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Crane AB, Jetti SK, Littleton JT. A stochastic RNA editing process targets a limited number of sites in individual Drosophila glutamatergic motoneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594696. [PMID: 38798345 PMCID: PMC11118563 DOI: 10.1101/2024.05.17.594696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
RNA editing is a post-transcriptional source of protein diversity and occurs across the animal kingdom. Given the complete profile of mRNA targets and their editing rate in individual cells is unclear, we analyzed single cell RNA transcriptomes from Drosophila larval tonic and phasic glutamatergic motoneuron subtypes to determine the most highly edited targets and identify cell-type specific editing. From ∼15,000 genes encoded in the genome, 316 high confidence A-to-I canonical RNA edit sites were identified, with 102 causing missense amino acid changes in proteins regulating membrane excitability, synaptic transmission, and cellular function. Some sites showed 100% editing in single neurons as observed with mRNAs encoding mammalian AMPA receptors. However, most sites were edited at lower levels and generated variable expression of edited and unedited mRNAs within individual neurons. Together, these data provide insights into how the RNA editing landscape alters protein function to modulate the properties of two well-characterized neuronal populations in Drosophila .
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Xu Y, Liu J, Zhao T, Song F, Tian L, Cai W, Li H, Duan Y. Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes. Int J Mol Sci 2023; 24:17126. [PMID: 38138955 PMCID: PMC10742984 DOI: 10.3390/ijms242417126] [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: 09/30/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuange Duan
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.X.); (J.L.); (T.Z.); (F.S.); (L.T.); (W.C.); (H.L.)
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Imbriano C, Moresi V, Belluti S, Renzini A, Cavioli G, Maretti E, Molinari S. Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives. Int J Mol Sci 2023; 24:15161. [PMID: 37894843 PMCID: PMC10606696 DOI: 10.3390/ijms242015161] [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: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which are N6-methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as a therapeutic approach. In this review, we aim to provide an overview of the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high-throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.
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Affiliation(s)
- Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy;
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Eleonora Maretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
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Vorobeva MA, Skvortsov DA, Pervouchine DD. Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing. Acta Naturae 2023; 15:23-31. [PMID: 38234601 PMCID: PMC10790352 DOI: 10.32607/actanaturae.26826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 01/19/2024] Open
Abstract
The regulation of alternative splicing in eukaryotic cells is carried out through the coordinated action of a large number of factors, including RNA-binding proteins and RNA structure. The RNA structure influences alternative splicing by blocking cis-regulatory elements, or bringing them closer or farther apart. In combination with RNA-binding proteins, it generates transcript conformations that help to achieve the necessary splicing outcome. However, the binding of regulatory proteins depends on RNA structure and, vice versa, the formation of RNA structure depends on the interaction with regulators. Therefore, RNA structure and RNA-binding proteins are inseparable components of common regulatory mechanisms. This review highlights examples of alternative splicing regulation by RNA-binding proteins, the regulation through local and long-range RNA structures, as well as how these elements work together, cooperate, and compete.
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Affiliation(s)
- M. A. Vorobeva
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. A. Skvortsov
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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Birk MA, Liscovitch-Brauer N, Dominguez MJ, McNeme S, Yue Y, Hoff JD, Twersky I, Verhey KJ, Sutton RB, Eisenberg E, Rosenthal JJC. Temperature-dependent RNA editing in octopus extensively recodes the neural proteome. Cell 2023; 186:2544-2555.e13. [PMID: 37295402 PMCID: PMC10445230 DOI: 10.1016/j.cell.2023.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 06/12/2023]
Abstract
In poikilotherms, temperature changes challenge the integration of physiological function. Within the complex nervous systems of the behaviorally sophisticated coleoid cephalopods, these problems are substantial. RNA editing by adenosine deamination is a well-positioned mechanism for environmental acclimation. We report that the neural proteome of Octopus bimaculoides undergoes massive reconfigurations via RNA editing following a temperature challenge. Over 13,000 codons are affected, and many alter proteins that are vital for neural processes. For two highly temperature-sensitive examples, recoding tunes protein function. For synaptotagmin, a key component of Ca2+-dependent neurotransmitter release, crystal structures and supporting experiments show that editing alters Ca2+ binding. For kinesin-1, a motor protein driving axonal transport, editing regulates transport velocity down microtubules. Seasonal sampling of wild-caught specimens indicates that temperature-dependent editing occurs in the field as well. These data show that A-to-I editing tunes neurophysiological function in response to temperature in octopus and most likely other coleoids.
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Affiliation(s)
- Matthew A Birk
- Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Biology, Saint Francis University, Loretto, PA 15940, USA
| | | | - Matthew J Dominguez
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Sean McNeme
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - J Damon Hoff
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - R Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Eli Eisenberg
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel.
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Tassinari V, La Rosa P, Guida E, Colopi A, Caratelli S, De Paolis F, Gallo A, Cenciarelli C, Sconocchia G, Dolci S, Cesarini V. Contribution of A-to-I RNA editing, M6A RNA Methylation, and Alternative Splicing to physiological brain aging and neurodegenerative diseases. Mech Ageing Dev 2023; 212:111807. [PMID: 37023929 DOI: 10.1016/j.mad.2023.111807] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Aging is a physiological and progressive phenomenon in all organisms' life cycle, characterized by the accumulation of degenerative processes triggered by several alterations within molecular pathways. These changes compromise cell fate, resulting in the loss of functions in tissues throughout the body, including the brain. Physiological brain aging has been linked to structural and functional alterations, as well as to an increased risk of neurodegenerative diseases. Post-transcriptional RNA modifications modulate mRNA coding properties, stability, translatability, expanding the coding capacity of the genome, and are involved in all cellular processes. Among mRNA post-transcriptional modifications, the A-to-I RNA editing, m6A RNA Methylation and Alternative Splicing play a critical role in all the phases of a neuronal cell life cycle and alterations in their mechanisms of action significantly contribute to aging and neurodegeneration. Here we review our current understanding of the contribution of A-to-I RNA editing, m6A RNA Methylation, and Alternative Splicing to physiological brain aging process and neurodegenerative diseases.
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Affiliation(s)
- Valentina Tassinari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Ambra Colopi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Sara Caratelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Francesca De Paolis
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Angela Gallo
- RNA Editing Lab., Oncohaematology Department, Cellular and Gene Therapy Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Cenciarelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Giuseppe Sconocchia
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Valeriana Cesarini
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
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Duan Y, Cai W, Li H. Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis. RNA (NEW YORK, N.Y.) 2023; 29:141-152. [PMID: 36649983 PMCID: PMC9891260 DOI: 10.1261/rna.079450.122] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/30/2022] [Indexed: 06/10/2023]
Abstract
The adaptiveness of nonsynonymous RNA editing (recoding) could be conferred by the flexibility of the temporal-spatially controllable proteomic diversity, or by its restorative effect which fixes unfavorable genomic mutations at the RNA level. These two complementary hypotheses, namely, the diversifying hypothesis and the restorative hypothesis, have distinct predictions on the landscape of RNA editing sites. We collected the chloroplast C-to-U RNA editomes of 21 vascular plants (11 angiosperms, four gymnosperms, and six ferns) from a previous study, aiming to testify whether the plant editomes typically conform to the restorative hypothesis. All predictions made by the restorative hypothesis are verified: (i) nonsynonymous editing sites are more frequent and have higher editing levels than synonymous sites; (ii) nonsynonymous editing levels are extremely high and show weak tissue-specificity in plants; (iii) on the inferred genomic sites with recent T-to-C mutations, nonsynonymous sites but not synonymous sites are compensated by C-to-U RNA editing. In conclusion, nonsynonymous C-to-U RNA editing in plants is adaptive due to its restorative effects. The recoding levels are high and are constantly required across the whole plant so that the recoding events could perfectly mimic DNA mutations. The evolutionary significance of plant RNA editing is systematically demonstrated at the genome-wide level.
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Affiliation(s)
- Yuange Duan
- Key Laboratory of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Key Laboratory of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Key Laboratory of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Women in the European Virus Bioinformatics Center. Viruses 2022; 14:1522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [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: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ana Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, 1349-008 Lisbon, Portugal
| | - Patricia Agudelo-Romero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Magda Bletsa
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Katherine Brown
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Claudia Claus
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology and Virology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Stefanie Deinhardt-Emmer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Li Deng
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Virology, Helmholtz Centre Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Caroline C. Friedel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - María Inés Gismondi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Agrobiotechnology and Molecular Biology (IABIMO), National Institute for Agriculture Technology (INTA), National Research Council (CONICET), Hurlingham B1686IGC, Argentina
- Department of Basic Sciences, National University of Luján, Luján B6702MZP, Argentina
| | - Evangelia Georgia Kostaki
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Denise Kühnert
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Urmila Kulkarni-Kale
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Karin J. Metzner
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Faculty of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Laura Miozzi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, 13353 Berlin, Germany
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Janina Rahlff
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, 391 82 Kalmar, Sweden
| | - Emma Thomson
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Charlotte Tumescheit
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Lia van der Hoek
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| | - Lore Van Espen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
- Institute for the Future, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Maryam Zaheri
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Neta Zuckerman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat Gan 52621, Israel
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
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9
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Tsybulskyi V, Meyer IM. ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence. Nucleic Acids Res 2022; 50:e85. [PMID: 35641016 PMCID: PMC9410897 DOI: 10.1093/nar/gkac405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/09/2022] [Indexed: 12/20/2022] Open
Abstract
There is an increased interest in the determination of RNA structures in vivo as it is now possible to probe them in a high-throughput manner, e.g. using SHAPE protocols. By now, there exist a range of computational methods that integrate experimental SHAPE-probing evidence into computational RNA secondary structure prediction. The state-of-the-art in this field is currently provided by computational methods that employ the minimum-free energy strategy for prediction RNA secondary structures with SHAPE-probing evidence. These methods, however, rely on the assumption that transcripts in vivo fold into the thermodynamically most stable configuration and ignore evolutionary evidence for conserved RNA structure features. We here present a new computational method, ShapeSorter, that predicts RNA structure features without employing the thermodynamic strategy. Instead, ShapeSorter employs a fully probabilistic framework to identify RNA structure features that are supported by evolutionary and SHAPE-probing evidence. Our method can capture RNA structure heterogeneity, pseudo-knotted RNA structures as well as transient and mutually exclusive RNA structure features. Moreover, it estimates P-values for the predicted RNA structure features which allows for easy filtering and ranking. We investigate the merits of our method in a comprehensive performance benchmarking and conclude that ShapeSorter has a significantly superior performance for predicting base-pairs than the existing state-of-the-art methods.
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Affiliation(s)
- Volodymyr Tsybulskyi
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.,Freie Universität Berlin, Department of Mathematics and Computer Science, Institute of Computer Science, Takustraße 9, 14195 Berlin, Germany
| | - Irmtraud M Meyer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.,Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Thielallee 63, 14195 Berlin, Germany.,Freie Universität Berlin, Department of Mathematics and Computer Science, Institute of Computer Science, Takustraße 9, 14195 Berlin, Germany
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10
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Yildirim E, Curtis R, Hwangbo DS. Roles of peripheral clocks: lessons from the fly. FEBS Lett 2022; 596:263-293. [PMID: 34862983 PMCID: PMC8844272 DOI: 10.1002/1873-3468.14251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 02/03/2023]
Abstract
To adapt to and anticipate rhythmic changes in the environment such as daily light-dark and temperature cycles, internal timekeeping mechanisms called biological clocks evolved in a diverse set of organisms, from unicellular bacteria to humans. These biological clocks play critical roles in organisms' fitness and survival by temporally aligning physiological and behavioral processes to the external cues. The central clock is located in a small subset of neurons in the brain and drives daily activity rhythms, whereas most peripheral tissues harbor their own clock systems, which generate metabolic and physiological rhythms. Since the discovery of Drosophila melanogaster clock mutants in the early 1970s, the fruit fly has become an extensively studied model organism to investigate the mechanism and functions of circadian clocks. In this review, we primarily focus on D. melanogaster to survey key discoveries and progresses made over the past two decades in our understanding of peripheral clocks. We discuss physiological roles and molecular mechanisms of peripheral clocks in several different peripheral tissues of the fly.
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Affiliation(s)
| | - Rachel Curtis
- Department of Biology, University of Louisville, Louisville, KY, USA
| | - Dae-Sung Hwangbo
- Department of Biology, University of Louisville, Louisville, KY, USA
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11
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Worpenberg L, Paolantoni C, Roignant JY. Functional interplay within the epitranscriptome: Reality or fiction? Bioessays 2021; 44:e2100174. [PMID: 34873719 DOI: 10.1002/bies.202100174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/11/2022]
Abstract
RNA modifications have recently emerged as an important regulatory layer of gene expression. The most prevalent and reversible modification on messenger RNA (mRNA), N6-methyladenosine, regulates most steps of RNA metabolism and its dysregulation has been associated with numerous diseases. Other modifications such as 5-methylcytosine and N1-methyladenosine have also been detected on mRNA but their abundance is lower and still debated. Adenosine to inosine RNA editing is widespread on coding and non-coding RNA and can alter mRNA decoding as well as protect against autoimmune diseases. 2'-O-methylation of the ribose and pseudouridine are widespread on ribosomal and transfer RNA and contribute to proper RNA folding and stability. While the understanding of the individual role of RNA modifications has now reached an unprecedented stage, still little is known about their interplay in the control of gene expression. In this review we discuss the examples where such interplay has been observed and speculate that with the progress of mapping technologies more of those will rapidly accumulate.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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12
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Yen YP, Chen JA. The m 6A epitranscriptome on neural development and degeneration. J Biomed Sci 2021; 28:40. [PMID: 34039354 PMCID: PMC8157406 DOI: 10.1186/s12929-021-00734-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent, conserved, and abundant RNA modification of the mRNAs of most eukaryotes, including mammals. Similar to epigenetic DNA modifications, m6A has been proposed to function as a critical regulator for gene expression. This modification is installed by m6A methylation "writers" (Mettl3/Mettl14 methyltransferase complex), and it can be reversed by demethylase "erasers" (Fto and Alkbh5). Furthermore, m6A can be recognized by "readers" (Ythdf and Ythdc families), which may be interpreted to affect mRNA splicing, stability, translation or localization. Levels of m6A methylation appear to be highest in the brain, where it plays important functions during embryonic stem cell differentiation, brain development, and neurodevelopmental disorders. Depletion of the m6A methylation writer Mettl14 from mouse embryonic nervous systems prolongs cell cycle progression of radial glia and extends cortical neurogenesis into postnatal stages. Recent studies further imply that dysregulated m6A methylation may be significantly correlated with neurodegenerative diseases. In this review, we give an overview of m6A modifications during neural development and associated disorders, and provide perspectives for studying m6A methylation.
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Affiliation(s)
- Ya-Ping Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
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13
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Sapiro AL, Freund EC, Restrepo L, Qiao HH, Bhate A, Li Q, Ni JQ, Mosca TJ, Li JB. Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons. Cell Rep 2021; 31:107654. [PMID: 32433963 PMCID: PMC7306179 DOI: 10.1016/j.celrep.2020.107654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/11/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Adenosine-to-inosine RNA editing, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, alters RNA sequences from those encoded by DNA. These editing events are dynamically regulated, but few trans regulators of ADARs are known in vivo. Here, we screen RNA-binding proteins for roles in editing regulation with knockdown experiments in the Drosophila brain. We identify zinc-finger protein at 72D (Zn72D) as a regulator of editing levels at a majority of editing sites in the brain. Zn72D both regulates ADAR protein levels and interacts with ADAR in an RNA-dependent fashion, and similar to ADAR, Zn72D is necessary to maintain proper neuromuscular junction architecture and fly mobility. Furthermore, Zn72D’s regulatory role in RNA editing is conserved because the mammalian homolog of Zn72D, Zfr, regulates editing in mouse primary neurons. The broad and conserved regulation of ADAR editing by Zn72D in neurons sustains critically important editing events. Sapiro et al. identify Drosophila Zn72D as an influential regulator of neuronal A-to-I RNA editing and synaptic morphology. Zn72D regulates ADAR levels and editing at a large subset of editing sites, providing insight into the maintenance of critical tissue-specific RNA editing events.
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Affiliation(s)
- Anne L Sapiro
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emily C Freund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lucas Restrepo
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Huan-Huan Qiao
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Amruta Bhate
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing, China
| | - Timothy J Mosca
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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14
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Duan Y, Tang X, Lu J. Evolutionary driving forces of A-to-I editing in metazoans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1666. [PMID: 33998151 DOI: 10.1002/wrna.1666] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/24/2021] [Indexed: 11/05/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is an evolutionarily conserved mechanism that converts adenosines to inosines in metazoans' transcriptomes. However, the landscapes of editomes have considerably changed during evolution. Here, we review some of our current knowledge of A-to-I editing in the metazoan transcriptomes, focusing on the possible evolutionary driving forces underlying the editing events. First, we review the evolution of ADAR gene family in animals. Then, we summarize the recent advances in characterizing the editomes of various metazoan species. Next, we highlight several factors contributing to the interspecies differences in editomes, including variations in copy number and expression patterns of ADAR genes, the differences in genomic architectures and contents, and the differences in the efficacy of natural selection. After that, we review the possible diversifying and restorative effects of the editing (recoding) events that change the protein sequences. Finally, we discuss the possible convergent evolution of RNA editing in distantly related clades. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
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15
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Martín AL, Mounir M, Meyer IM. CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo. Nucleic Acids Res 2021; 49:e19. [PMID: 33095878 PMCID: PMC7913772 DOI: 10.1093/nar/gkaa900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/16/2020] [Accepted: 09/30/2020] [Indexed: 11/14/2022] Open
Abstract
RNA structure formation in vivo happens co-transcriptionally while the transcript is being made. The corresponding co-transcriptional folding pathway typically involves transient RNA structure features that are not part of the final, functional RNA structure. These transient features can play important functional roles of their own and also influence the formation of the final RNA structure in vivo. We here present CoBold, a computational method for identifying different functional classes of transient RNA structure features that can either aid or hinder the formation of a known reference RNA structure. Our method takes as input either a single RNA or a corresponding multiple-sequence alignment as well as a known reference RNA secondary structure and identifies different classes of transient RNA structure features that could aid or prevent the formation of the given RNA structure. We make CoBold available via a web-server which includes dedicated data visualisation.
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Affiliation(s)
- Adrián López Martín
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Mohamed Mounir
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Irmtraud M Meyer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.,Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Thielallee 63, 14195 Berlin, Germany
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16
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Duan Y, Dou S, Porath HT, Huang J, Eisenberg E, Lu J. A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution. iScience 2021; 24:101983. [PMID: 33458624 PMCID: PMC7797907 DOI: 10.1016/j.isci.2020.101983] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/18/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Social insects exhibit extensive phenotypic diversities among the genetically similar individuals, suggesting a role for the epigenetic regulations beyond the genome level. The ADAR-mediated adenosine-to-inosine (A-to-I) RNA editing, an evolutionarily conserved mechanism, facilitates adaptive evolution by expanding proteomic diversities. Here, we characterize the A-to-I RNA editome of honeybees (Apis mellifera), identifying 407 high-confidence A-to-I editing sites. Editing is most abundant in the heads and shows signatures for positive selection. Editing behavior differs between foragers and nurses, suggesting a role for editing in caste differentiation. Although only five sites are conserved between bees and flies, an unexpectedly large number of genes exhibit editing in both species, albeit at different locations, including the nonsynonymous auto-editing of Adar. This convergent evolution, where the same target genes independently acquire recoding events in distant diverged clades, together with the signals of adaptation observed in honeybees alone, further supports the notion of recoding being adaptive. Nonsynonymous editing sites in honeybees were under positive selection Differential editing may contribute to the phenotypic diversity between sub-castes Target genes acquire editing in different clades, suggesting convergent evolution
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan 52900, Israel
| | - Jiaxing Huang
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
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17
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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18
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Grau-Bové X, Weetman D. RNA editing: an overlooked source of fine-scale adaptation in insect vectors? CURRENT OPINION IN INSECT SCIENCE 2020; 40:48-55. [PMID: 32599511 DOI: 10.1016/j.cois.2020.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
RNA editing is a source of molecular diversity that regulates the functional repertoire of animal transcriptomes. Multiple studies in Drosophila have revealed that conserved editing events can be a source of evolutionary adaptations, and there is a solid body of evidence linking editing and the fine-tuning of neural genes, which are often targeted by insecticides used in vector control. Yet, despite these suggestive connections, genome-wide analyses of editing in insect vectors are conspicuously lacking. Future advances will require complementing the growing wealth of vector genomes with targeted transcriptome analyses. Here, we review recent investigations of the genetic footprints of adaptive RNA editing in insects and provide an overview of new methodologies applicable to studies of RNA editing in insect vectors.
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Affiliation(s)
- Xavier Grau-Bové
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
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19
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Kapoor U, Licht K, Amman F, Jakobi T, Martin D, Dieterich C, Jantsch MF. ADAR-deficiency perturbs the global splicing landscape in mouse tissues. Genome Res 2020; 30:1107-1118. [PMID: 32727871 PMCID: PMC7462079 DOI: 10.1101/gr.256933.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
Adenosine-to-inosine RNA editing and pre-mRNA splicing largely occur cotranscriptionally and influence each other. Here, we use mice deficient in either one of the two editing enzymes ADAR (ADAR1) or ADARB1 (ADAR2) to determine the transcriptome-wide impact of RNA editing on splicing across different tissues. We find that ADAR has a 100× higher impact on splicing than ADARB1, although both enzymes target a similar number of substrates with a large common overlap. Consistently, differentially spliced regions frequently harbor ADAR editing sites. Moreover, catalytically dead ADAR also impacts splicing, demonstrating that RNA binding of ADAR affects splicing. In contrast, ADARB1 editing sites are found enriched 5′ of differentially spliced regions. Several of these ADARB1-mediated editing events change splice consensus sequences, therefore strongly influencing splicing of some mRNAs. A significant overlap between differentially edited and differentially spliced sites suggests evolutionary selection toward splicing being regulated by editing in a tissue-specific manner.
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Affiliation(s)
- Utkarsh Kapoor
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Konstantin Licht
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Fabian Amman
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria.,Institute of Theoretical Biochemistry, University of Vienna, A-1090 Vienna, Austria
| | - Tobias Jakobi
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, University Hospital, D-96120 Heidelberg, Germany
| | - David Martin
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Christoph Dieterich
- Department of Internal Medicine III and Klaus Tschira Institute for Computational Cardiology, Section of Bioinformatics and Systems Cardiology, University Hospital, D-96120 Heidelberg, Germany
| | - Michael F Jantsch
- Center of Anatomy and Cell Biology, Department of Cell and Developmental Biology, Medical University of Vienna, A-1090 Vienna, Austria
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20
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Taylor K, Sobczak K. Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control. Int J Mol Sci 2020; 21:ijms21145161. [PMID: 32708277 PMCID: PMC7404189 DOI: 10.3390/ijms21145161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.
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21
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Tang SJ, Shen H, An O, Hong H, Li J, Song Y, Han J, Tay DJT, Ng VHE, Bellido Molias F, Leong KW, Pitcheshwar P, Yang H, Chen L. Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development. Nat Commun 2020; 11:799. [PMID: 32034135 PMCID: PMC7005744 DOI: 10.1038/s41467-020-14621-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/16/2020] [Indexed: 12/18/2022] Open
Abstract
RNA editing and splicing are the two major processes that dynamically regulate human transcriptome diversity. Despite growing evidence of crosstalk between RNA editing enzymes (mainly ADAR1) and splicing machineries, detailed mechanistic explanations and their biological importance in diseases, such as cancer are still lacking. Herein, we identify approximately a hundred high-confidence splicing events altered by ADAR1 and/or ADAR2, and ADAR1 or ADAR2 protein can regulate cassette exons in both directions. We unravel a binding tendency of ADARs to dsRNAs that involves GA-rich sequences for editing and splicing regulation. ADAR1 edits an intronic splicing silencer, leading to recruitment of SRSF7 and repression of exon inclusion. We also present a mechanism through which ADAR2 binds to dsRNA formed between GA-rich sequences and polypyrimidine (Py)-tract and precludes access of U2AF65 to 3' splice site. Furthermore, we find these ADARs-regulated splicing changes per se influence tumorigenesis, not merely byproducts of ADARs editing and binding.
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Affiliation(s)
- Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Fernando Bellido Molias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Ka Wai Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Priyankaa Pitcheshwar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117594, Singapore.
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22
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Christofi T, Zaravinos A. RNA editing in the forefront of epitranscriptomics and human health. J Transl Med 2019; 17:319. [PMID: 31547885 PMCID: PMC6757416 DOI: 10.1186/s12967-019-2071-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022] Open
Abstract
Post-transcriptional modifications have been recently expanded with the addition of RNA editing, which is predominantly mediated by adenosine and cytidine deaminases acting on DNA and RNA. Here, we review the full spectrum of physiological processes in which these modifiers are implicated, among different organisms. Adenosine to inosine (A-to-I) editors, members of the ADAR and ADAT protein families are important regulators of alternative splicing and transcriptional control. On the other hand, cytidine to uridine (C-to-U) editors, members of the AID/APOBEC family, are heavily implicated in innate and adaptive immunity with important roles in antibody diversification and antiviral response. Physiologically, these enzymes are present in the nucleus and/or the cytoplasm, where they modify various RNA molecules, including miRNAs, tRNAs apart from mRNAs, whereas DNA editing is also possible by some of them. The expansion of next generation sequencing technologies provided a wealth of data regarding such modifications. RNA editing has been implicated in various disorders including cancer, and neurological diseases of the brain or the central nervous system. It is also related to cancer heterogeneity and the onset of carcinogenesis. Response to treatment can also be affected by the RNA editing status where drug efficacy is significantly compromised. Studying RNA editing events can pave the way to the identification of new disease biomarkers, and provide a more personalised therapy to various diseases.
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Affiliation(s)
- Theodoulakis Christofi
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404, Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404, Nicosia, Cyprus. .,Centre for Risk and Decision Sciences (CERIDES), 2404, Nicosia, Cyprus.
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23
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Licht K, Kapoor U, Amman F, Picardi E, Martin D, Bajad P, Jantsch MF. A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing. Genome Res 2019; 29:1453-1463. [PMID: 31427386 PMCID: PMC6724681 DOI: 10.1101/gr.242636.118] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 07/25/2019] [Indexed: 11/25/2022]
Abstract
Pre-mRNA-splicing and adenosine to inosine (A-to-I) RNA-editing occur mostly cotranscriptionally. During A-to-I editing, a genomically encoded adenosine is deaminated to inosine by adenosine deaminases acting on RNA (ADARs). Editing-competent stems are frequently formed between exons and introns. Consistently, studies using reporter assays have shown that splicing efficiency can affect editing levels. Here, we use Nascent-seq and identify ∼90,000 novel A-to-I editing events in the mouse brain transcriptome. Most novel sites are located in intronic regions. Unlike previously assumed, we show that both ADAR (ADAR1) and ADARB1 (ADAR2) can edit repeat elements and regular transcripts to the same extent. We find that inhibition of splicing primarily increases editing levels at hundreds of sites, suggesting that reduced splicing efficiency extends the exposure of intronic and exonic sequences to ADAR enzymes. Lack of splicing factors NOVA1 or NOVA2 changes global editing levels, demonstrating that alternative splicing factors can modulate RNA editing. Finally, we show that intron retention rates correlate with editing levels across different brain tissues. We therefore demonstrate that splicing efficiency is a major factor controlling tissue-specific differences in editing levels.
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Affiliation(s)
- Konstantin Licht
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Utkarsh Kapoor
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Fabian Amman
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria.,Institute of Theoretical Biochemistry, University of Vienna, A-1090 Vienna, Austria
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, I-70126 Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, I-70126 Bari, Italy
| | - David Martin
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Prajakta Bajad
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
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24
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Masachis S, Tourasse NJ, Lays C, Faucher M, Chabas S, Iost I, Darfeuille F. A genetic selection reveals functional metastable structures embedded in a toxin-encoding mRNA. eLife 2019; 8:47549. [PMID: 31411564 PMCID: PMC6733600 DOI: 10.7554/elife.47549] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/14/2019] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional regulation plays important roles to fine-tune gene expression in bacteria. In particular, regulation of type I toxin-antitoxin (TA) systems is achieved through sophisticated mechanisms involving toxin mRNA folding. Here, we set up a genetic approach to decipher the molecular underpinnings behind the regulation of a type I TA in Helicobacter pylori. We used the lethality induced by chromosomal inactivation of the antitoxin to select mutations that suppress toxicity. We found that single point mutations are sufficient to allow cell survival. Mutations located either in the 5’ untranslated region or within the open reading frame of the toxin hamper its translation by stabilizing stem-loop structures that sequester the Shine-Dalgarno sequence. We propose that these short hairpins correspond to metastable structures that are transiently formed during transcription to avoid premature toxin expression. This work uncovers the co-transcriptional inhibition of translation as an additional layer of TA regulation in bacteria.
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Affiliation(s)
- Sara Masachis
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, Bordeaux, France
| | - Nicolas J Tourasse
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, Bordeaux, France
| | - Claire Lays
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, Bordeaux, France
| | - Marion Faucher
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, Bordeaux, France
| | - Sandrine Chabas
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, Bordeaux, France
| | - Isabelle Iost
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, Bordeaux, France
| | - Fabien Darfeuille
- University of Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, Bordeaux, France
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25
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Abstract
A fundamental question in contemporary neuroscience is how the remarkable cellular diversity required for the intricate function of the nervous system is achieved. Here, we bridge the gap between a cellular machinery that is known to diversify the transcriptome and the existence of distinct neuronal populations that compose the Drosophila brain. Adenosine-to-inosine (A-to-I) RNA editing is a ubiquitous mechanism that generates transcriptomic diversity in cells by recoding certain adenosines within the pre-mRNA sequence into inosines. We present a spatial map of RNA editing across different neuronal populations in Drosophila brain. Each neuronal population has a distinct editing signature, with the majority of differential editing occurring in highly conserved regions of transcripts that encode ion channels and other essential neuronal genes. Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a ubiquitous mechanism that generates transcriptomic diversity. This process is particularly important for proper neuronal function; however, little is known about how RNA editing is dynamically regulated between the many functionally distinct neuronal populations of the brain. Here, we present a spatial RNA editing map in the Drosophila brain and show that different neuronal populations possess distinct RNA editing signatures. After purifying and sequencing RNA from genetically marked groups of neuronal nuclei, we identified a large number of editing sites and compared editing levels in hundreds of transcripts across nine functionally different neuronal populations. We found distinct editing repertoires for each population, including sites in repeat regions of the transcriptome and differential editing in highly conserved and likely functional regions of transcripts that encode essential neuronal genes. These changes are site-specific and not driven by changes in Adar expression, suggesting a complex, targeted regulation of editing levels in key transcripts. This fine-tuning of the transcriptome between different neurons by RNA editing may account for functional differences between distinct populations in the brain.
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26
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John D, Weirick T, Dimmeler S, Uchida S. RNAEditor: easy detection of RNA editing events and the introduction of editing islands. Brief Bioinform 2018; 18:993-1001. [PMID: 27694136 DOI: 10.1093/bib/bbw087] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Indexed: 12/30/2022] Open
Abstract
RNA editing of adenosine residues to inosine ('A-to-I editing') is the most common RNA modification event detectible with RNA sequencing (RNA-seq). While not directly detectable, inosine is read by next-generation sequencers as guanine. Therefore, mapping RNA-seq reads to their corresponding reference genome can detect potential editing events by identifying 'A-to-G' conversions. However, one must exercise caution when searching for editing sites, as A-to-G conversions also arise from sequencing errors as well as mutations. To address these complexities, several algorithms and software products have been developed to accurately identify editing events. Here, we survey currently available methods to analyze RNA editing events and introduce a new easy-to-use bioinformatics tool 'RNAEditor' for the detection of RNA editing events. During the development of RNAEditor, we noticed editing often happened in clusters, which we named 'editing islands'. We developed a clustering algorithm to find editing islands and included it in RNAEditor. RNAEditor is freely available at http://rnaeditor.uni-frankfurt.de. We anticipate that RNAEditor will provide biologists with an easy-to-use tool for studying RNA editing events and the newly defined editing islands.
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27
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Hsiao YHE, Bahn JH, Yang Y, Lin X, Tran S, Yang EW, Quinones-Valdez G, Xiao X. RNA editing in nascent RNA affects pre-mRNA splicing. Genome Res 2018; 28:812-823. [PMID: 29724793 PMCID: PMC5991522 DOI: 10.1101/gr.231209.117] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/26/2018] [Indexed: 12/21/2022]
Abstract
In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress in understanding their global RNA targets and regulatory pathways. However, the interplay between individual steps of RNA processing, an essential aspect of gene regulation, remains poorly understood. By sequencing the RNA of different subcellular fractions, we examined the timing of adenosine-to-inosine (A-to-I) RNA editing and its impact on alternative splicing. We observed that >95% A-to-I RNA editing events occurred in the chromatin-associated RNA prior to polyadenylation. We report about 500 editing sites in the 3' acceptor sequences that can alter splicing of the associated exons. These exons are highly conserved during evolution and reside in genes with important cellular function. Furthermore, we identified a second class of exons whose splicing is likely modulated by RNA secondary structures that are recognized by the RNA editing machinery. The genome-wide analyses, supported by experimental validations, revealed remarkable interplay between RNA editing and splicing and expanded the repertoire of functional RNA editing sites.
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Affiliation(s)
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yun Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Xianzhi Lin
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Stephen Tran
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Ei-Wen Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
| | | | - Xinshu Xiao
- Department of Bioengineering
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
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28
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Bakhtiarizadeh MR, Salehi A, Rivera RM. Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing. PLoS One 2018; 13:e0193316. [PMID: 29470549 PMCID: PMC5823453 DOI: 10.1371/journal.pone.0193316] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/08/2018] [Indexed: 12/30/2022] Open
Abstract
RNA editing increases the diversity of the transcriptome and proteome. Adenosine-to-inosine (A-to-I) editing is the predominant type of RNA editing in mammals and it is catalyzed by the adenosine deaminases acting on RNA (ADARs) family. Here, we used a largescale computational analysis of transcriptomic data from brain, heart, colon, lung, spleen, kidney, testes, skeletal muscle and liver, from three adult animals in order to identify RNA editing sites in bovine. We developed a computational pipeline and used a rigorous strategy to identify novel editing sites from RNA-Seq data in the absence of corresponding DNA sequence information. Our methods take into account sequencing errors, mapping bias, as well as biological replication to reduce the probability of obtaining a false-positive result. We conducted a detailed characterization of sequence and structural features related to novel candidate sites and found 1,600 novel canonical A-to-I editing sites in the nine bovine tissues analyzed. Results show that these sites 1) occur frequently in clusters and short interspersed nuclear elements (SINE) repeats, 2) have a preference for guanines depletion/enrichment in the flanking 5′/3′ nucleotide, 3) occur less often in coding sequences than other regions of the genome, and 4) have low evolutionary conservation. Further, we found that a positive correlation exists between expression of ADAR family members and tissue-specific RNA editing. Most of the genes with predicted A-to-I editing in each tissue were significantly enriched in biological terms relevant to the function of the corresponding tissue. Lastly, the results highlight the importance of the RNA editome in nervous system regulation. The present study extends the list of RNA editing sites in bovine and provides pipelines that may be used to investigate the editome in other organisms.
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Affiliation(s)
| | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Rocío Melissa Rivera
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
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29
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Duan Y, Dou S, Zhang H, Wu C, Wu M, Lu J. Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution. Mol Biol Evol 2018; 35:132-148. [PMID: 29048557 PMCID: PMC5850729 DOI: 10.1093/molbev/msx274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The adenosine-to-inosine (A-to-I) RNA editomes have been systematically characterized in various metazoan species, and many editing sites were found in clusters. However, it remains unclear whether the clustered editing sites tend to be linked in the same RNA molecules or not. By adopting a method originally designed to detect linkage disequilibrium of DNA mutations, we examined the editomes of ten metazoan species and detected extensive linkage of editing in Drosophila and cephalopods. The prevalent linkages of editing in these two clades, many of which are conserved between closely related species and might be associated with the adaptive proteomic recoding, are maintained by natural selection at the cost of genome evolution. Nevertheless, in worms and humans, we only detected modest proportions of linked editing events, the majority of which were not conserved. Furthermore, the linkage of editing in coding regions of worms and humans might be overall deleterious, which drives the evolution of DNA sites to escape promiscuous editing. Altogether, our results suggest that the linkage landscape of A-to-I editing has evolved during metazoan evolution. This present study also suggests that linkage of editing should be considered in elucidating the functional consequences of RNA editing.
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Mingming Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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30
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Meyer IM. In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression. Methods 2017; 120:3-16. [PMID: 28433606 DOI: 10.1016/j.ymeth.2017.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/16/2017] [Accepted: 04/14/2017] [Indexed: 01/26/2023] Open
Abstract
RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts. The picture that now emerges is that RNA structures constitute an additional layer of information that can be encoded in any RNA transcript (and on top of other layers of information such as protein-context) in order to exert a wide range of functional roles. Moreover, different encoded RNA structures can be expressed at different stages of a transcript's life in order to alter the transcript's behaviour depending on its actual cellular context. Similar to the concept of alternative splicing for protein-coding genes, where a single transcript can yield different proteins depending on cellular context, it is thus appropriate to propose the notion of alternative RNA structure expression for any given transcript. This review introduces several computational strategies that my group developed to detect different aspects of RNA structure expression in vivo. Two aspects are of particular interest to us: (1) RNA secondary structure features that emerge during co-transcriptional folding and (2) functional RNA structure features that are expressed at different times of a transcript's life and potentially mutually exclusive.
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Affiliation(s)
- Irmtraud M Meyer
- Laboratory of Bioinformatics of RNA Structure and Transcriptome Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin-Buch, Germany; Institute of Chemistry and Biochemistry, Free University, Thielallee 63, 14195 Berlin, Germany.
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Thomas JM, Beal PA. How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs. Bioessays 2017; 39. [PMID: 28217931 DOI: 10.1002/bies.201600187] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Deamination of adenosine in RNA to form inosine has wide ranging consequences on RNA function including amino acid substitution to give proteins not encoded in the genome. What determines which adenosines in an mRNA are subject to this modification reaction? The answer lies in an understanding of the mechanism and substrate recognition properties of adenosine deaminases that act on RNA (ADARs). Our recent publication of X-ray crystal structures of the human ADAR2 deaminase domain bound to RNA editing substrates shed considerable light on how the catalytic domains of these enzymes bind RNA and promote adenosine deamination. Here we review in detail the deaminase domain-RNA contact surfaces and present models of how full length ADARs, bearing double stranded RNA-binding domains (dsRBDs) and deaminase domains, could process naturally occurring substrate RNAs.
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Affiliation(s)
- Justin M Thomas
- Department of Chemistry, University of California, Davis, CA, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, CA, USA
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Gong J, Liu C, Liu W, Xiang Y, Diao L, Guo AY, Han L. LNCediting: a database for functional effects of RNA editing in lncRNAs. Nucleic Acids Res 2016; 45:D79-D84. [PMID: 27651464 PMCID: PMC5210611 DOI: 10.1093/nar/gkw835] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 01/23/2023] Open
Abstract
RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome. To provide a useful resource for the functional effects of RNA editing in long noncoding RNAs (lncRNAs), we systematically analyzed the A-to-I editing sites in lncRNAs across human, rhesus, mouse, and fly, and observed an appreciable number of RNA editing sites which can significantly impact the secondary structures of lncRNAs and lncRNA–miRNA interactions. All the data were compiled into LNCediting, a user-friendly database (http://bioinfo.life.hust.edu.cn/LNCediting/). LNCediting provides customized tools to predict functional effects of novel editing sites in lncRNAs. We hope that it will become an important resource for exploring functions of RNA editing sites in lncRNAs.
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Affiliation(s)
- Jing Gong
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Chunjie Liu
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Wei Liu
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
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