1
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Zhu Z, Lu J. Development and assessment of an RNA editing-based risk model for the prognosis of cervical cancer patients. Medicine (Baltimore) 2024; 103:e38116. [PMID: 38728474 PMCID: PMC11081546 DOI: 10.1097/md.0000000000038116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
RNA editing, as an epigenetic mechanism, exhibits a strong correlation with the occurrence and development of cancers. Nevertheless, few studies have been conducted to investigate the impact of RNA editing on cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). In order to study the connection between RNA editing and CESC patients' prognoses, we obtained CESC-related information from The Cancer Genome Atlas (TCGA) database and randomly allocated the patients into the training group or testing group. An RNA editing-based risk model for CESC patients was established by Cox regression analysis and least absolute shrinkage and selection operator (LASSO). According to the median score generated by this RNA editing-based risk model, patients were categorized into subgroups with high and low risks. We further constructed the nomogram by risk scores and clinical characteristics and analyzed the impact of RNA editing levels on host gene expression levels and adenosine deaminase acting on RNA. Finally, we also compared the biological functions and pathways of differentially expressed genes (DEGs) between different subgroups by enrichment analysis. In this risk model, we screened out 6 RNA editing sites with significant prognostic value. The constructed nomogram performed well in forecasting patients' prognoses. Furthermore, the level of RNA editing at the prognostic site exhibited a strong correlation with host gene expression. In the high-risk subgroup, we observed multiple biological functions and pathways associated with immune response, cell proliferation, and tumor progression. This study establishes an RNA editing-based risk model that helps forecast patients' prognoses and offers a new understanding of the underlying mechanism of RNA editing in CESC.
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Affiliation(s)
- Zihan Zhu
- Department of Biostatistics, School of Public Health, Nanjing Medical University 101 Longmian Avenue, Nanjing, P.R. China
| | - Jing Lu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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2
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Li W, Bu M, Hu R, Jiang S, Chen L, Somero GN. Tissue-specific temperature dependence of RNA editing levels in zebrafish. BMC Biol 2023; 21:262. [PMID: 37981664 PMCID: PMC10659053 DOI: 10.1186/s12915-023-01738-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/16/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND RNA editing by adenosine deaminase acting on RNA (ADAR) occurs in all metazoans and fulfils several functions. Here, we examined effects of acclimation temperature (27 °C, 18 °C,13 °C) on editing patterns in six tissues of zebrafish (Danio rerio). RESULTS Sites and total amounts of editing differed among tissues. Brain showed the highest levels, followed by gill and skin. In these highly edited tissues, decreases in temperatures led to large increases in total amounts of editing and changes in specific edited sites. Gene ontology analysis showed both similarities (e.g., endoplasmic reticulum stress response) and differences in editing among tissues. The majority of edited sites were in transcripts of transposable elements and the 3'UTR regions of protein coding genes. By experimental validation, translation efficiency was directly related to extent of editing of the 3'UTR region of an mRNA. CONCLUSIONS RNA editing increases 3'UTR polymorphism and affects efficiency of translation. Such editing may lead to temperature-adaptive changes in the proteome through altering relative amounts of synthesis of different proteins.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Mengdi Bu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Ruiqin Hu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.
- International Research Center for Marine Biosciences, Ministry of Science and Technology, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China.
| | - George N Somero
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, 93950, USA.
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3
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Mahapatra A, Dhakal A, Noguchi A, Vadlamani P, Hundley HA. ADAR-mediated regulation of PQM-1 expression in neurons impacts gene expression throughout C. elegans and regulates survival from hypoxia. PLoS Biol 2023; 21:e3002150. [PMID: 37747897 PMCID: PMC10553819 DOI: 10.1371/journal.pbio.3002150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/05/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA-binding protein (RBP), ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RBP, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia, phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important posttranscriptional gene regulatory mechanism in Caenorhabditis elegans that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
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Affiliation(s)
- Ananya Mahapatra
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington, Indiana, United States of America
| | - Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine–Bloomington, Bloomington, Indiana, United States of America
| | - Aika Noguchi
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine–Bloomington, Bloomington, Indiana, United States of America
| | - Heather A. Hundley
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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4
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Rangan KJ, Reck-Peterson SL. RNA recoding in cephalopods tailors microtubule motor protein function. Cell 2023; 186:2531-2543.e11. [PMID: 37295401 PMCID: PMC10467349 DOI: 10.1016/j.cell.2023.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/05/2023] [Accepted: 04/24/2023] [Indexed: 06/12/2023]
Abstract
RNA editing is a widespread epigenetic process that can alter the amino acid sequence of proteins, termed "recoding." In cephalopods, most transcripts are recoded, and recoding is hypothesized to be an adaptive strategy to generate phenotypic plasticity. However, how animals use RNA recoding dynamically is largely unexplored. We investigated the function of cephalopod RNA recoding in the microtubule motor proteins kinesin and dynein. We found that squid rapidly employ RNA recoding in response to changes in ocean temperature, and kinesin variants generated in cold seawater displayed enhanced motile properties in single-molecule experiments conducted in the cold. We also identified tissue-specific recoded squid kinesin variants that displayed distinct motile properties. Finally, we showed that cephalopod recoding sites can guide the discovery of functional substitutions in non-cephalopod kinesin and dynein. Thus, RNA recoding is a dynamic mechanism that generates phenotypic plasticity in cephalopods and can inform the characterization of conserved non-cephalopod proteins.
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Affiliation(s)
- Kavita J Rangan
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | - Samara L Reck-Peterson
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
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5
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Mahapatra A, Dhakal A, Noguchi A, Vadlamani P, Hundley HA. ADARs employ a neural-specific mechanism to regulate PQM-1 expression and survival from hypoxia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539519. [PMID: 37205482 PMCID: PMC10187282 DOI: 10.1101/2023.05.05.539519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA binding protein, ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RNA binding protein, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia; phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important post-transcriptional gene regulatory mechanism that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
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Affiliation(s)
- Ananya Mahapatra
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington IN, 47405 USA
| | - Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine – Bloomington, Bloomington IN, 47405 USA
| | - Aika Noguchi
- Department of Biology, Indiana University, Bloomington IN 47405 USA
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine – Bloomington, Bloomington IN, 47405 USA
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6
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Morelli KH, Smargon AA, Yeo GW. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders. RNA (NEW YORK, N.Y.) 2023; 29:489-497. [PMID: 36693761 PMCID: PMC10019361 DOI: 10.1261/rna.079519.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Disruptions in RNA processing play critical roles in the pathogenesis of neurological diseases. In this Perspective, we discuss recent progress in the development of RNA-targeting therapeutic modalities. We focus on progress, limitations, and opportunities in a new generation of therapies engineered from RNA binding proteins and other endogenous RNA regulatory macromolecules to treat human neurological disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
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7
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Somero GN. Turning a page: remaining a top competitor in an evolving publication ecosystem. J Exp Biol 2023; 226:286582. [PMID: 36637438 DOI: 10.1242/jeb.245153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Journal of Experimental Biology (JEB) is celebrating its first 100 years this year. My own relationship with the journal spans over six decades and encompasses a variety of roles: reader, author, Editor (1995-2000), Editorial Advisory Board member (2000 to present) and Director on the board of its publisher, The Company of Biologists (2003-2009). I was therefore delighted when the journal Editors asked me to write a Perspective to reflect on how the journal and the publishing environment in which it competes have evolved over this long period, and to peek into my crystal ball and comment on what the future might hold for the journal and the primary fields it covers: comparative-environmental-evolutionary physiology, neuroethology and biomechanics.
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Affiliation(s)
- George N Somero
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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8
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Çakır U, Gabed N, Brunet M, Roucou X, Kryvoruchko I. Mosaic translation hypothesis: chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability. FEBS J 2023; 290:370-378. [PMID: 34743413 DOI: 10.1111/febs.16269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/03/2021] [Accepted: 11/05/2021] [Indexed: 02/05/2023]
Abstract
How many different proteins can be produced from a single spliced transcript? Genome annotation projects overlook the coding potential of reading frames other than that of the reference open reading frames (refORFs). Recently, alternative open reading frames (altORFs) and their translational products, alternative proteins, have been shown to carry out important functions in various organisms. AltORFs overlapping refORFs or other altORFs in a different reading frame may be involved in one fundamental mechanism so far overlooked. A few years ago, it was proposed that altORFs may act as building blocks for chimeric (mosaic) polypeptides, which are produced via multiple ribosomal frameshifting events from a single mature transcript. We adopt terminology from that earlier discussion and call this mechanism mosaic translation. This way of extracting and combining genetic information may significantly increase proteome diversity. Thus, we hypothesize that this mechanism may have contributed to the flexibility and adaptability of organisms to a variety of environmental conditions. Specialized ribosomes acting as sensors probably played a central role in this process. Importantly, mosaic translation may be the main source of protein diversity in genomes that lack alternative splicing. The idea of mosaic translation is a testable hypothesis, although its direct demonstration is challenging. Should mosaic translation occur, we would currently highly underestimate the complexity of translation mechanisms and thus the proteome.
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Affiliation(s)
- Umut Çakır
- Molecular Biology and Genetics Department, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Noujoud Gabed
- Cellular and Molecular Biology Department, Oran High School of Biological Sciences (ESSBO), Oran, Algeria
| | - Marie Brunet
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, QC, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), QC, Canada
| | - Xavier Roucou
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), QC, Canada.,Department of Biochemistry and Functional Genomics, Université de Sherbrooke, QC, Canada
| | - Igor Kryvoruchko
- Molecular Biology and Genetics Department, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
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9
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Cuddleston WH, Fan X, Sloofman L, Liang L, Mossotto E, Moore K, Zipkowitz S, Wang M, Zhang B, Wang J, Sestan N, Devlin B, Roeder K, Sanders SJ, Buxbaum JD, Breen MS. Spatiotemporal and genetic regulation of A-to-I editing throughout human brain development. Cell Rep 2022; 41:111585. [PMID: 36323256 PMCID: PMC9704047 DOI: 10.1016/j.celrep.2022.111585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 07/06/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Posttranscriptional RNA modifications by adenosine-to-inosine (A-to-I) editing are abundant in the brain, yet elucidating functional sites remains challenging. To bridge this gap, we investigate spatiotemporal and genetically regulated A-to-I editing sites across prenatal and postnatal stages of human brain development. More than 10,000 spatiotemporally regulated A-to-I sites were identified that occur predominately in 3' UTRs and introns, as well as 37 sites that recode amino acids in protein coding regions with precise changes in editing levels across development. Hyper-edited transcripts are also enriched in the aging brain and stabilize RNA secondary structures. These features are conserved in murine and non-human primate models of neurodevelopment. Finally, thousands of cis-editing quantitative trait loci (edQTLs) were identified with unique regulatory effects during prenatal and postnatal development. Collectively, this work offers a resolved atlas linking spatiotemporal variation in editing levels to genetic regulatory effects throughout distinct stages of brain maturation.
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Affiliation(s)
- Winston H Cuddleston
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xuanjia Fan
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lindsay Liang
- Department of Psychiatry and Behavioral Sciences and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Enrico Mossotto
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kendall Moore
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah Zipkowitz
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Icahn Institute for Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Comparative Medicine, Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, CT 06510, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA
| | - Kathryn Roeder
- Carnegie Mellon University, Statistics & Data Science Department, Pittsburgh, PA 15213, USA
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael S Breen
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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10
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Genome and transcriptome mechanisms driving cephalopod evolution. Nat Commun 2022; 13:2427. [PMID: 35508532 PMCID: PMC9068888 DOI: 10.1038/s41467-022-29748-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 03/28/2022] [Indexed: 11/27/2022] Open
Abstract
Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing. “Cephalopods are known for their large nervous systems, complex behaviors, and morphological innovations. Here, the authors find that soft-bodied cephalopod genomes are more rearranged than other extant molluscs and that mRNA editing patterns are associated with the nervous system and repetitive elements”.
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11
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Shoshan Y, Liscovitch-Brauer N, Rosenthal JJC, Eisenberg E. Adaptive Proteome Diversification by Nonsynonymous A-to-I RNA Editing in Coleoid Cephalopods. Mol Biol Evol 2021; 38:3775-3788. [PMID: 34022057 PMCID: PMC8382921 DOI: 10.1093/molbev/msab154] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
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Affiliation(s)
- Yoav Shoshan
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | - Noa Liscovitch-Brauer
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
| | | | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
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12
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Vesely C, Jantsch MF. An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing. Genes (Basel) 2021; 12:1026. [PMID: 34356042 PMCID: PMC8304401 DOI: 10.3390/genes12071026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-editing by adenosine deaminases acting on RNA (ADARs) converts adenosines to inosines in structured RNAs. Inosines are read as guanosines by most cellular machineries. A to I editing has two major functions: first, marking endogenous RNAs as "self", therefore helping the innate immune system to distinguish repeat- and endogenous retrovirus-derived RNAs from invading pathogenic RNAs; and second, recoding the information of the coding RNAs, leading to the translation of proteins that differ from their genomically encoded versions. It is obvious that these two important biological functions of ADARs will differ during development, in different tissues, upon altered physiological conditions or after exposure to pathogens. Indeed, different levels of ADAR-mediated editing have been observed in different tissues, as a response to altered physiology or upon pathogen exposure. In this review, we describe the dynamics of A to I editing and summarize the known and likely mechanisms that will lead to global but also substrate-specific regulation of A to I editing.
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Affiliation(s)
| | - Michael F. Jantsch
- Division of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria;
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13
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Li X, Wu J, Xiao X, Rong Y, Yang H, Li J, Zhou Q, Zhou W, Shi J, Qi H, Du H. Characterization and complexity of transcriptome in Gymnocypris przewalskii using single-molecule long-read sequencing and RNA-seq. DNA Res 2021; 28:6275749. [PMID: 33989386 PMCID: PMC8320875 DOI: 10.1093/dnares/dsab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/11/2021] [Indexed: 11/30/2022] Open
Abstract
The Tibetan Schizothoracinae fish Gymnocypris przewalskii has the ability to adapt to the extreme plateau environment, making it an ideal biological material for evolutionary biology research. However, the lack of well-annotated reference genomes has limited the study of the molecular genetics of G. przewalskii. To characterize its transcriptome features, we first used long-read sequencing technology in combination with RNA-seq for transcriptomic analysis. A total of 159,053 full-length (FL) transcripts were captured by Iso-Seq, having a mean length of 3,445 bp with N50 value of 4,348. Of all FL transcripts, 145,169 were well-annotated in the public database and 134,537 contained complete open reading frames. There were 4,149 pairs of alternative splicing events, of which three randomly selected were defined by RT–PCR and sequencing, and 13,293 long non-coding RNAs detected, based on all-vs.-all BLAST. A total of 118,185 perfect simple sequence repeats were identified from FL transcripts. The FL transcriptome might provide basis for further research of G. przewalskii.
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Affiliation(s)
- Xindan Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Jinming Wu
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Xinping Xiao
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Yifeng Rong
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Haile Yang
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Junyi Li
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Qiong Zhou
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China
| | - Weiguo Zhou
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Jianquan Shi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hongfang Qi
- The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
| | - Hao Du
- Key Laboratory of freshwater biodiversity conservation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China.,College of Marine Science, Shanghai Ocean University, Shanghai 201306, China.,The Rescue and Rehabilitation Center of Naked Carps in Lake Qinghai, Xining, Qinghai 810016, China
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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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Malik TN, Doherty EE, Gaded VM, Hill TM, Beal PA, Emeson RB. Regulation of RNA editing by intracellular acidification. Nucleic Acids Res 2021; 49:4020-4036. [PMID: 33721028 PMCID: PMC8053123 DOI: 10.1093/nar/gkab157] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/03/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022] Open
Abstract
The hydrolytic deamination of adenosine-to-inosine (A-to-I) by RNA editing is a widespread post-transcriptional modification catalyzed by the adenosine deaminase acting on RNA (ADAR) family of proteins. ADAR-mediated RNA editing modulates cellular pathways involved in innate immunity, RNA splicing, RNA interference, and protein recoding, and has been investigated as a strategy for therapeutic intervention of genetic disorders. Despite advances in basic and translational research, the mechanisms regulating RNA editing are poorly understood. Though several trans-acting regulators of editing have been shown to modulate ADAR protein expression, previous studies have not identified factors that modulate ADAR catalytic activity. Here, we show that RNA editing increases upon intracellular acidification, and that these effects are predominantly explained by both enhanced ADAR base-flipping and deamination rate at acidic pH. We also show that the extent of RNA editing increases with the reduction in pH associated with conditions of cellular hypoxia.
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Affiliation(s)
- Turnee N Malik
- Training Program in Neuroscience, Vanderbilt University, Nashville, TN 37232, USA
| | - Erin E Doherty
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
| | - Vandana M Gaded
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
| | - Theodore M Hill
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
| | - Ronald B Emeson
- Training Program in Neuroscience, Vanderbilt University, Nashville, TN 37232, USA.,Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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16
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Breton S, Ghiselli F, Milani L. Mitochondrial Short-Term Plastic Responses and Long-Term Evolutionary Dynamics in Animal Species. Genome Biol Evol 2021; 13:6248094. [PMID: 33892508 PMCID: PMC8290114 DOI: 10.1093/gbe/evab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
How do species respond or adapt to environmental changes? The answer to this depends partly on mitochondrial epigenetics and genetics, new players in promoting adaptation to both short- and long-term environmental changes. In this review, we explore how mitochondrial epigenetics and genetics mechanisms, such as mtDNA methylation, mtDNA-derived noncoding RNAs, micropeptides, mtDNA mutations, and adaptations, can contribute to animal plasticity and adaptation. We also briefly discuss the challenges in assessing mtDNA adaptive evolution. In sum, this review covers new advances in the field of mitochondrial genomics, many of which are still controversial, and discusses processes still somewhat obscure, and some of which are still quite speculative and require further robust experimentation.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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17
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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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18
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Malik TN, Cartailler JP, Emeson RB. Quantitative Analysis of Adenosine-to-Inosine RNA Editing. Methods Mol Biol 2021; 2181:97-111. [PMID: 32729077 DOI: 10.1007/978-1-0716-0787-9_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The conversion of adenosine to inosine (A to I) by RNA editing represents a common posttranscriptional mechanism for diversification of both the transcriptome and proteome, and is a part of the cellular response for innate immune tolerance. Due to its preferential base-pairing with cytosine (C), inosine (I) is recognized as guanosine (G) by reverse transcriptase, as well as the cellular splicing and translation machinery. A-to-I editing events appear as A-G discrepancies between genomic DNA and cDNA sequences. Molecular analyses of RNA editing have leveraged these nucleoside differences to quantify RNA editing in ensemble populations of RNA transcripts and within individual cDNAs using high-throughput sequencing or Sanger sequencing-derived analysis of electropherogram peak heights. Here, we briefly review and compare these methods of RNA editing quantification, as well as provide experimental protocols by which such analyses may be achieved.
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Affiliation(s)
- Turnee N Malik
- Training Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jean-Philippe Cartailler
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ronald B Emeson
- Training Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA. .,Departments of Pharmacology, Biochemistry and Psychiatry & Behavioral Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.
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19
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Erdmann EA, Mahapatra A, Mukherjee P, Yang B, Hundley HA. To protect and modify double-stranded RNA - the critical roles of ADARs in development, immunity and oncogenesis. Crit Rev Biochem Mol Biol 2020; 56:54-87. [PMID: 33356612 DOI: 10.1080/10409238.2020.1856768] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) are present in all animals and function to both bind double-stranded RNA (dsRNA) and catalyze the deamination of adenosine (A) to inosine (I). As inosine is a biological mimic of guanosine, deamination by ADARs changes the genetic information in the RNA sequence and is commonly referred to as RNA editing. Millions of A-to-I editing events have been reported for metazoan transcriptomes, indicating that RNA editing is a widespread mechanism used to generate molecular and phenotypic diversity. Loss of ADARs results in lethality in mice and behavioral phenotypes in worm and fly model systems. Furthermore, alterations in RNA editing occur in over 35 human pathologies, including several neurological disorders, metabolic diseases, and cancers. In this review, a basic introduction to ADAR structure and target recognition will be provided before summarizing how ADARs affect the fate of cellular RNAs and how researchers are using this knowledge to engineer ADARs for personalized medicine. In addition, we will highlight the important roles of ADARs and RNA editing in innate immunity and cancer biology.
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Affiliation(s)
- Emily A Erdmann
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Priyanka Mukherjee
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
| | - Boyoon Yang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
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20
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Molecular Plasticity in Animal Pigmentation: Emerging Processes Underlying Color Changes. Integr Comp Biol 2020; 60:1531-1543. [DOI: 10.1093/icb/icaa142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synopsis
Animal coloration has been rigorously studied and has provided morphological implications for fitness with influences over social behavior, predator–prey interactions, and sexual selection. In vertebrates, its study has developed our understanding across diverse fields ranging from behavior to molecular biology. In the search for underlying molecular mechanisms, many have taken advantage of pedigree-based and genome-wide association screens to reveal the genetic architecture responsible for pattern variation that occurs in early development. However, genetic differences do not provide a full picture of the dynamic changes in coloration that are most prevalent across vertebrates at the molecular level. Changes in coloration that occur in adulthood via phenotypic plasticity rely on various social, visual, and dietary cues independent of genetic variation. Here, I will review the contributions of pigment cell biology to animal color changes and recent studies describing their molecular underpinnings and function. In this regard, conserved epigenetic processes such as DNA methylation play a role in lending plasticity to gene regulation as it relates to chromatophore function. Lastly, I will present African cichlids as emerging models for the study of pigmentation and molecular plasticity for animal color changes. I posit that these processes, in a dialog with environmental stimuli, are important regulators of variation and the selective advantages that accompany a change in coloration for vertebrate animals.
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21
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Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020; 215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes.
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Affiliation(s)
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405
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22
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Alonso LM, Marder E. Temperature compensation in a small rhythmic circuit. eLife 2020; 9:e55470. [PMID: 32484437 PMCID: PMC7332291 DOI: 10.7554/elife.55470] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/31/2020] [Indexed: 12/28/2022] Open
Abstract
Temperature affects the conductances and kinetics of the ionic channels that underlie neuronal activity. Each membrane conductance has a different characteristic temperature sensitivity, which raises the question of how neurons and neuronal circuits can operate robustly over wide temperature ranges. To address this, we employed computational models of the pyloric network of crabs and lobsters. We produced multiple different models that exhibit a triphasic pyloric rhythm over a range of temperatures and explored the dynamics of their currents and how they change with temperature. Temperature can produce smooth changes in the relative contributions of the currents to neural activity so that neurons and networks undergo graceful transitions in the mechanisms that give rise to their activity patterns. Moreover, responses of the models to deletions of a current can be different at high and low temperatures, indicating that even a well-defined genetic or pharmacological manipulation may produce qualitatively distinct effects depending on the temperature.
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Affiliation(s)
- Leandro M Alonso
- Volen Center and Biology Department, Brandeis UniversityWalthamUnited States
| | - Eve Marder
- Volen Center and Biology Department, Brandeis UniversityWalthamUnited States
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23
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Non-Coding RNAs in Lung Tumor Initiation and Progression. Int J Mol Sci 2020; 21:ijms21082774. [PMID: 32316322 PMCID: PMC7215285 DOI: 10.3390/ijms21082774] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/07/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is one of the deadliest forms of cancer affecting society today. Non-coding RNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), through the transcriptional, post-transcriptional, and epigenetic changes they impose, have been found to be dysregulated to affect lung cancer tumorigenesis and metastasis. This review will briefly summarize hallmarks involved in lung cancer initiation and progression. For initiation, these hallmarks include tumor initiating cells, immortalization, activation of oncogenes and inactivation of tumor suppressors. Hallmarks involved in lung cancer progression include metastasis and drug tolerance and resistance. The targeting of these hallmarks with non-coding RNAs can affect vital metabolic and cell signaling pathways, which as a result can potentially have a role in cancerous and pathological processes. By further understanding non-coding RNAs, researchers can work towards diagnoses and treatments to improve early detection and clinical response.
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24
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Mwanzia VM, Nzei JM, Yan DY, Kamau PW, Chen JM, Li ZZ. The complete chloroplast genomes of two species in threatened monocot genus Caldesia in China. Genetica 2019; 147:381-390. [PMID: 31654262 DOI: 10.1007/s10709-019-00079-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
Caldesia is a genus in the family Alismataceae mainly found in the tropical and temperate regions of the Northern hemisphere. In China, two species, Caldesia parnassifolia, and Caldesia grandis are recorded as critically endangered in sporadic regions. Available protection of the genetic resource of these threatened species has been impeded due to limited genomic information. Here, we sequence the whole chloroplast (cp) genome of the two Caldesia species using high throughput sequencing technology. The whole cp genomes of C. parnassifolia and C. grandis were 167,647 bp and 168,500 bp, respectively with a typical quadripartite structure. There were 115 unique genes with 81 protein-coding genes, 31 tRNA genes, and four rRNA genes. Both species showed a GC content of 37.1%. A duplication of two tRNA genes and a ~ 6 kb inversion region in the LSC was noted in both species. Mononucleotide simple sequence repeats (SSRs) A/T were most abundant for both Caldesia species. High nucleotide variability was recorded in ycf1 gene and trnK-UUU/rps16 intergenic spacer region. All RNA editing conversions were C-U in 23 and 24 protein-coding genes for C. parnassifolia and C. grandis, respectively. Phylogenetic analysis placed both Caldesia species as sister to Sagittaria lichuanensis. This study will be useful for further evolutionary, systematic researches and conservation of the genus Caldesia.
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Affiliation(s)
- Virginia M Mwanzia
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - John M Nzei
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Dong-Ying Yan
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Tibet, China.,College of Science, Tibet University, Tibet, China
| | | | - Jin-Ming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Zhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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25
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Tzelepis K, Rausch O, Kouzarides T. RNA-modifying enzymes and their function in a chromatin context. Nat Struct Mol Biol 2019; 26:858-862. [PMID: 31582848 PMCID: PMC7613430 DOI: 10.1038/s41594-019-0312-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/30/2019] [Indexed: 12/29/2022]
Abstract
Exciting research has connected specific RNA modifications to chromatin, providing evidence for co-transcriptional deposition and function in gene regulation. Here we review insights gained from studying the co-transcriptional roles of RNA modifications, and their influence in normal and disease contexts. We also discuss how the availability of novel technical approaches could raise the translational potential of targeting RNA-modifying enzymes for the treatment of disease.
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Affiliation(s)
- Konstantinos Tzelepis
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - Oliver Rausch
- Storm Therapeutics Ltd, Babraham Research Campus, Cambridge, UK
| | - Tony Kouzarides
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
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26
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Abstract
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance. However, systematic mapping of the editome across the animal kingdom has revealed that most A-to-I editing sites are located within mobile elements in non-coding parts of the genome. Editing of these non-coding sites is thought to have a critical role in protecting against activation of innate immunity by self-transcripts. Both recoding and non-coding events have implications for genome evolution and, when deregulated, may lead to disease. Finally, ADARs are now being adapted for RNA engineering purposes.
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27
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Myszczyński K, Ślipiko M, Sawicki J. Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends. Int J Mol Sci 2019; 20:E2963. [PMID: 31216623 PMCID: PMC6627324 DOI: 10.3390/ijms20122963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/04/2023] Open
Abstract
RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.
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Affiliation(s)
- Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
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28
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Hughes SC, Simmonds AJ. Drosophila mRNA Localization During Later Development: Past, Present, and Future. Front Genet 2019; 10:135. [PMID: 30899273 PMCID: PMC6416162 DOI: 10.3389/fgene.2019.00135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple mechanisms tightly regulate mRNAs during their transcription, translation, and degradation. Of these, the physical localization of mRNAs to specific cytoplasmic regions is relatively easy to detect; however, linking localization to functional regulatory roles has been more difficult to establish. Historically, Drosophila melanogaster is a highly effective model to identify localized mRNAs and has helped identify roles for this process by regulating various cell activities. The majority of the well-characterized functional roles for localizing mRNAs to sub-regions of the cytoplasm have come from the Drosophila oocyte and early syncytial embryo. At present, relatively few functional roles have been established for mRNA localization within the relatively smaller, differentiated somatic cell lineages characteristic of later development, beginning with the cellular blastoderm, and the multiple cell lineages that make up the gastrulating embryo, larva, and adult. This review is divided into three parts—the first outlines past evidence for cytoplasmic mRNA localization affecting aspects of cellular activity post-blastoderm development in Drosophila. The majority of these known examples come from highly polarized cell lineages such as differentiating neurons. The second part considers the present state of affairs where we now know that many, if not most mRNAs are localized to discrete cytoplasmic regions in one or more somatic cell lineages of cellularized embryos, larvae or adults. Assuming that the phenomenon of cytoplasmic mRNA localization represents an underlying functional activity, and correlation with the encoded proteins suggests that mRNA localization is involved in far more than neuronal differentiation. Thus, it seems highly likely that past-identified examples represent only a small fraction of localization-based mRNA regulation in somatic cells. The last part highlights recent technological advances that now provide an opportunity for probing the role of mRNA localization in Drosophila, moving beyond cataloging the diversity of localized mRNAs to a similar understanding of how localization affects mRNA activity.
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Affiliation(s)
- Sarah C Hughes
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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29
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Healy TM, Schulte PM. Patterns of alternative splicing in response to cold acclimation in fish. ACTA ACUST UNITED AC 2019; 222:jeb.193516. [PMID: 30692167 DOI: 10.1242/jeb.193516] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/23/2019] [Indexed: 12/26/2022]
Abstract
Phenotypic plasticity is an important aspect of an organism's response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative, as a result of increases or decreases in the amounts of specific transcripts, or qualitative, as a result of the expression of alternative transcripts from the same gene (e.g. via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold acclimation. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for 426 to 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a set of genes with expression patterns that respond qualitatively to prolonged exposure to cold temperatures across fishes.
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Affiliation(s)
- Timothy M Healy
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| | - Patricia M Schulte
- The University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
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30
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Abstract
Long double-stranded RNAs (dsRNAs) are abundantly expressed in animals, in which they frequently occur in introns and 3' untranslated regions of mRNAs. Functions of long, cellular dsRNAs are poorly understood, although deficiencies in adenosine deaminases that act on RNA, or ADARs, promote their recognition as viral dsRNA and an aberrant immune response. Diverse dsRNA-binding proteins bind cellular dsRNAs, hinting at additional roles. Understanding these roles is facilitated by mapping the genomic locations that express dsRNA in various tissues and organisms. ADAR editing provides a signature of dsRNA structure in cellular transcripts. In this review, we detail approaches to map ADAR editing sites and dsRNAs genome-wide, with particular focus on high-throughput sequencing methods and considerations for their successful application to the detection of editing sites and dsRNAs.
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Affiliation(s)
- Daniel P Reich
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112
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31
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Stillman JH. Heat Waves, the New Normal: Summertime Temperature Extremes Will Impact Animals, Ecosystems, and Human Communities. Physiology (Bethesda) 2019; 34:86-100. [DOI: 10.1152/physiol.00040.2018] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A consequence of climate change is the increased frequency and severity of extreme heat waves. This is occurring now as most of the warmest summers and most intense heat waves ever recorded have been during the past decade. In this review, I describe the ways in which animals and human populations are likely to respond to increased extreme heat, suggest how to study those responses, and reflect on the importance of those studies for countering the devastating impacts of climate change.
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Affiliation(s)
- Jonathon H. Stillman
- Estuary and Ocean Science Center and Department of Biology, San Francisco State University, San Francisco, California
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32
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Handley MT, Reddy K, Wills J, Rosser E, Kamath A, Halachev M, Falkous G, Williams D, Cox P, Meynert A, Raymond ES, Morrison H, Brown S, Allan E, Aligianis I, Jackson AP, Ramsahoye BH, von Kriegsheim A, Taylor RW, Finch AJ, FitzPatrick DR. ITPase deficiency causes a Martsolf-like syndrome with a lethal infantile dilated cardiomyopathy. PLoS Genet 2019; 15:e1007605. [PMID: 30856165 PMCID: PMC6428344 DOI: 10.1371/journal.pgen.1007605] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 03/21/2019] [Accepted: 12/27/2018] [Indexed: 12/30/2022] Open
Abstract
Typical Martsolf syndrome is characterized by congenital cataracts, postnatal microcephaly, developmental delay, hypotonia, short stature and biallelic hypomorphic mutations in either RAB3GAP1 or RAB3GAP2. Genetic analysis of 85 unrelated "mutation negative" probands with Martsolf or Martsolf-like syndromes identified two individuals with different homozygous null mutations in ITPA, the gene encoding inosine triphosphate pyrophosphatase (ITPase). Both probands were from multiplex families with a consistent, lethal and highly distinctive disorder; a Martsolf-like syndrome with infantile-onset dilated cardiomyopathy. Severe ITPase-deficiency has been previously reported with infantile epileptic encephalopathy (MIM 616647). ITPase acts to prevent incorporation of inosine bases (rI/dI) into RNA and DNA. In Itpa-null cells dI was undetectable in genomic DNA. dI could be identified at a low level in mtDNA without detectable mitochondrial genome instability, mtDNA depletion or biochemical dysfunction of the mitochondria. rI accumulation was detectable in proband-derived lymphoblastoid RNA. In Itpa-null mouse embryos rI was detectable in the brain and kidney with the highest level seen in the embryonic heart (rI at 1 in 385 bases). Transcriptome and proteome analysis in mutant cells revealed no major differences with controls. The rate of transcription and the total amount of cellular RNA also appeared normal. rI accumulation in RNA-and by implication rI production-correlates with the severity of organ dysfunction in ITPase deficiency but the basis of the cellulopathy remains cryptic. While we cannot exclude cumulative minor effects, there are no major anomalies in the production, processing, stability and/or translation of mRNA.
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Affiliation(s)
- Mark T. Handley
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Section of Genetics, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kigndom
| | - Kaalak Reddy
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- University of Florida College of Medicine, Center for NeuroGenetics, Gainesville, United States of America
| | - Jimi Wills
- Edinburgh Cancer Research Centre, MRC Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond St Hospital, London, United Kingdom
| | - Archith Kamath
- Medical School, University of Oxford, John Radcliffe Hospital Oxford United Kingdom
| | - Mihail Halachev
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Denise Williams
- Department of Clinical Genetics, Birmingham Women's and Children's NHSFT, Birmingham, United Kingdom
| | - Phillip Cox
- Department of Histopathology, Birmingham Women's and Children's NHSFT, Birmingham United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Eleanor S. Raymond
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Harris Morrison
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Brown
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Emma Allan
- CBS-IGMM Transgenic Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Irene Aligianis
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew P. Jackson
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Bernard H. Ramsahoye
- Centre for Genetic and Experimental Medicine, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex von Kriegsheim
- Edinburgh Cancer Research Centre, MRC Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew J. Finch
- Edinburgh Cancer Research Centre, MRC Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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33
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Sharma S, Wang J, Alqassim E, Portwood S, Cortes Gomez E, Maguire O, Basse PH, Wang ES, Segal BH, Baysal BE. Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells. Genome Biol 2019; 20:37. [PMID: 30791937 PMCID: PMC6383285 DOI: 10.1186/s13059-019-1651-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 02/12/2019] [Indexed: 12/30/2022] Open
Abstract
Background Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes and macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear. Results Here, we show that the related cytidine deaminase, APOBEC3G, induces site-specific C-to-U RNA editing in natural killer cells, lymphoma cell lines, and, to a lesser extent, CD8-positive T cells upon cellular crowding and hypoxia. In contrast to expectations from its anti-HIV-1 function, the highest expression of APOBEC3G is shown to be in cytotoxic lymphocytes. RNA-seq analysis of natural killer cells subjected to cellular crowding and hypoxia reveals widespread C-to-U mRNA editing that is enriched for genes involved in mRNA translation and ribosome function. APOBEC3G promotes Warburg-like metabolic remodeling in HuT78 T cells under similar conditions. Hypoxia-induced RNA editing by APOBEC3G can be mimicked by the inhibition of mitochondrial respiration and occurs independently of HIF-1α. Conclusions APOBEC3G is an endogenous RNA editing enzyme in primary natural killer cells and lymphoma cell lines. This RNA editing is induced by cellular crowding and mitochondrial respiratory inhibition to promote adaptation to hypoxic stress. Electronic supplementary material The online version of this article (10.1186/s13059-019-1651-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shraddha Sharma
- Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.,Present Address: Translate Bio, Lexington, MA, 02421, USA
| | - Jianmin Wang
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Emad Alqassim
- Department of Internal Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Scott Portwood
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Eduardo Cortes Gomez
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Orla Maguire
- Department of Flow and Image Cytometry, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Per H Basse
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Eunice S Wang
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Brahm H Segal
- Department of Internal Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Bora E Baysal
- Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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34
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Trontti K, Väänänen J, Sipilä T, Greco D, Hovatta I. Strong conservation of inbred mouse strain microRNA loci but broad variation in brain microRNAs due to RNA editing and isomiR expression. RNA (NEW YORK, N.Y.) 2018; 24:643-655. [PMID: 29445025 PMCID: PMC5900563 DOI: 10.1261/rna.064881.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by (i) identifying miRNA SNPs in whole-genome sequence data from 36 strains, and (ii) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of six strains, to facilitate the study of miRNAs in neurobehavioral phenotypes. miRNA loci were strongly conserved among the 36 strains, but even the highly conserved seed region contained 16 SNPs. In contrast, we identified RNA editing in 58.9% of miRNAs, including 11 consistent editing events in the seed region. We confirmed the functional significance of three conserved edits in the miR-379/410 cluster, demonstrating that edited miRNAs gained novel target mRNAs not recognized by the unedited miRNAs. We found significant interstrain differences in miRNA and isomiR expression: Of 779 miRNAs expressed in Hpc and 719 in FCx, 262 were differentially expressed (190 in Hpc, 126 in FCx, 54 in both). We also identified 32 novel miRNA candidates using miRNA prediction tools. Our studies provide the first comprehensive analysis of SNP, isomiR, and RNA editing variation in miRNA loci across inbred mouse strains, and a detailed catalog of expressed miRNAs in Hpc and FCx in six commonly used strains. These findings will facilitate the molecular analysis of neurological and behavioral phenotypes in this model organism.
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Affiliation(s)
- Kalevi Trontti
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Juho Väänänen
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Tessa Sipilä
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Dario Greco
- Insitute of Biotechnology, University of Helsinki, Helsinki FI-00790, Finland
| | - Iiris Hovatta
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
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35
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Pan S, Bruford MW, Wang Y, Lin Z, Gu Z, Hou X, Deng X, Dixon A, Graves JAM, Zhan X. Transcription-Associated Mutation Promotes RNA Complexity in Highly Expressed Genes-A Major New Source of Selectable Variation. Mol Biol Evol 2018; 35:1104-1119. [PMID: 29420738 PMCID: PMC5913671 DOI: 10.1093/molbev/msy017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Alternatively spliced transcript isoforms are thought to play a critical role for functional diversity. However, the mechanism generating the enormous diversity of spliced transcript isoforms remains unknown, and its biological significance remains unclear. We analyzed transcriptomes in saker falcons, chickens, and mice to show that alternative splicing occurs more frequently, yielding more isoforms, in highly expressed genes. We focused on hemoglobin in the falcon, the most abundantly expressed genes in blood, finding that alternative splicing produces 10-fold more isoforms than expected from the number of splice junctions in the genome. These isoforms were produced mainly by alternative use of de novo splice sites generated by transcription-associated mutation (TAM), not by the RNA editing mechanism normally invoked. We found that high expression of globin genes increases mutation frequencies during transcription, especially on nontranscribed DNA strands. After DNA replication, transcribed strands inherit these somatic mutations, creating de novo splice sites, and generating multiple distinct isoforms in the cell clone. Bisulfate sequencing revealed that DNA methylation may counteract this process by suppressing TAM, suggesting DNA methylation can spatially regulate RNA complexity. RNA profiling showed that falcons living on the high Qinghai-Tibetan Plateau possess greater global gene expression levels and higher diversity of mean to high abundance isoforms (reads per kilobases per million mapped reads ≥18) than their low-altitude counterparts, and we speculate that this may enhance their oxygen transport capacity under low-oxygen environments. Thus, TAM-induced RNA diversity may be physiologically significant, providing an alternative strategy in lifestyle evolution.
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Affiliation(s)
- Shengkai Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Michael W Bruford
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Organisms and Environment Division, School of Biosciences and Sustainable Place Institute, Cardiff University, Cardiff, United Kingdom
| | - Yusong Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China
| | - Zhongru Gu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xian Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xuemei Deng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Andrew Dixon
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Emirates Falconers' Club, Abu Dhabi, UAE
| | | | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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36
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Somero GN. RNA thermosensors: how might animals exploit their regulatory potential? J Exp Biol 2018; 221:221/4/jeb162842. [DOI: 10.1242/jeb.162842] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
ABSTRACT
The secondary and tertiary orders of RNA structure are crucial for a suite of RNA-related functions, including regulation of translation, gene expression and RNA turnover. The temperature sensitivity of RNA secondary and tertiary structures is exploited by bacteria to fabricate RNA thermosensing systems that allow a rapid adaptive response to temperature change. RNA thermometers (RNATs) present in non-coding regions of certain mRNAs of pathogenic bacteria enable rapid upregulation of translation of virulence proteins when the temperature of the bacterium rises after entering a mammalian host. Rapid upregulation of translation of bacterial heat-shock proteins likewise is governed in part by RNATs. Turnover of mRNA may be regulated by temperature-sensitive RNA structures. Whereas the roles of temperature-sensitive RNA structures similar to RNATs in Eukarya and Archaea are largely unknown, there would appear to be a potential for all taxa to adaptively regulate their thermal physiology through exploitation of RNA-based thermosensory responses akin to those of bacteria. In animals, these responses might include regulation of translation of stress-induced proteins, alternative splicing of messenger RNA precursors, differential expression of allelic proteins, modulation of activities of small non-coding RNAs, regulation of mRNA turnover and control of RNA editing. New methods for predicting, detecting and experimentally modifying RNA secondary structure offer promising windows into these fascinating aspects of RNA biochemistry. Elucidating whether animals too have exploited the types of RNA thermosensing tools that are used so effectively by bacteria seems likely to provide exciting new insights into the mechanisms of evolutionary adaptation and acclimatization to temperature.
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Affiliation(s)
- George N. Somero
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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37
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Gebhardt A, Laudenbach BT, Pichlmair A. Discrimination of Self and Non-Self Ribonucleic Acids. J Interferon Cytokine Res 2018; 37:184-197. [PMID: 28475460 DOI: 10.1089/jir.2016.0092] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Most virus infections are controlled through the innate and adaptive immune system. A surprisingly limited number of so-called pattern recognition receptors (PRRs) have the ability to sense a large variety of virus infections. The reason for the broad activity of PRRs lies in the ability to recognize viral nucleic acids. These nucleic acids lack signatures that are present in cytoplasmic cellular nucleic acids and thereby marking them as pathogen-derived. Accumulating evidence suggests that these signatures, which are predominantly sensed by a class of PRRs called retinoic acid-inducible gene I (RIG-I)-like receptors and other proteins, are not unique to viruses but rather resemble immature forms of cellular ribonucleic acids generated by cellular polymerases. RIG-I-like receptors, and other cellular antiviral proteins, may therefore have mainly evolved to sense nonprocessed nucleic acids typically generated by primitive organisms and pathogens. This capability has not only implications on induction of antiviral immunity but also on the function of cellular proteins to handle self-derived RNA with stimulatory potential.
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Affiliation(s)
- Anna Gebhardt
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry , Munich, Germany
| | | | - Andreas Pichlmair
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry , Munich, Germany
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38
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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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Teichert I, Dahlmann TA, Kück U, Nowrousian M. RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes. Genome Biol Evol 2017; 9:855-868. [PMID: 28338982 PMCID: PMC5381528 DOI: 10.1093/gbe/evx052] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 12/16/2022] Open
Abstract
RNA editing is a post-transcriptional process that modifies RNA molecules leading to transcript sequences that differ from their template DNA. A-to-I editing was found to be widely distributed in nuclear transcripts of metazoa, but was detected in fungi only recently in a study of the filamentous ascomycete Fusarium graminearum that revealed extensive A-to-I editing of mRNAs in sexual structures (fruiting bodies). Here, we searched for putative RNA editing events in RNA-seq data from Sordaria macrospora and Pyronema confluens, two distantly related filamentous ascomycetes, and in data from the Taphrinomycete Schizosaccharomyces pombe. Like F. graminearum, S. macrospora is a member of the Sordariomycetes, whereas P. confluens belongs to the early-diverging group of Pezizomycetes. We found extensive A-to-I editing in RNA-seq data from sexual mycelium from both filamentous ascomycetes, but not in vegetative structures. A-to-I editing was not detected in different stages of meiosis of S. pombe. A comparison of A-to-I editing in S. macrospora with F. graminearum and P. confluens, respectively, revealed little conservation of individual editing sites. An analysis of RNA-seq data from two sterile developmental mutants of S. macrospora showed that A-to-I editing is strongly reduced in these strains. Sequencing of cDNA fragments containing more than one editing site from P. confluens showed that at the beginning of sexual development, transcripts were incompletely edited or unedited, whereas in later stages transcripts were more extensively edited. Taken together, these data suggest that A-to-I RNA editing is an evolutionary conserved feature during fruiting body development in filamentous ascomycetes.
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Affiliation(s)
- Ines Teichert
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Germany
| | - Tim A Dahlmann
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Germany
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Germany
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40
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Oakes E, Anderson A, Cohen-Gadol A, Hundley HA. Adenosine Deaminase That Acts on RNA 3 (ADAR3) Binding to Glutamate Receptor Subunit B Pre-mRNA Inhibits RNA Editing in Glioblastoma. J Biol Chem 2017; 292:4326-4335. [PMID: 28167531 DOI: 10.1074/jbc.m117.779868] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/05/2017] [Indexed: 01/08/2023] Open
Abstract
RNA editing is a cellular process that precisely alters nucleotide sequences, thus regulating gene expression and generating protein diversity. Over 60% of human transcripts undergo adenosine to inosine RNA editing, and editing is required for normal development and proper neuronal function of animals. Editing of one adenosine in the transcript encoding the glutamate receptor subunit B, glutamate receptor ionotropic AMPA 2 (GRIA2), modifies a codon, replacing the genomically encoded glutamine (Q) with arginine (R); thus this editing site is referred to as the Q/R site. Editing at the Q/R site of GRIA2 is essential, and reduced editing of GRIA2 transcripts has been observed in patients suffering from glioblastoma. In glioblastoma, incorporation of unedited GRIA2 subunits leads to a calcium-permeable glutamate receptor, which can promote cell migration and tumor invasion. In this study, we identify adenosine deaminase that acts on RNA 3 (ADAR3) as an important regulator of Q/R site editing, investigate its mode of action, and detect elevated ADAR3 expression in glioblastoma tumors compared with adjacent brain tissue. Overexpression of ADAR3 in astrocyte and astrocytoma cell lines inhibits RNA editing at the Q/R site of GRIA2 Furthermore, the double-stranded RNA binding domains of ADAR3 are required for repression of RNA editing. As the Q/R site of GRIA2 is specifically edited by ADAR2, we suggest that ADAR3 directly competes with ADAR2 for binding to GRIA2 transcript, inhibiting RNA editing, as evidenced by the direct binding of ADAR3 to the GRIA2 pre-mRNA. Finally, we provide evidence that both ADAR2 and ADAR3 expression contributes to the relative level of GRIA2 editing in tumors from patients suffering from glioblastoma.
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Affiliation(s)
| | - Ashley Anderson
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405 and
| | - Aaron Cohen-Gadol
- Department of Neurological Surgery, Goodman Campbell Brain and Spine, Indianapolis, Indiana 46202
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, Indiana 47405 and
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41
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Danan-Gotthold M, Guyon C, Giraud M, Levanon EY, Abramson J. Extensive RNA editing and splicing increase immune self-representation diversity in medullary thymic epithelial cells. Genome Biol 2016; 17:219. [PMID: 27776542 PMCID: PMC5078920 DOI: 10.1186/s13059-016-1079-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/05/2016] [Indexed: 01/28/2023] Open
Abstract
Background In order to become functionally competent but harmless mediators of the immune system, T cells undergo a strict educational program in the thymus, where they learn to discriminate between self and non-self. This educational program is, to a large extent, mediated by medullary thymic epithelial cells that have a unique capacity to express, and subsequently present, a large fraction of body antigens. While the scope of promiscuously expressed genes by medullary thymic epithelial cells is well-established, relatively little is known about the expression of variants that are generated by co-transcriptional and post-transcriptional processes. Results Our study reveals that in comparison to other cell types, medullary thymic epithelial cells display significantly higher levels of alternative splicing, as well as A-to-I and C-to-U RNA editing, which thereby further expand the diversity of their self-antigen repertoire. Interestingly, Aire, the key mediator of promiscuous gene expression in these cells, plays a limited role in the regulation of these transcriptional processes. Conclusions Our results highlight RNA processing as another layer by which the immune system assures a comprehensive self-representation in the thymus which is required for the establishment of self-tolerance and prevention of autoimmunity. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1079-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Clotilde Guyon
- Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France
| | - Matthieu Giraud
- Department of Infection Immunity and Inflammation, Cochin Institute, Paris, France
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel.
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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Bryant CD, Yazdani N. RNA-binding proteins, neural development and the addictions. GENES BRAIN AND BEHAVIOR 2016; 15:169-86. [PMID: 26643147 DOI: 10.1111/gbb.12273] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022]
Abstract
Transcriptional and post-transcriptional regulation of gene expression defines the neurobiological mechanisms that bridge genetic and environmental risk factors with neurobehavioral dysfunction underlying the addictions. More than 1000 genes in the eukaryotic genome code for multifunctional RNA-binding proteins (RBPs) that can regulate all levels of RNA biogenesis. More than 50% of these RBPs are expressed in the brain where they regulate alternative splicing, transport, localization, stability and translation of RNAs during development and adulthood. Dysfunction of RBPs can exert global effects on their targetomes that underlie neurodegenerative disorders such as Alzheimer's and Parkinson's diseases as well as neurodevelopmental disorders, including autism and schizophrenia. Here, we consider the evidence that RBPs influence key molecular targets, neurodevelopment, synaptic plasticity and neurobehavioral dysfunction underlying the addictions. Increasingly well-powered genome-wide association studies in humans and mammalian model organisms combined with ever more precise transcriptomic and proteomic approaches will continue to uncover novel and possibly selective roles for RBPs in the addictions. Key challenges include identifying the biological functions of the dynamic RBP targetomes from specific cell types throughout subcellular space (e.g. the nuclear spliceome vs. the synaptic translatome) and time and manipulating RBP programs through post-transcriptional modifications to prevent or reverse aberrant neurodevelopment and plasticity underlying the addictions.
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Affiliation(s)
- C D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - N Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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Chen W, Feng P, Ding H, Lin H. PAI: Predicting adenosine to inosine editing sites by using pseudo nucleotide compositions. Sci Rep 2016; 6:35123. [PMID: 27725762 PMCID: PMC5057124 DOI: 10.1038/srep35123] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/20/2016] [Indexed: 12/24/2022] Open
Abstract
The adenosine to inosine (A-to-I) editing is the most prevalent kind of RNA editing and involves in many biological processes. Accurate identification of A-to-I editing site is invaluable for better understanding its biological functions. Due to the limitations of experimental methods, in the present study, a support vector machine based-model, called PAI, is proposed to identify A-to-I editing site in D. melanogaster. In this model, RNA sequences are encoded by "pseudo dinucleotide composition" into which six RNA physiochemical properties were incorporated. PAI achieves promising performances in jackknife test and independent dataset test, indicating that it holds very high potential to become a useful tool for identifying A-to-I editing site. For the convenience of experimental scientists, a web-server was constructed for PAI and it is freely accessible at http://lin.uestc.edu.cn/server/PAI.
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Affiliation(s)
- Wei Chen
- Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, China
| | - Pengmian Feng
- School of Public Health, North China University of Science and Technology, Tangshan, 063000, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Liu H, Wang Q, He Y, Chen L, Hao C, Jiang C, Li Y, Dai Y, Kang Z, Xu JR. Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes. Genome Res 2016; 26:499-509. [PMID: 26934920 PMCID: PMC4817773 DOI: 10.1101/gr.199877.115] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/22/2016] [Indexed: 01/10/2023]
Abstract
Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (ADAR) orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals. However, during this study with the PUK1(FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium graminearum, we found that two tandem stop codons, UA(1831)GUA(1834)G, in its kinase domain were changed to UG(1831)GUG(1834)G by RNA editing in perithecia. To confirm A-to-I editing of PUK1 transcripts, strand-specific RNA-seq data were generated with RNA isolated from conidia, hyphae, and perithecia. PUK1 was almost specifically expressed in perithecia, and 90% of transcripts were edited to UG(1831)GUG(1834)G. Genome-wide analysis identified 26,056 perithecium-specific A-to-I editing sites. Unlike those in animals, 70.5% of A-to-I editing sites inF. graminearum occur in coding regions, and more than two-thirds of them result in amino acid changes, including editing of 69PUK1-like pseudogenes with stop codons in ORFs.PUK1orthologs and other pseudogenes also displayed stage-specific expression and editing in Neurospora crassa and F. verticillioides Furthermore,F. graminearum differs from animals in the sequence preference and structure selectivity of A-to-I editing sites. Whereas A's embedded in RNA stems are targeted by ADARs, RNA editing inF. graminearum preferentially targets A's in hairpin loops, which is similar to the anticodon loop of tRNA targeted by adenosine deaminases acting on tRNA (ADATs). Overall, our results showed that A-to-I RNA editing occurs specifically during sexual reproduction and mainly in the coding regions in filamentous ascomycetes, involving adenosine deamination mechanisms distinct from metazoan ADARs.
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Affiliation(s)
- Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi He
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingfeng Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chaofeng Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Yafeng Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
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45
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Evolution of Plasticity: Mechanistic Link between Development and Reversible Acclimation. Trends Ecol Evol 2016; 31:237-249. [PMID: 26846962 DOI: 10.1016/j.tree.2016.01.004] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 12/29/2015] [Accepted: 01/07/2016] [Indexed: 11/24/2022]
Abstract
Phenotypic characteristics of animals can change independently from changes in the genetic code. These plastic phenotypic responses are important for population persistence in changing environments. Plasticity can be induced during early development, with persistent effects on adult phenotypes, and it can occur reversibly throughout life (acclimation). These manifestations of plasticity have been viewed as separate processes. Here we argue that developmental conditions not only change mean trait values but also modify the capacity for acclimation. Acclimation counteracts the potentially negative effects of phenotype-environment mismatches resulting from epigenetic modifications during early development. Developmental plasticity is therefore also beneficial when environmental conditions change within generations. Hence, the evolution of reversible acclimation can no longer be viewed as independent from developmental processes.
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46
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Characterization and Expression of the Lucina pectinata Oxygen and Sulfide Binding Hemoglobin Genes. PLoS One 2016; 11:e0147977. [PMID: 26824233 PMCID: PMC4732748 DOI: 10.1371/journal.pone.0147977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/11/2016] [Indexed: 12/30/2022] Open
Abstract
The clam Lucina pectinata lives in sulfide-rich muds and houses intracellular symbiotic bacteria that need to be supplied with hydrogen sulfide and oxygen. This clam possesses three hemoglobins: hemoglobin I (HbI), a sulfide-reactive protein, and hemoglobin II (HbII) and III (HbIII), which are oxygen-reactive. We characterized the complete gene sequence and promoter regions for the oxygen reactive hemoglobins and the partial structure and promoters of the HbI gene from Lucina pectinata. We show that HbI has two mRNA variants, where the 5'end had either a sequence of 96 bp (long variant) or 37 bp (short variant). The gene structure of the oxygen reactive Hbs is defined by having 4-exons/3-introns with conservation of intron location at B12.2 and G7.0 and the presence of pre-coding introns, while the partial gene structure of HbI has the same intron conservation but appears to have a 5-exon/ 4-intron structure. A search for putative transcription factor binding sites (TFBSs) was done with the promoters for HbII, HbIII, HbI short and HbI long. The HbII, HbIII and HbI long promoters showed similar predicted TFBSs. We also characterized MITE-like elements in the HbI and HbII gene promoters and intronic regions that are similar to sequences found in other mollusk genomes. The gene expression levels of the clam Hbs, from sulfide-rich and sulfide-poor environments showed a significant decrease of expression in the symbiont-containing tissue for those clams in a sulfide-poor environment, suggesting that the sulfide concentration may be involved in the regulation of these proteins. Gene expression evaluation of the two HbI mRNA variants indicated that the longer variant is expressed at higher levels than the shorter variant in both environments.
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47
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Advani VM, Dinman JD. Reprogramming the genetic code: The emerging role of ribosomal frameshifting in regulating cellular gene expression. Bioessays 2015; 38:21-6. [PMID: 26661048 PMCID: PMC4749135 DOI: 10.1002/bies.201500131] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Reading frame maintenance is a critical property of ribosomes. However, a number of genetic elements have been described that can induce ribosomes to shift on mRNAs, the most well understood of which are a class that directs ribosomal slippage by one base in 5' (‐1) direction. This is referred to as programmed ‐1 ribosomal frameshifting (‐1 PRF). Recently, a new ‐1 PRF promoting element was serendipitously discovered in a study examining the effects of stretches of adenosines in the coding sequences of mRNAs. Here, we discuss this finding, recent studies describing how ‐1 PRF is used to control gene expression in eukaryotes, and how ‐1 PRF is itself regulated. The implications of dysregulation of ‐1 PRF on human health are examined, as are possible new areas in which novel ‐1 PRF promoting elements might be discovered. Also watch the https://youtu.be/1mPXIINCRcY.
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Affiliation(s)
- Vivek M Advani
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
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48
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Abstract
Adenosine deaminases acting on RNA (ADARs) convert adenosine to inosine in double-stranded RNA. This A-to-I editing occurs not only in protein-coding regions of mRNAs, but also frequently in non-coding regions that contain inverted Alu repeats. Editing of coding sequences can result in the expression of functionally altered proteins that are not encoded in the genome, whereas the significance of Alu editing remains largely unknown. Certain microRNA (miRNA) precursors are also edited, leading to reduced expression or altered function of mature miRNAs. Conversely, recent studies indicate that ADAR1 forms a complex with Dicer to promote miRNA processing, revealing a new function of ADAR1 in the regulation of RNA interference.
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49
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Deffit SN, Hundley HA. To edit or not to edit: regulation of ADAR editing specificity and efficiency. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:113-27. [PMID: 26612708 DOI: 10.1002/wrna.1319] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/15/2015] [Accepted: 10/20/2015] [Indexed: 11/08/2022]
Abstract
Hundreds to millions of adenosine (A)-to-inosine (I) modifications are present in eukaryotic transcriptomes and play an essential role in the creation of proteomic and phenotypic diversity. As adenosine and inosine have different base-pairing properties, the functional consequences of these modifications or 'edits' include altering coding potential, splicing, and miRNA-mediated gene silencing of transcripts. However, rather than serving as a static control of gene expression, A-to-I editing provides a means to dynamically rewire the genetic code during development and in a cell-type specific manner. Interestingly, during normal development, in specific cells, and in both neuropathological diseases and cancers, the extent of RNA editing does not directly correlate with levels of the substrate mRNA or the adenosine deaminase that act on RNA (ADAR) editing enzymes, implying that cellular factors are required for spatiotemporal regulation of A-to-I editing. The factors that affect the specificity and extent of ADAR activity have been thoroughly dissected in vitro. Yet, we still lack a complete understanding of how specific ADAR family members can selectively deaminate certain adenosines while others cannot. Additionally, in the cellular environment, ADAR specificity and editing efficiency is likely to be influenced by cellular factors, which is currently an area of intense investigation. Data from many groups have suggested two main mechanisms for controlling A-to-I editing in the cell: (1) regulating ADAR accessibility to target RNAs and (2) protein-protein interactions that directly alter ADAR enzymatic activity. Recent studies suggest cis- and trans-acting RNA elements, heterodimerization and RNA-binding proteins play important roles in regulating RNA editing levels in vivo. WIREs RNA 2016, 7:113-127. doi: 10.1002/wrna.1319.
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Affiliation(s)
- Sarah N Deffit
- Medical Sciences Program, Indiana University, Bloomington, IN, USA
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