNAs, suggesting the existence of alternative export pathways. Our results highlight nuclear mRNA export as a limiting factor in mRNA metabolism and gene regulation.
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Affiliation(s)
- Jason M. Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Katharina Moos
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Till Baar
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Kerstin C. Maier
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kristina Zumer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Achim Tresch
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
- Center for Data and Simulation Science, University of Cologne, Cologne, Germany
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8
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Mercier BC, Labaronne E, Cluet D, Guiguettaz L, Fontrodona N, Bicknell A, Corbin A, Wencker M, Aube F, Modolo L, Jouravleva K, Auboeuf D, Moore MJ, Ricci EP. Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation. Genome Res 2024; 34:394-409. [PMID: 38508694 PMCID: PMC11067875 DOI: 10.1101/gr.277863.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
mRNA translation and decay are tightly interconnected processes both in the context of mRNA quality-control pathways and for the degradation of functional mRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions, and the recruitment of specific proteins to ribosomes is an important determinant of mRNA turnover. However, the extent to which translation-dependent mRNA decay (TDD) and translation-independent mRNA decay (TID) pathways participate in the degradation of mRNAs has not been studied yet. Here we describe a comprehensive analysis of basal and signal-induced TDD and TID in mouse primary CD4+ T cells. Our results indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner. Our analysis further identifies the length of untranslated regions, the density of ribosomes, and GC3 content as important determinants of TDD magnitude. Consistently, all transcripts that undergo changes in ribosome density within their coding sequence upon T cell activation display a corresponding change in their TDD level. Moreover, we reveal a dynamic modulation in the relationship between GC3 content and TDD upon T cell activation, with a reversal in the impact of GC3- and AU3-rich codons. Altogether, our data show a strong and dynamic interconnection between mRNA translation and decay in mammalian primary cells.
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Affiliation(s)
- Blandine C Mercier
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Emmanuel Labaronne
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
- ADLIN Science, 9100 Evry-Courcouronnes, France
| | - David Cluet
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Laura Guiguettaz
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Nicolas Fontrodona
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Alicia Bicknell
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Antoine Corbin
- Centre International de Recherche en Infectiologie Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Mélanie Wencker
- Centre International de Recherche en Infectiologie Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Fabien Aube
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Laurent Modolo
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Karina Jouravleva
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Didier Auboeuf
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France
| | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Emiliano P Ricci
- Laboratory of Biology and Modeling of the Cell (LBMC), Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293, 69007 Lyon, France;
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9
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Berg K, Lodha M, Delazer I, Bartosik K, Garcia YC, Hennig T, Wolf E, Dölken L, Lusser A, Prusty B, Erhard F. Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data. Nucleic Acids Res 2024; 52:e35. [PMID: 38381903 PMCID: PMC11039982 DOI: 10.1093/nar/gkae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 01/25/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Nucleoside analogues like 4-thiouridine (4sU) are used to metabolically label newly synthesized RNA. Chemical conversion of 4sU before sequencing induces T-to-C mismatches in reads sequenced from labelled RNA, allowing to obtain total and labelled RNA expression profiles from a single sequencing library. Cytotoxicity due to extended periods of labelling or high 4sU concentrations has been described, but the effects of extensive 4sU labelling on expression estimates from nucleotide conversion RNA-seq have not been studied. Here, we performed nucleotide conversion RNA-seq with escalating doses of 4sU with short-term labelling (1h) and over a progressive time course (up to 2h) in different cell lines. With high concentrations or at later time points, expression estimates were biased in an RNA half-life dependent manner. We show that bias arose by a combination of reduced mappability of reads carrying multiple conversions, and a global, unspecific underrepresentation of labelled RNA emerging during library preparation and potentially global reduction of RNA synthesis. We developed a computational tool to rescue unmappable reads, which performed favourably compared to previous read mappers, and a statistical method, which could fully remove remaining bias. All methods developed here are freely available as part of our GRAND-SLAM pipeline and grandR package.
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Affiliation(s)
- Kevin Berg
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Manivel Lodha
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Isabel Delazer
- Medical University of Innsbruck, Biocenter, Institute of Molecular Biology, Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Yilliam Cruz Garcia
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Thomas Hennig
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
- Institute of Biochemistry, University of Kiel, Kiel, Germany
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Alexandra Lusser
- Medical University of Innsbruck, Biocenter, Institute of Molecular Biology, Innsbruck, Austria
| | - Bhupesh K Prusty
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Florian Erhard
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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10
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McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. A kinetic dichotomy between mitochondrial and nuclear gene expression processes. Mol Cell 2024; 84:1541-1555.e11. [PMID: 38503286 PMCID: PMC11236289 DOI: 10.1016/j.molcel.2024.02.028] [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: 09/05/2023] [Revised: 12/12/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS subunit biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared with nuclear mRNAs, mt-mRNAs were produced 1,100-fold more, degraded 7-fold faster, and accumulated to 160-fold higher levels. Quantitative modeling and depletion of mitochondrial factors LRPPRC and FASTKD5 identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.
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Affiliation(s)
- Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gyan Prakash
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iliana Soto
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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11
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Ohashi S, Nakamura M, Acharyya S, Inagaki M, Abe N, Kimura Y, Hashiya F, Abe H. Development and Comparison of 4-Thiouridine to Cytidine Base Conversion Reaction. ACS OMEGA 2024; 9:9300-9308. [PMID: 38434802 PMCID: PMC10905967 DOI: 10.1021/acsomega.3c08516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/14/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
To study transcriptome dynamics without harming cells, it is essential to convert chemical bases. 4-Thiouridine (4sU) is a biocompatible uridine analogue that can be converted into a cytidine analogue. Although several reactions can convert 4sU into a cytidine analogue, few studies have compared the features of these reactions. In this study, we performed three reported base conversion reactions, including osmium tetroxide, iodoacetamide, and sodium periodate treatment, as well as a new reaction using 2,4-dinitrofluorobenzene. We compared the reaction time, conversion efficacy, and effects on reverse transcription. These reactions successfully converted 4sU into a cytidine analogue quantitatively using trinucleotides. However, the conversion efficacy and effect on reverse transcription vary depending on the reaction with the RNA transcript. OsO4 treatment followed by NH4Cl treatment showed the best base-conversion efficiency. Nevertheless, each reaction has its own advantages and disadvantages as a tool for studying the transcriptome. Therefore, it is crucial to select the appropriate reaction for the target of interest.
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Affiliation(s)
- Sana Ohashi
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Mayu Nakamura
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Susit Acharyya
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Masahito Inagaki
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Naoko Abe
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yasuaki Kimura
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Fumitaka Hashiya
- Research
Center for Material Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroshi Abe
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Research
Center for Material Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Institute
for Glyco-core Research (iGCORE), Nagoya
University, Nagoya, Aichi 464-8602, Japan
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12
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Fuchs J, Jamontas R, Hoock MH, Oltmanns J, Golinelli-Pimpaneau B, Schünemann V, Pierik AJ, Meškys R, Aučynaitė A, Boll M. TudS desulfidases recycle 4-thiouridine-5'-monophosphate at a catalytic [4Fe-4S] cluster. Commun Biol 2023; 6:1092. [PMID: 37891428 PMCID: PMC10611767 DOI: 10.1038/s42003-023-05450-5] [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: 07/14/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
In all domains of life, transfer RNAs (tRNAs) contain post-transcriptionally sulfur-modified nucleosides such as 2- and 4-thiouridine. We have previously reported that a recombinant [4Fe-4S] cluster-containing bacterial desulfidase (TudS) from an uncultured bacterium catalyzes the desulfuration of 2- and 4-thiouracil via a [4Fe-5S] cluster intermediate. However, the in vivo function of TudS enzymes has remained unclear and direct evidence for substrate binding to the [4Fe-4S] cluster during catalysis was lacking. Here, we provide kinetic evidence that 4-thiouridine-5'-monophosphate rather than sulfurated tRNA, thiouracil, thiouridine or 4-thiouridine-5'-triphosphate is the preferred substrate of TudS. The occurrence of sulfur- and substrate-bound catalytic intermediates was uncovered from the observed switch of the S = 3/2 spin state of the catalytic [4Fe-4S] cluster to a S = 1/2 spin state upon substrate addition. We show that a putative gene product from Pseudomonas putida KT2440 acts as a TudS desulfidase in vivo and conclude that TudS-like enzymes are widespread desulfidases involved in recycling and detoxifying tRNA-derived 4-thiouridine monophosphate nucleosides for RNA synthesis.
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Affiliation(s)
- Jonathan Fuchs
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Rapolas Jamontas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257, Vilnius, Lithuania
| | - Maren Hellen Hoock
- Department of Physics, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Jonathan Oltmanns
- Department of Physics, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris, CEDEX 05, France
| | - Volker Schünemann
- Department of Physics, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Antonio J Pierik
- Department of Chemistry, RPTU Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257, Vilnius, Lithuania
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257, Vilnius, Lithuania
| | - Matthias Boll
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany.
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13
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McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527880. [PMID: 36824735 PMCID: PMC9948965 DOI: 10.1101/2023.02.09.527880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared to nuclear mRNAs, mt-mRNAs were produced 700-fold higher, degraded 5-fold faster, and accumulated to 170-fold higher levels. Quantitative modeling and depletion of mitochondrial factors, LRPPRC and FASTKD5, identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.
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Affiliation(s)
- Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gyan Prakash
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M. Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iliana Soto
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Current affiliation: Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - L. Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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14
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Rummel T, Sakellaridi L, Erhard F. grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis. Nat Commun 2023; 14:3559. [PMID: 37321987 PMCID: PMC10272207 DOI: 10.1038/s41467-023-39163-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
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Affiliation(s)
- Teresa Rummel
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Lygeri Sakellaridi
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany.
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstr. 4, 93053, Regensburg, Germany.
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15
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Gupta M, Wang J, Garfio CM, Vandewalle A, Spitale RC. Cycloaddition enabled mutational profiling of 5-vinyluridine in RNA. Chem Commun (Camb) 2023; 59:3257-3260. [PMID: 36815680 PMCID: PMC10089805 DOI: 10.1039/d3cc00043e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We report the detection of 5-vinyluridine (5-VUrd) in RNA at single nucleotide resolution via mutational profiling. Maleimide cycloadducts with 5-VUrd in RNA cause a stop in primer extension during reverse transcription, and the full-length cDNA product from reverse transcription contains misincorporation across the cycloadduct site.
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Affiliation(s)
- Mrityunjay Gupta
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
| | - Jingtian Wang
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Chely M Garfio
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Abigail Vandewalle
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
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16
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Studying miRNA-mRNA Interactions: An Optimized CLIP-Protocol for Endogenous Ago2-Protein. Methods Protoc 2022; 5:mps5060096. [PMID: 36548138 PMCID: PMC9781880 DOI: 10.3390/mps5060096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Transcriptome-wide analysis of RNA-binding partners is commonly achieved using UV crosslinking and immunoprecipitation (CLIP). Individual-nucleotide-resolution CLIP (iCLIP)enables identification of the specific position of the protein-RNA interaction. In addition to RNA-binding proteins (RBPs), microRNA (miRNA)-mRNA interactions also play a crucial role in the regulation of gene expression. Argonaute-2 (Ago2) mediates miRNA binding to a multitude of mRNA target sites, enabling the identification of miRNA-mRNA interactions by employing modified Ago2-CLIP protocols. Here, we describe an Ago2-specific CLIP protocol optimized for the use of small quantities of cell material, targeting endogenous Ago2 while avoiding possible methodological biases such as metabolic labeling or Ago2 overexpression and applying the latest advances in CLIP library preparation, the iCLIP2 protocol. In particular, we focus on the optimization of lysis conditions and improved radioactive labeling of the 5' end of the miRNA.
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17
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mTOR- and LARP1-dependent regulation of TOP mRNA poly(A) tail and ribosome loading. Cell Rep 2022; 41:111548. [DOI: 10.1016/j.celrep.2022.111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 08/30/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
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18
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Gupta M, Levine SR, Spitale RC. Probing Nascent RNA with Metabolic Incorporation of Modified Nucleosides. Acc Chem Res 2022; 55:2647-2659. [PMID: 36073807 DOI: 10.1021/acs.accounts.2c00347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The discovery of previously unknown functional roles of RNA in biological systems has led to increased interest in revealing novel RNA molecules as therapeutic targets and the development of tools to better understand the role of RNA in cells. RNA metabolic labeling broadens the scope of studying RNA by incorporating of unnatural nucleobases and nucleosides with bioorthogonal handles that can be utilized for chemical modification of newly synthesized cellular RNA. Such labeling of RNA provides access to applications including measurement of the rates of synthesis and decay of RNA, cellular imaging for RNA localization, and selective enrichment of nascent RNA from the total RNA pool. Several unnatural nucleosides and nucleobases have been shown to be incorporated into RNA by endogenous RNA synthesis machinery of the cells. RNA metabolic labeling can also be performed in a cell-specific manner, where only cells expressing an essential enzyme incorporate the unnatural nucleobase into their RNA. Although several discoveries have been enabled by the current RNA metabolic labeling methods, some key challenges still exist: (i) toxicity of unnatural analogues, (ii) lack of RNA-compatible conjugation chemistries, and (iii) background incorporation of modified analogues in cell-specific RNA metabolic labeling. In this Account, we showcase work done in our laboratory to overcome these challenges faced by RNA metabolic labeling.To begin, we discuss the cellular pathways that have been utilized to perform RNA metabolic labeling and study the interaction between nucleosides and nucleoside kinases. Then we discuss the use of vinyl nucleosides for metabolic labeling and demonstrate the low toxicity of 5-vinyluridine (5-VUrd) compared to other widely used nucleosides. Next, we discuss cell-specific RNA metabolic labeling with unnatural nucleobases, which requires the expression of a specific phosphoribosyl transferase (PRT) enzyme for incorporation of the nucleobase into RNA. In the course of this work, we discovered the enzyme uridine monophosphate synthase (UMPS), which is responsible for nonspecific labeling with modified uracil nucleobases. We were able to overcome this background labeling by discovering a mutant uracil PRT (UPRT) that demonstrates highly specific RNA metabolic labeling with 5-vinyluracil (5-VU). Furthermore, we discuss the optimization of inverse-electron-demand Diels-Alder (IEDDA) reactions for performing chemical modification of vinyl nucleosides to achieve covalent conjugation of RNA without transcript degradation. Finally, we highlight our latest endeavor: the development of mutually orthogonal chemical reactions for selective labeling of 5-VUrd and 2-vinyladenosine (2-VAdo), which allows for potential use of multiple vinyl nucleosides for simultaneous investigation of multiple cellular processes involving RNA. We hope that our methods and discoveries encourage scientists studying biological systems to include RNA metabolic labeling in their toolkit for studying RNA and its role in biological systems.
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19
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Poetz F, Lebedeva S, Schott J, Lindner D, Ohler U, Stoecklin G. Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation. Genome Biol 2022; 23:193. [PMID: 36096941 PMCID: PMC9465963 DOI: 10.1186/s13059-022-02760-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/23/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Cytoplasmic polyadenylation element-binding protein 4 (CPEB4) is known to associate with cytoplasmic polyadenylation elements (CPEs) located in the 3' untranslated region (UTR) of specific mRNAs and assemble an activator complex promoting the translation of target mRNAs through cytoplasmic polyadenylation. RESULTS Here, we find that CPEB4 is part of an alternative repressor complex that mediates mRNA degradation by associating with the evolutionarily conserved CCR4-NOT deadenylase complex. We identify human CPEB4 as an RNA-binding protein (RBP) with enhanced association to poly(A) RNA upon inhibition of class I histone deacetylases (HDACs), a condition known to cause widespread degradation of poly(A)-containing mRNA. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis using endogenously tagged CPEB4 in HeLa cells reveals that CPEB4 preferentially binds to the 3'UTR of immediate early gene mRNAs, at G-containing variants of the canonical U- and A-rich CPE located in close proximity to poly(A) sites. By transcriptome-wide mRNA decay measurements, we find that the strength of CPEB4 binding correlates with short mRNA half-lives and that loss of CPEB4 expression leads to the stabilization of immediate early gene mRNAs. Akin to CPEB4, we demonstrate that CPEB1 and CPEB2 also confer mRNA instability by recruitment of the CCR4-NOT complex. CONCLUSIONS While CPEB4 was previously known for its ability to stimulate cytoplasmic polyadenylation, our findings establish an additional function for CPEB4 as the RNA adaptor of a repressor complex that enhances the degradation of short-lived immediate early gene mRNAs.
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Affiliation(s)
- Fabian Poetz
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Svetlana Lebedeva
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany
| | - Johanna Schott
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Doris Lindner
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Uwe Ohler
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany
- Department of Biology, Humboldt Universität Berlin, 10099, Berlin, Germany
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany.
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany.
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20
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Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem 2022; 298:101924. [PMID: 35413291 PMCID: PMC8994257 DOI: 10.1016/j.jbc.2022.101924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 10/25/2022] Open
Abstract
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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21
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Koliński M, Kałużna E, Piwecka M. RNA–protein interactomes as invaluable resources to study RNA viruses: Insights from SARS CoV‐2 studies. WIRES RNA 2022; 13:e1727. [PMID: 35343064 PMCID: PMC9111084 DOI: 10.1002/wrna.1727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/27/2022]
Abstract
Understanding the molecular mechanisms of severe respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is essential for the successful development of therapeutic strategies against the COVID‐19 pandemic. Numerous studies have focused on the identification of host factors and cellular pathways involved in the viral replication cycle. The speed and magnitude of hijacking the translation machinery of host mRNA, and shutting down host transcription are still not well understood. Since SARS‐CoV‐2 relies on host RNA‐binding proteins for the infection progression, several efforts have been made to define the SARS‐CoV‐2 RNA‐bound proteomes (RNA–protein interactomes). Methodologies that enable the systemic capture of protein interactors of given RNA in vivo have been adapted for the identification of the SARS‐CoV‐2 RNA interactome. The obtained proteomic data aided by genome‐wide and targeted CRISPR perturbation screens, revealed host factors with either pro‐ or anti‐viral activity and highlighted cellular processes and factors involved in host response. We focus here on the recent studies on SARS‐CoV‐2 RNA–protein interactomes, with regard to both the technological aspects of RNA interactome capture methods and the obtained results. We also summarize several related studies, which were used in the interpretation of the SARS‐CoV‐2 RNA–protein interactomes. These studies provided the selection of host factors that are potentially suitable candidates for antiviral therapy. Finally, we underscore the importance of RNA–protein interactome studies in regard to the effective development of antiviral strategies against current and future threats. This article is categorized under:RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Methods > RNA Analyses in Cells
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Affiliation(s)
- Marcin Koliński
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
| | - Ewelina Kałużna
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
| | - Monika Piwecka
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
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22
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Li R, Zou Z, Wang W, Zou P. Metabolic incorporation of electron-rich ribonucleosides enhances APEX-seq for profiling spatially restricted nascent transcriptome. Cell Chem Biol 2022; 29:1218-1231.e8. [PMID: 35245437 DOI: 10.1016/j.chembiol.2022.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 07/30/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
The spatial arrangement of newly synthesized transcriptome in eukaryotic cells underlies various biological processes including cell proliferation and differentiation. In this study, we combine metabolic incorporation of electron-rich ribonucleosides (e.g., 6-thioguanosine and 4-thiouridine) with a peroxidase-mediated proximity-dependent RNA labeling technique (APEX-seq) to develop a sensitive method, termed MERR APEX-seq, for selectively profiling newly transcribed RNAs at specific subcellular locations in live cells. We demonstrate that MERR APEX-seq is 20-fold more efficient than APEX-seq and offers both high spatial specificity and high coverage in mitochondrial matrix. At the ER membrane, 91% of the transcripts captured by MERR APEX-seq encode for secretory pathway proteins, thus demonstrating the high spatial specificity of MERR APEX-seq in open subcellular compartments. Application of MERR APEX-seq to the nuclear lamina of human cells reveals a local transcriptome of 1,012 RNAs, many of which encode for nuclear proteins involved in histone modification, chromosomal structure maintenance, and RNA processing.
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Affiliation(s)
- Ran Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhongyu Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Wentao Wang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Peng Zou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China; Chinese Institute for Brain Research (CIBR), Beijing 102206, China.
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23
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Kalesh K, Wei W, Mantilla BS, Roumeliotis TI, Choudhary J, Denny PW. Transcriptome-Wide Identification of Coding and Noncoding RNA-Binding Proteins Defines the Comprehensive RNA Interactome of Leishmania mexicana. Microbiol Spectr 2022; 10:e0242221. [PMID: 35138191 PMCID: PMC8826732 DOI: 10.1128/spectrum.02422-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
Proteomic profiling of RNA-binding proteins in Leishmania is currently limited to polyadenylated mRNA-binding proteins, leaving proteins that interact with nonadenylated RNAs, including noncoding RNAs and pre-mRNAs, unidentified. Using a combination of unbiased orthogonal organic phase separation methodology and tandem mass tag-labeling-based high resolution quantitative proteomic mass spectrometry, we robustly identified 2,417 RNA-binding proteins, including 1289 putative novel non-poly(A)-RNA-binding proteins across the two main Leishmania life cycle stages. Eight out of 20 Leishmania deubiquitinases, including the recently characterized L. mexicana DUB2 with an elaborate RNA-binding protein interactome were exclusively identified in the non-poly(A)-RNA-interactome. Additionally, an increased representation of WD40 repeat domains were observed in the Leishmania non-poly(A)-RNA-interactome, thus uncovering potential involvement of this protein domain in RNA-protein interactions in Leishmania. We also characterize the protein-bound RNAs using RNA-sequencing and show that in addition to protein coding transcripts ncRNAs are also enriched in the protein-RNA interactome. Differential gene expression analysis revealed enrichment of 142 out of 195 total L. mexicana protein kinase genes in the protein-RNA-interactome, suggesting important role of protein-RNA interactions in the regulation of the Leishmania protein kinome. Additionally, we characterize the quantitative changes in RNA-protein interactions in hundreds of Leishmania proteins following inhibition of heat shock protein 90 (Hsp90). Our results show that the Hsp90 inhibition in Leishmania causes widespread disruption of RNA-protein interactions in ribosomal proteins, proteasomal proteins and translation factors in both life cycle stages, suggesting downstream effect of the inhibition on protein synthesis and degradation pathways in Leishmania. This study defines the comprehensive RNA interactome of Leishmania and provides in-depth insight into the widespread involvement of RNA-protein interactions in Leishmania biology. IMPORTANCE Advances in proteomics and mass spectrometry have revealed the mRNA-binding proteins in many eukaryotic organisms, including the protozoan parasites Leishmania spp., the causative agents of leishmaniasis, a major infectious disease in over 90 tropical and subtropical countries. However, in addition to mRNAs, which constitute only 2 to 5% of the total transcripts, many types of non-coding RNAs participate in crucial biological processes. In Leishmania, RNA-binding proteins serve as primary gene regulators. Therefore, transcriptome-wide identification of RNA-binding proteins is necessary for deciphering the distinctive posttranscriptional mechanisms of gene regulation in Leishmania. Using a combination of highly efficient orthogonal organic phase separation method and tandem mass tag-labeling-based quantitative proteomic mass spectrometry, we provide unprecedented comprehensive molecular definition of the total RNA interactome across the two main Leishmania life cycle stages. In addition, we characterize for the first time the quantitative changes in RNA-protein interactions in Leishmania following inhibition of heat shock protein 90, shedding light into hitherto unknown large-scale downstream molecular effect of the protein inhibition in the parasite. This work provides insight into the importance of total RNA-protein interactions in Leishmania, thus significantly expanding our knowledge of the emergence of RNA-protein interactions in Leishmania biology.
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Affiliation(s)
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Brian S. Mantilla
- Department of Biosciences, Durham University, Durham, United Kingdom
| | | | - Jyoti Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, United Kingdom
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom
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24
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Fakhraldeen SA, Berry SM, Beebe DJ, Roopra A, Bisbach CM, Spiegelman VS, Niemi NM, Alexander CM. Enhanced immunoprecipitation techniques for the identification of RNA-binding protein partners: IGF2BP1 interactions in mammary epithelial cells. J Biol Chem 2022; 298:101649. [PMID: 35104504 PMCID: PMC8891971 DOI: 10.1016/j.jbc.2022.101649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 11/24/2022] Open
Abstract
RNA-binding proteins (RBPs) regulate the expression of large cohorts of RNA species to produce programmatic changes in cellular phenotypes. To describe the function of RBPs within a cell, it is key to identify their mRNA-binding partners. This is often done by crosslinking nucleic acids to RBPs, followed by chemical release of the nucleic acid fragments for analysis. However, this methodology is lengthy, which involves complex processing with attendant sample losses, thus large amounts of starting materials and prone to artifacts. To evaluate potential alternative technologies, we tested “exclusion-based” purification of immunoprecipitates (IFAST or SLIDE) and report here that these methods can efficiently, rapidly, and specifically isolate RBP–RNA complexes. The analysis requires less than 1% of the starting material required for techniques that include crosslinking. Depending on the antibody used, 50% to 100% starting protein can be retrieved, facilitating the assay of endogenous levels of RBPs; the isolated ribonucleoproteins are subsequently analyzed using standard techniques, to provide a comprehensive portrait of RBP complexes. Using exclusion-based techniques, we show that the mRNA-binding partners for RBP IGF2BP1 in cultured mammary epithelial cells are enriched in mRNAs important for detoxifying superoxides (specifically glutathione peroxidase [GPX]-1 and GPX-2) and mRNAs encoding mitochondrial proteins. We show that these interactions are functionally significant, as loss of function of IGF2BP1 leads to destabilization of GPX mRNAs and reduces mitochondrial membrane potential and oxygen consumption. We speculate that this underlies a consistent requirement for IGF2BP1 for the expression of clonogenic activity in vitro.
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Affiliation(s)
- Saja A Fakhraldeen
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Scott M Berry
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Celia M Bisbach
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Vladimir S Spiegelman
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Natalie M Niemi
- Department of Biochemistry & Molecular Biophysics, Washington University in St Louis
| | - Caroline M Alexander
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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25
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Braun C, Knüppel R, Perez-Fernandez J, Ferreira-Cerca S. Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil. Methods Mol Biol 2022; 2533:199-213. [PMID: 35796990 PMCID: PMC9761907 DOI: 10.1007/978-1-0716-2501-9_12] [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] [Indexed: 06/15/2023]
Abstract
RNA molecules and their expression dynamics play essential roles in the establishment of complex cellular phenotypes and/or in the rapid cellular adaption to environmental changes. Accordingly, analyzing RNA expression remains an important step to understand the molecular basis controlling the formation of cellular phenotypes, cellular homeostasis or disease progression. Steady-state RNA levels in the cells are controlled by the sum of highly dynamic molecular processes contributing to RNA expression and can be classified in transcription, maturation and degradation. The main goal of analyzing RNA dynamics is to disentangle the individual contribution of these molecular processes to the life cycle of a given RNA under different physiological conditions. In the recent years, the use of nonradioactive nucleotide/nucleoside analogs and improved chemistry, in combination with time-dependent and high-throughput analysis, have greatly expanded our understanding of RNA metabolism across various cell types, organisms, and growth conditions.In this chapter, we describe a step-by-step protocol allowing pulse labeling of RNA with the nonradioactive nucleotide analog, 4-thiouracil , in the eukaryotic model organism Saccharomyces cerevisiae and the model archaeon Haloferax volcanii .
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Affiliation(s)
- Christina Braun
- Biochemistry III-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Robert Knüppel
- Biochemistry III-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Jorge Perez-Fernandez
- Biochemistry III-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
- Department of Experimental Biology, University of Jaen, Jaén, Spain.
| | - Sébastien Ferreira-Cerca
- Biochemistry III-Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany.
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26
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Challal D, Colin J, Villa T, Libri D. A Modified Cross-Linking Analysis of cDNAs (CRAC ) Protocol for Detecting RNA-Protein Interactions and Transcription at Single-Nucleotide Resolution. Methods Mol Biol 2022; 2477:35-55. [PMID: 35524110 DOI: 10.1007/978-1-0716-2257-5_3] [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] [Indexed: 06/14/2023]
Abstract
Detecting protein-RNA interactions in vivo is essential for deciphering many important cellular pathways. Several methods have been described for this purpose, among which cross-linking analysis of cDNA, CRAC. This method relies on a first step of UV cross-linking of living yeast cells and several subsequent steps of purification of the protein-RNA complexes, some of which under denaturing condition. Without altering the general principle of the method, we have modified and improved the protocol, with the specific aim of sequencing the nascent RNA isolated from transcription complexes and generate high-resolution and directional transcription maps.
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Affiliation(s)
- Drice Challal
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
- Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France
| | - Jessie Colin
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
- Ecole Pratique des Hautes Etudes - PSL Research university, Paris, France
- Unité Biologie des ARN des Pathogènes Fongiques, Institut Pasteur, Paris, France
| | - Tommaso Villa
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France.
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27
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Abstract
The control of mRNA stability is fundamental to gene regulation, and a deeper understanding of this post-transcriptional regulatory step can provide key insights into gene function. Measuring mRNA half-lives directly, however, is challenging. The most common strategies for evaluating mRNA stability and decay involve blocking general transcription and then measuring the decline in mRNA levels over time. The downside of these approaches, however, is that they severely impact cell function and viability, indirectly perturbing gene expression. Here, we describe Roadblock-qPCR, a simple method for measuring mRNA decay kinetics in living cells that is both economical and quick. Cells are first incubated with the nucleoside analog 4-thiouridine (4sU), which is readily incorporated into nascent mRNAs during transcription. RNA is then extracted and treated with N-ethylmaleimide (NEM), a sulfhydryl alkylating agent that selectively modifies 4sU, before proceeding to cDNA synthesis. Because the NEM-modified 4sU creates a chemical "roadblock" that interferes with reverse transcription, this treatment ultimately results in the depletion of the nascent 4sU-containing transcripts from the cDNA pool. As such, the decay rate of the non-4sU-labeled pre-existing mRNAs can be monitored by quantitative PCR (qPCR). In combination with spike-in standards, this approach can be used to efficiently and accurately measure the half-lives of endogenous mRNAs with a wide range of stabilities, while avoiding the artifacts of transcription shutoff strategies. © 2022 Wiley Periodicals LLC. Basic Protocol: Roadblock-qPCR Support Protocol: Synthesis of spike-in mRNA.
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Affiliation(s)
- Maegan J. Watson
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06510
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06510,To whom correspondence should be addressed.
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28
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Altieri JAC, Hertel KJ. The influence of 4-thiouridine labeling on pre-mRNA splicing outcomes. PLoS One 2021; 16:e0257503. [PMID: 34898625 PMCID: PMC8668116 DOI: 10.1371/journal.pone.0257503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Metabolic labeling is a widely used tool to investigate different aspects of pre-mRNA splicing and RNA turnover. The labeling technology takes advantage of native cellular machineries where a nucleotide analog is readily taken up and incorporated into nascent RNA. One such analog is 4-thiouridine (4sU). Previous studies demonstrated that the uptake of 4sU at elevated concentrations (>50μM) and extended exposure led to inhibition of rRNA synthesis and processing, presumably induced by changes in RNA secondary structure. Thus, it is possible that 4sU incorporation may also interfere with splicing efficiency. To test this hypothesis, we carried out splicing analyses of pre-mRNA substrates with varying levels of 4sU incorporation (0-100%). We demonstrate that increased incorporation of 4sU into pre-mRNAs decreased splicing efficiency. The overall impact of 4sU labeling on pre-mRNA splicing efficiency negatively correlates with the strength of splice site signals such as the 3' and the 5' splice sites. Introns with weaker splice sites are more affected by the presence of 4sU. We also show that transcription by T7 polymerase and pre-mRNA degradation kinetics were impacted at the highest levels of 4sU incorporation. Increased incorporation of 4sU caused elevated levels of abortive transcripts, and fully labeled pre-mRNA is more stable than its uridine-only counterpart. Cell culture experiments show that a small number of alternative splicing events were modestly, but statistically significantly influenced by metabolic labeling with 4sU at concentrations considered to be tolerable (40 μM). We conclude that at high 4sU incorporation rates small, but noticeable changes in pre-mRNA splicing can be detected when splice sites deviate from consensus. Given these potential 4sU artifacts, we suggest that appropriate controls for metabolic labeling experiments need to be included in future labeling experiments.
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Affiliation(s)
- Jessie A. C. Altieri
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Klemens J. Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
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29
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Kleiner RE. Interrogating the transcriptome with metabolically incorporated ribonucleosides. Mol Omics 2021; 17:833-841. [PMID: 34635895 DOI: 10.1039/d1mo00334h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA is a central player in biological processes, but there remain major gaps in our understanding of transcriptomic processes and the underlying biochemical mechanisms regulating RNA in cells. A powerful strategy to facilitate molecular analysis of cellular RNA is the metabolic incorporation of chemical probes. In this review, we discuss current approaches for RNA metabolic labeling with modified ribonucleosides and their integration with Next-Generation Sequencing, mass spectrometry-based proteomics, and fluorescence microscopy in order to interrogate RNA behavior in its native context.
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Affiliation(s)
- Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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30
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Guo X, Tariq M, Lai Y, Kanwal S, Lv Y, Wang X, Li N, Jiang M, Meng J, Hu J, Yuan J, Luo Z, Ward C, Volpe G, Wang D, Yin M, Qin B, Zhang B, Bao X, Esteban MA. Capture of the newly transcribed RNA interactome using click chemistry. Nat Protoc 2021; 16:5193-5219. [PMID: 34697467 DOI: 10.1038/s41596-021-00609-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Application of synthetic nucleoside analogues to capture newly transcribed RNAs has unveiled key features of RNA metabolism. Whether this approach could be adapted to isolate the RNA-bound proteome (RNA interactome) was, however, unexplored. We have developed a new method (capture of the newly transcribed RNA interactome using click chemistry, or RICK) for the systematic identification of RNA-binding proteins based on the incorporation of 5-ethynyluridine into newly transcribed RNAs followed by UV cross-linking and click chemistry-mediated biotinylation. The RNA-protein adducts are then isolated by affinity capture using streptavidin-coated beads. Through high-throughput RNA sequencing and mass spectrometry, the RNAs and proteins can be elucidated globally. A typical RICK experimental procedure takes only 1 d, excluding the steps of cell preparation, 5-ethynyluridine labeling, validation (silver staining, western blotting, quantitative reverse-transcription PCR (qRT-PCR) or RNA sequencing (RNA-seq)) and proteomics. Major advantages of RICK are the capture of RNA-binding proteins interacting with any type of RNA and, particularly, the ability to discern between newly transcribed and steady-state RNAs through controlled labeling. Thanks to its versatility, RICK will facilitate the characterization of the total and newly transcribed RNA interactome in different cell types and conditions.
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Affiliation(s)
- Xiangpeng Guo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Muqddas Tariq
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shahzina Kanwal
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiwei Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Na Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mengling Jiang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jin Meng
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Jieyi Hu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianwen Yuan
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Dongye Wang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Menghui Yin
- Laboratory of RNA Chemical Biology, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Baoming Qin
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Biliang Zhang
- Laboratory of RNA Chemical Biology, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
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31
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Gupta M, Singha M, Rasale DB, Zhou Z, Bhandari S, Beasley S, Sakr J, Parker SM, Spitale RC. Mutually Orthogonal Bioconjugation of Vinyl Nucleosides for RNA Metabolic Labeling. Org Lett 2021; 23:7183-7187. [PMID: 34496205 DOI: 10.1021/acs.orglett.1c02584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a strategy for the orthogonal conjugation of the vinyl nucleosides, 5-vinyluridine (5-VU) and 2-vinyladenosine (2-VA), via selective reactivity with maleimide and tris(2-carboxyethyl)phosphine (TCEP), respectively. The orthogonality was investigated using density functional theory (DFT) and confirmed by reactions with vinyl nucleosides. Further, these chemistries were used to modify RNA for fluorescent cell imaging. These reactions allow for the expanded use of RNA metabolic labeling to study nascent RNA expression within different RNA populations.
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Affiliation(s)
- Mrityunjay Gupta
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Monika Singha
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Dnyaneshwar B Rasale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Zehao Zhou
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Srijana Bhandari
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Samantha Beasley
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Jasmine Sakr
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Robert C Spitale
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
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32
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Fan Z, Qin W. [Advances in technologies for large-scale enrichment and identification of ribonucleic acid-protein complexes]. Se Pu 2021; 39:105-111. [PMID: 34227341 PMCID: PMC9274842 DOI: 10.3724/sp.j.1123.2020.07019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
核糖核酸(RNA)在细胞中并非单独存在,从它们产生到被降解的过程中与大量蛋白质发生相互作用,RNA结合蛋白(RNA-binding proteins, RBPs)能与RNA结合形成RNA-蛋白质复合物(RP复合物),并以这种复合物的形式发挥生理功能。RNAs或RBPs任一组分的异常与缺失都会影响RP复合物的正常生理功能,从而导致疾病的发生,如代谢异常、肌肉萎缩症、自身免疫性疾病和癌症。因此,定性定量分析RBPs及其在正常细胞和肿瘤细胞中与RNAs靶标之间的复杂相互作用网络有助于挖掘RP复合物在肿瘤发生发展中的作用,开发肿瘤生物标志物和新的治疗方式。要深入研究和理解RNAs与RBPs的相互作用网络,须依赖组学技术对RP复合物进行大规模鉴定。而作为在组学层面系统性解析RP复合物组成、含量和功能的第一步,大规模富集RP复合物极具挑战性。为了解决这一难题,研究者们发展了各种富集鉴定策略。该文针对RP复合物富集策略的最新进展进行了综述,包括紫外光交联和免疫沉淀(crosslinking and immunoprecipitation, CLIP)及其衍生技术、基于“点击化学”的富集策略和基于相分离的富集策略,比较分析了它们的技术原理、优缺点,以方便研究者们选择合适的策略来解决感兴趣的生物学问题。该文最后总结了当前的RP复合物富集方法仍然存在富集效率低和操作繁琐等亟需解决的技术挑战,为富集策略的发展提供了研究方向。
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Affiliation(s)
- Zhiya Fan
- Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), State Key Laboratory of Proteomics, Beijing 102206, China
| | - Weijie Qin
- Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), State Key Laboratory of Proteomics, Beijing 102206, China
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van’t Sant LJ, White JJ, Hoeijmakers JHJ, Vermeij WP, Jaarsma D. In vivo 5-ethynyluridine (EU) labelling detects reduced transcription in Purkinje cell degeneration mouse mutants, but can itself induce neurodegeneration. Acta Neuropathol Commun 2021; 9:94. [PMID: 34020718 PMCID: PMC8139001 DOI: 10.1186/s40478-021-01200-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent staining of newly transcribed RNA via metabolic labelling with 5-ethynyluridine (EU) and click chemistry enables visualisation of changes in transcription, such as in conditions of cellular stress. Here, we tested whether EU labelling can be used to examine transcription in vivo in mouse models of nervous system disorders. We show that injection of EU directly into the cerebellum results in reproducible labelling of newly transcribed RNA in cerebellar neurons and glia, with cell type-specific differences in relative labelling intensities, such as Purkinje cells exhibiting the highest levels. We also observed EU-labelling accumulating into cytoplasmic inclusions, indicating that EU, like other modified uridines, may introduce non-physiological properties in labelled RNAs. Additionally, we found that EU induces Purkinje cell degeneration nine days after EU injection, suggesting that EU incorporation not only results in abnormal RNA transcripts, but also eventually becomes neurotoxic in highly transcriptionally-active neurons. However, short post-injection intervals of EU labelling in both a Purkinje cell-specific DNA repair-deficient mouse model and a mouse model of spinocerebellar ataxia 1 revealed reduced transcription in Purkinje cells compared to controls. We combined EU labelling with immunohistology to correlate altered EU staining with pathological markers, such as genotoxic signalling factors. These data indicate that the EU-labelling method provided here can be used to identify changes in transcription in vivo in nervous system disease models.
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Abstract
The identity and metabolism of RNAs are often governed by their 5' and 3' ends. Single gene loci produce a variety of transcript isoforms, varying primarily in their RNA 3' end status and consequently facing radically different cellular fates. Knowledge about RNA termini is therefore key to understanding the diverse RNA output from individual transcription units. In addition, the 3' end of a nascent RNA at the catalytic center of RNA polymerase provides a precise and strand-specific measure of the transcription process. Here, we describe a modified RNA 3' end sequencing method, that utilizes the in vivo metabolic labeling of RNA followed by its purification and optional in vitro polyadenylation to provide a comprehensive view of all RNA 3' ends. The strategy offers the advantages of (i) nucleotide resolution mapping of RNA 3' ends, (ii) increased sequencing depth of lowly abundant RNA and (iii) inference of RNA 3' end polyadenylation status. We have used the method to study RNA decay and transcription termination mechanisms with the potential utility to a wider range of biological questions.
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Affiliation(s)
- Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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35
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Sutton EC, DeRose VJ. Early nucleolar responses differentiate mechanisms of cell death induced by oxaliplatin and cisplatin. J Biol Chem 2021; 296:100633. [PMID: 33819479 PMCID: PMC8131322 DOI: 10.1016/j.jbc.2021.100633] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Recent reports provide evidence that the platinum chemotherapeutic oxaliplatin causes cell death via ribosome biogenesis stress, while cisplatin causes cell death via the DNA damage response (DDR). Underlying differences in mechanisms that might initiate disparate routes to cell death by these two broadly used platinum compounds have not yet been carefully explored. Additionally, prior studies had demonstrated that cisplatin can also inhibit ribosome biogenesis. Therefore, we sought to directly compare the initial influences of oxaliplatin and cisplatin on nucleolar processes and on the DDR. Using pulse-chase experiments, we found that at equivalent doses, oxaliplatin but not cisplatin significantly inhibited ribosomal RNA (rRNA) synthesis by Pol I, but neither compound affected rRNA processing. Inhibition of rRNA synthesis occurred as early as 90 min after oxaliplatin treatment in A549 cells, concurrent with the initial redistribution of the nucleolar protein nucleophosmin (NPM1). We observed that the nucleolar protein fibrillarin began to redistribute by 6 h after oxaliplatin treatment and formed canonical nucleolar caps by 24 h. In cisplatin-treated cells, DNA damage, as measured by γH2AX immunofluorescence, was more extensive, whereas nucleolar organization was unaffected. Taken together, our results demonstrate that oxaliplatin causes early nucleolar disruption via inhibition of rRNA synthesis accompanied by NPM1 relocalization and subsequently causes extensive nucleolar reorganization, while cisplatin causes early DNA damage without significant nucleolar disruption. These data support a model in which, at clinically relevant doses, cisplatin kills cells via the canonical DDR, and oxaliplatin kills cells via ribosome biogenesis stress, specifically via rapid inhibition of rRNA synthesis.
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Affiliation(s)
- Emily C Sutton
- Department of Biology, University of Oregon, Eugene, Oregon, USA; Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Victoria J DeRose
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA; Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, USA.
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36
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Larke MSC, Schwessinger R, Nojima T, Telenius J, Beagrie RA, Downes DJ, Oudelaar AM, Truch J, Graham B, Bender MA, Proudfoot NJ, Higgs DR, Hughes JR. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Mol Cell 2021; 81:983-997.e7. [PMID: 33539786 PMCID: PMC7612206 DOI: 10.1016/j.molcel.2021.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 09/25/2020] [Accepted: 01/02/2021] [Indexed: 12/16/2022]
Abstract
Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key question is how transcriptional enhancers influence these events to control gene expression. Here, we present an approach that evaluates the level and change in promoter-proximal transcription (initiation and pausing) in the context of differential gene expression, genome-wide. This combinatorial approach shows that in primary cells, control of gene expression during differentiation is achieved predominantly via changes in transcription initiation rather than via release of Pol II pausing. Using genetically engineered mouse models, deleted for functionally validated enhancers of the α- and β-globin loci, we confirm that these elements regulate Pol II recruitment and/or initiation to modulate gene expression. Together, our data show that gene expression during differentiation is regulated predominantly at the level of initiation and that enhancers are key effectors of this process.
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Affiliation(s)
- Martin S C Larke
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Julia Truch
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M A Bender
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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37
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The search for RNA-binding proteins: a technical and interdisciplinary challenge. Biochem Soc Trans 2021; 49:393-403. [PMID: 33492363 PMCID: PMC7925008 DOI: 10.1042/bst20200688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins are customarily regarded as important facilitators of gene expression. In recent years, RNA–protein interactions have also emerged as a pervasive force in the regulation of homeostasis. The compendium of proteins with provable RNA-binding function has swelled from the hundreds to the thousands astride the partnership of mass spectrometry-based proteomics and RNA sequencing. At the foundation of these advances is the adaptation of RNA-centric capture methods that can extract bound protein that has been cross-linked in its native environment. These methods reveal snapshots in time displaying an extensive network of regulation and a wealth of data that can be used for both the discovery of RNA-binding function and the molecular interfaces at which these interactions occur. This review will focus on the impact of these developments on our broader perception of post-transcriptional regulation, and how the technical features of current capture methods, as applied in mammalian systems, create a challenging medium for interpretation by systems biologists and target validation by experimental researchers.
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38
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Watson M, Park Y, Thoreen C. Roadblock-qPCR: A simple and inexpensive strategy for targeted measurements of mRNA stability. RNA (NEW YORK, N.Y.) 2020; 27:rna.076885.120. [PMID: 33288682 PMCID: PMC7901842 DOI: 10.1261/rna.076885.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
The stability of mRNAs is fundamental to determining expression level and dynamics. Nonetheless, current approaches for measuring transcript half-lives (e.g. transcription shutoff) are generally toxic or technically complex. Here we describe an alternative strategy for targeted measurements of endogenous mRNA stability that is simple, inexpensive, and non-toxic. Cells are first metabolically labelled with the nucleoside analog 4-thiouridine (4sU). Extracted mRNA can then be treated with the thiol-reactive compound N-ethylmaleimide. This compound modifies 4sU nucleotides and sterically interferes with reverse transcription of 4sU-containing transcripts, disrupting their conversion into cDNA. The decay rate of non-4sU-containing pre-existing mRNA can then be monitored by quantitative PCR (qPCR). Importantly, this approach avoids the biochemical isolation of 4sU-labelled transcripts and/or RNA-seq analysis required for other metabolic-labelling strategies. In summary, our method combines the simplicity of "transcription shutoff" strategies with the accuracy of metabolic-labelling strategies for measurements of mRNA stability across a wide range of half-lives.
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39
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Perez-Perri JI, Noerenberg M, Kamel W, Lenz CE, Mohammed S, Hentze MW, Castello A. Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture. Nat Protoc 2020; 16:27-60. [PMID: 33208978 DOI: 10.1038/s41596-020-00404-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
Interactions between RNA-binding proteins (RBPs) and RNAs are critical to cell biology. However, methods to comprehensively and quantitatively assess these interactions within cells were lacking. RNA interactome capture (RIC) uses in vivo UV crosslinking, oligo(dT) capture, and proteomics to identify RNA-binding proteomes. Recent advances have empowered RIC to quantify RBP responses to biological cues such as metabolic imbalance or virus infection. Enhanced RIC exploits the stronger binding of locked nucleic acid (LNA)-containing oligo(dT) probes to poly(A) tails to maximize RNA capture selectivity and efficiency, profoundly improving signal-to-noise ratios. The subsequent analytical use of SILAC and TMT proteomic approaches, together with high-sensitivity sample preparation and tailored statistical data analysis, substantially improves RIC's quantitative accuracy and reproducibility. This optimized approach is an extension of the original RIC protocol. It takes 3 d plus 2 weeks for proteomics and data analysis and will enable the study of RBP dynamics under different physiological and pathological conditions.
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Affiliation(s)
| | - Marko Noerenberg
- Department of Biochemistry, University of Oxford, Oxford, UK.,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, Scotland, UK
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Caroline E Lenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, UK.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK.,The Rosalind Franklin Institute, Oxfordshire, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, Oxford, UK. .,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, Scotland, UK.
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40
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Clip for studying protein-RNA interactions that regulate virus replication. Methods 2020; 183:84-92. [PMID: 31765715 DOI: 10.1016/j.ymeth.2019.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 01/24/2023] Open
Abstract
Viral and cellular RNA-binding proteins regulate numerous key steps in the replication of diverse virus genera. Viruses efficiently co-opt the host cell machinery for purposes such as transcription, splicing and subcellular localization of viral genomes. Though viral RNAs often need to resemble cellular RNAs to effectively utilize the cellular machinery, they still retain unique sequence and structural features for recognition by viral proteins for processes such as RNA polymerization, RNA export and selective packaging into virus particles. While beneficial for virus replication, distinct features of viral nucleic acids can also be recognized as foreign by several host defense proteins. Development of the crosslinking immunoprecipitation coupled with sequencing (CLIP) approach has allowed the study of viral and cellular RNA binding proteins that regulate critical aspects of viral replication in unprecedented detail. By combining immunoprecipitation of covalently crosslinked protein-RNA complexes with high-throughput sequencing, CLIP provides a global account of RNA sequences bound by RNA-binding proteins of interest in physiological settings and at near-nucleotide resolution. Here, we describe the step-by-step application of the CLIP methodology within the context of two cellular splicing regulatory proteins, hnRNP A1 and hnRNP H1 that regulate HIV-1 splicing. In principle, this versatile protocol can be applied to many other viral and cellular RNA-binding proteins.
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41
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the "fifth" ribonucleotide in 1951. Since then, the ever-increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal-Hreidarsson syndrome, Bowen-Conradi syndrome, or Williams-Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Phillip J. McCown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Agnieszka Ruszkowska
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
- Present address:
Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
| | - Charlotte N. Kunkler
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Kurtis Breger
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jacob P. Hulewicz
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew C. Wang
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Noah A. Springer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jessica A. Brown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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42
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Wang D, Zhang Y, Kleiner RE. Cell- and Polymerase-Selective Metabolic Labeling of Cellular RNA with 2'-Azidocytidine. J Am Chem Soc 2020; 142:14417-14421. [PMID: 32786764 DOI: 10.1021/jacs.0c04566] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Metabolic labeling of cellular RNA is a powerful approach to investigate RNA biology. In addition to revealing whole transcriptome dynamics, targeted labeling strategies can be used to study individual RNA subpopulations within complex systems. Here, we describe a strategy for cell- and polymerase-selective RNA labeling with 2'-azidocytidine (2'-AzCyd), a modified nucleoside amenable to bioorthogonal labeling with SPAAC chemistry. In contrast to 2'-OH-containing pyrimidine ribonucleosides, which rely upon uridine-cytidine kinase 2 (UCK2) for activation, 2'-AzCyd is phosphorylated by deoxycytidine kinase (dCK), and we find that expression of dCK mediates cell-selective 2'-AzCyd labeling. Further, 2'-AzCyd is primarily incorporated into rRNA and displays low cytotoxicity and high labeling efficiency. We apply our system to analyze the turnover of rRNA during ribophagy induced by oxidative stress or mTOR inhibition to show that 28S and 18S rRNAs undergo accelerated degradation. Taken together, our work provides a general approach for studying dynamic RNA behavior with cell and polymerase specificity and reveals fundamental insights into nucleotide and nucleic acid metabolism.
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Affiliation(s)
- Danyang Wang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Yu Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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43
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Abstract
RNA proximity ligation is a set of molecular biology techniques used to analyze the conformations and spatial proximity of RNA molecules within cells. A typical experiment starts with cross-linking of a biological sample using UV light or psoralen, followed by partial fragmentation of RNA, RNA-RNA ligation, library preparation, and high-throughput sequencing. In the past decade, proximity ligation has been used to study structures of individual RNAs, networks of interactions between small RNAs and their targets, and whole RNA-RNA interactomes, in models ranging from bacteria to animal tissues and whole animals. Here, we provide an overview of the field, highlight the main findings, review the recent experimental and computational developments, and provide troubleshooting advice for new users. In the final section, we draw parallels between DNA and RNA proximity ligation and speculate on possible future research directions.
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Affiliation(s)
- Grzegorz Kudla
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
| | - Yue Wan
- Stem Cell and Regenerative Medicine, Genome Institute of Singapore, Singapore 138672.,School of Biological Sciences, Nanyang Technological University, Singapore 637551.,Department of Biochemistry, National University of Singapore, Singapore 117596
| | - Aleksandra Helwak
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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44
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Chen Y, Wu F, Chen Z, He Z, Wei Q, Zeng W, Chen K, Xiao F, Yuan Y, Weng X, Zhou Y, Zhou X. Acrylonitrile-Mediated Nascent RNA Sequencing for Transcriptome-Wide Profiling of Cellular RNA Dynamics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1900997. [PMID: 32328408 PMCID: PMC7175251 DOI: 10.1002/advs.201900997] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 01/25/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
RNA sequencing has greatly facilitated gene expression studies but is weak in studying temporal RNA dynamics; this issue can be addressed by analyzing nascent RNAs. A famous method for nascent RNA analysis is metabolic labeling with noncanonic nucleoside followed by affinity purification, however, purification processes can always introduce biases into data analysis. Here, a chemical method for nascent RNA sequencing that avoids affinity purification based on acrylonitrile-mediated uridine-to-cytidine (U-to-C) conversion (AMUC-seq) via 4-thiouridine (s4U) cyanoethylation is presented. This method converts s4U base-pairing with guanine through the nucleophilic addition of s4U to acrylonitrile. The high reaction efficiency permits AMUC-seq directly and efficiently to recover nascent RNA information from total RNAs. AMUC-seq is validated by being used to detect mRNA half-lives and investigating the direct gene targets of a G-quadruplex stabilizer, which can be regarded as potential anticancer drug, in human cells. Thousands of direct gene targets of this drug are verified (these genes are significantly enriched in cancer such as SRC and HRAS). AMUC-seq also confirms G-quadruplex stabilization that impacts RNA polyadenylation. These results show AMUC-seq is qualified for the study of temporal RNA dynamics, and it can be a promising strategy to study the therapeutic mechanism of transcription-modulating drugs.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Fan Wu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Zonggui Chen
- The Institute for Advanced StudiesWuhan UniversityWuhan430072P. R. China
| | - Zhiyong He
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Qi Wei
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Weiwu Zeng
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Kun Chen
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Feng Xiao
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Yushu Yuan
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Yu Zhou
- The Institute for Advanced StudiesWuhan UniversityWuhan430072P. R. China
- State Key Laboratory of VirologyCollege of Life SciencesWuhan UniversityWuhan430072P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
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45
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Szabo EX, Reichert P, Lehniger MK, Ohmer M, de Francisco Amorim M, Gowik U, Schmitz-Linneweber C, Laubinger S. Metabolic Labeling of RNAs Uncovers Hidden Features and Dynamics of the Arabidopsis Transcriptome. THE PLANT CELL 2020; 32:871-887. [PMID: 32060173 PMCID: PMC7145469 DOI: 10.1105/tpc.19.00214] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 01/14/2020] [Accepted: 02/11/2020] [Indexed: 05/05/2023]
Abstract
Transcriptome analysis by RNA sequencing (RNA-seq) has become an indispensable research tool in modern plant biology. Virtually all RNA-seq studies provide a snapshot of the steady state transcriptome, which contains valuable information about RNA populations at a given time but lacks information about the dynamics of RNA synthesis and degradation. Only a few specialized sequencing techniques, such as global run-on sequencing, have been used to provide information about RNA synthesis rates in plants. Here, we demonstrate that RNA labeling with the modified, nontoxic uridine analog 5-ethynyl uridine (5-EU) in Arabidopsis (Arabidopsis thaliana) seedlings provides insight into plant transcriptome dynamics. Pulse labeling with 5-EU revealed nascent and unstable RNAs, RNA processing intermediates generated by splicing, and chloroplast RNAs. Pulse-chase experiments with 5-EU allowed us to determine RNA stabilities without the need for chemical transcription inhibitors such as actinomycin and cordycepin. Inhibitor-free, genome-wide analysis of polyadenylated RNA stability via 5-EU pulse-chase experiments revealed RNAs with shorter half-lives than those reported after chemical inhibition of transcription. In summary, our results indicate that the Arabidopsis nascent transcriptome contains unstable RNAs and RNA processing intermediates and suggest that polyadenylated RNAs have low stability in plants. Our technique lays the foundation for easy, affordable, nascent transcriptome analysis and inhibitor-free analysis of RNA stability in plants.
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Affiliation(s)
- Emese Xochitl Szabo
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
| | - Philipp Reichert
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
| | | | - Marilena Ohmer
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | | | - Udo Gowik
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
| | | | - Sascha Laubinger
- Institute for Biology and Environmental Science, University of Oldenburg, 26129 Oldenburg, Germany
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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46
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Smith T, Villanueva E, Queiroz RML, Dawson CS, Elzek M, Urdaneta EC, Willis AE, Beckmann BM, Krijgsveld J, Lilley KS. Organic phase separation opens up new opportunities to interrogate the RNA-binding proteome. Curr Opin Chem Biol 2020; 54:70-75. [PMID: 32131038 DOI: 10.1016/j.cbpa.2020.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023]
Abstract
Protein-RNA interactions regulate all aspects of RNA metabolism and are crucial to the function of catalytic ribonucleoproteins. Until recently, the available technologies to capture RNA-bound proteins have been biased toward poly(A) RNA-binding proteins (RBPs) or involve molecular labeling, limiting their application. With the advent of organic-aqueous phase separation-based methods, we now have technologies that efficiently enrich the complete suite of RBPs and enable quantification of RBP dynamics. These flexible approaches to study RBPs and their bound RNA open up new research avenues for systems-level interrogation of protein-RNA interactions.
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Affiliation(s)
- Tom Smith
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Eneko Villanueva
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Rayner M L Queiroz
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Charlotte S Dawson
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Mohamed Elzek
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Erika C Urdaneta
- Humboldt University Berlin, IRI Life Sciences, Philippstr. 13 10115 Berlin, Germany
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Leicester, LE1 7BH, UK
| | - Benedikt M Beckmann
- Humboldt University Berlin, IRI Life Sciences, Philippstr. 13 10115 Berlin, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center, Im Neuenheimer Feld 581, Heidelberg, Germany; Heidelberg University, Medical Faculty, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Kathryn S Lilley
- Cambridge Center for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
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47
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Biasini A, Marques AC. A Protocol for Transcriptome-Wide Inference of RNA Metabolic Rates in Mouse Embryonic Stem Cells. Front Cell Dev Biol 2020; 8:97. [PMID: 32175319 PMCID: PMC7056730 DOI: 10.3389/fcell.2020.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/07/2020] [Indexed: 12/16/2022] Open
Abstract
The relative ease of mouse Embryonic Stem Cells (mESCs) culture and the potential of these cells to differentiate into any of the three primary germ layers: ectoderm, endoderm and mesoderm (pluripotency), makes them an ideal and frequently used ex vivo system to dissect how gene expression changes impact cell state and differentiation. These efforts are further supported by the large number of constitutive and inducible mESC mutants established with the aim of assessing the contributions of different pathways and genes to cell homeostasis and gene regulation. Gene product abundance is controlled by the modulation of the rates of RNA synthesis, processing, and degradation. The ability to determine the relative contribution of these different RNA metabolic rates to gene expression control using standard RNA-sequencing approaches, which only capture steady state abundance of transcripts, is limited. In contrast, metabolic labeling of RNA with 4-thiouridine (4sU) coupled with RNA-sequencing, allows simultaneous and reproducible inference of transcriptome wide synthesis, processing, and degradation rates. Here we describe, a detailed protocol for 4sU metabolic labeling in mESCs that requires short 4sU labeling times at low concentration and minimally impacts cellular homeostasis. This approach presents a versatile method for in-depth characterization of the gene regulatory strategies governing gene steady state abundance in mESC.
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Affiliation(s)
- Adriano Biasini
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ana Claudia Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
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48
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An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. Nat Methods 2020; 17:311-318. [PMID: 32015544 PMCID: PMC8518020 DOI: 10.1038/s41592-019-0726-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022]
Abstract
Tissues and organs are composed of diverse cell types, which poses a major challenge for cell-specific gene expression profiling. Current metabolic labeling methods rely on the inability of mammalian cells to incorporate exogenous pyrimidine analogs, which are then co-opted by ectopically-expressed enzymes. We demonstrate that mammalian cells can incorporate uracil analogs and characterize the enzymatic pathways responsible for high background incorporation. To overcome these limitations, we developed a novel small-molecule/enzyme pair consisting of uridine-cytidine kinase 2 (UCK2) and 2’-azidouridine (2’AzUd). We demonstrate that 2’AzUd is only incorporated in UCK2-expressing cells and characterize selectivity mechanisms using molecular dynamics and X-ray crystallography. Furthermore, this pair can be used to purify and track RNA from specific cellular populations, making it ideal for high-resolution cell-specific RNA labeling. Overall, these results reveal novel aspects of mammalian salvage pathways and serve as a new benchmark for designing, characterizing and evaluating cell-specific biomolecule labeling methodologies.
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49
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Gregersen LH, Mitter R, Svejstrup JQ. Using TT chem-seq for profiling nascent transcription and measuring transcript elongation. Nat Protoc 2020; 15:604-627. [PMID: 31915390 DOI: 10.1038/s41596-019-0262-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/29/2019] [Indexed: 01/08/2023]
Abstract
The dynamics of transcription can be studied genome wide by high-throughput sequencing of nascent and newly synthesized RNA. 4-thiouridine (4SU) labeling in vivo enables the specific capture of such new transcripts, with 4SU residues being tagged by biotin linkers and captured using streptavidin beads before library production and high-throughput sequencing. To achieve high-resolution profiles of transcribed regions, an RNA fragmentation step before biotin tagging was introduced, in an approach known as transient transcriptome sequencing (TT-seq). We recently introduced a chemical approach for RNA fragmentation that we refer to as TTchem-seq. We describe how TTchem-seq can be used in combination with transient inhibition of early elongation using the reversible CDK9 inhibitor, 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB), to measure RNA polymerase II (RNAPII) elongation rates in vivo, a technique we call DRB/TTchem-seq. Here, we provide detailed protocols for carrying out TTchem-seq and DRB/TTchem-seq, including computational analysis. Experiments and data analysis can be performed over a period of 10-13 d and require molecular biology and bioinformatics skills.
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Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK.
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50
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Lusser A, Gasser C, Trixl L, Piatti P, Delazer I, Rieder D, Bhasin JM, Riml C, Amort T, Micura R. Thiouridine-to-Cytidine Conversion Sequencing (TUC-Seq) to Measure mRNA Transcription and Degradation Rates. Methods Mol Biol 2020; 2062:191-211. [PMID: 31768978 DOI: 10.1007/978-1-4939-9822-7_10] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The study of RNA dynamics, specifically RNA transcription and decay rates, has gained increasing attention in recent years because various mechanisms have been discovered that affect mRNA half-life, thereby ultimately controlling protein output. Therefore, there is a need for methods enabling minimally invasive, simple and high-throughput determination of RNA stability that can be applied to determine RNA transcription and decay rates in cells and organisms. We have recently developed a protocol which we named TUC-seq to directly distinguish newly synthesized transcripts from the preexisting pool of transcripts by metabolic labeling of nascent RNAs with 4-thiouridine (4sU) followed by osmium tetroxide-mediated conversion of 4sU to cytidine (C) and direct sequencing. In contrast to other related methods (SLAM-seq, TimeLapse-seq), TUC-seq converts 4sU to a native C instead of an alkylated or otherwise modified nucleoside derivative. TUC-seq can be applied to any cell type that is amenable to 4sU labeling. By employing different labeling strategies (pulse or pulse-chase labeling), it is suitable for a broad field of applications and provides a fast and highly efficient means to determine mRNA transcription and decay rates.
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Affiliation(s)
- Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
| | - Catherina Gasser
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
| | - Lukas Trixl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Isabel Delazer
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Christian Riml
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria
| | - Thomas Amort
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronald Micura
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, Leopold Franzens University, Innsbruck, Austria.
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