1
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Schneider N, Steinberg R, Ben-David A, Valensi J, David-Kadoch G, Rosenwasser Z, Banin E, Levanon EY, Sharon D, Ben-Aroya S. A pipeline for identifying guide RNA sequences that promote RNA editing of nonsense mutations that cause inherited retinal diseases. Mol Ther Nucleic Acids 2024; 35:102130. [PMID: 38375504 PMCID: PMC10875612 DOI: 10.1016/j.omtn.2024.102130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024]
Abstract
Adenosine deaminases acting on RNA (ADARs) are endogenous enzymes catalyzing the deamination of adenosines to inosines, which are then read as guanosines during translation. This ability to recode makes ADAR an attractive therapeutic tool to edit genetic mutations and reprogram genetic information at the mRNA level. Using the endogenous ADARs and guiding them to a selected target has promising therapeutic potential. Indeed, different studies have reported several site-directed RNA-editing approaches for making targeted base changes in RNA molecules. The basic strategy has been to use guide RNAs (gRNAs) that hybridize and form a double-stranded RNA (dsRNA) structure with the desired RNA target because of ADAR activity in regions of dsRNA formation. Here we report on a novel pipeline for identifying disease-causing variants as candidates for RNA editing, using a yeast-based screening system to select efficient gRNAs for editing of nonsense mutations, and test them in a human cell line reporter system. We have used this pipeline to modify the sequence of transcripts carrying nonsense mutations that cause inherited retinal diseases in the FAM161A, KIZ, TRPM1, and USH2A genes. Our approach can serve as a basis for gene therapy intervention in knockin mouse models and ultimately in human patients.
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Affiliation(s)
- Nina Schneider
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ricky Steinberg
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Amit Ben-David
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Johanna Valensi
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Galit David-Kadoch
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Zohar Rosenwasser
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Eyal Banin
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Erez Y. Levanon
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Dror Sharon
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shay Ben-Aroya
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
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2
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Levanon EY, Cohen-Fultheim R, Eisenberg E. In search of critical dsRNA targets of ADAR1. Trends Genet 2024; 40:250-259. [PMID: 38160061 DOI: 10.1016/j.tig.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Recent studies have underscored the pivotal role of adenosine-to-inosine RNA editing, catalyzed by ADAR1, in suppressing innate immune interferon responses triggered by cellular double-stranded RNA (dsRNA). However, the specific ADAR1 editing targets crucial for this regulatory function remain elusive. We review analyses of transcriptome-wide ADAR1 editing patterns and their evolutionary dynamics, which offer valuable insights into this unresolved query. The growing appreciation of the significance of immunogenic dsRNAs and their editing in inflammatory and autoimmune diseases and cancer calls for a more comprehensive understanding of dsRNA immunogenicity, which may promote our understanding of these diseases and open doors to therapeutic avenues.
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Affiliation(s)
- Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
| | - Roni Cohen-Fultheim
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv, University, Tel Aviv 6997801, Israel.
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3
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Dadush A, Merdler-Rabinowicz R, Gorelik D, Feiglin A, Buchumenski I, Pal LR, Ben-Aroya S, Ruppin E, Levanon EY. DNA and RNA base editors can correct the majority of pathogenic single nucleotide variants. NPJ Genom Med 2024; 9:16. [PMID: 38409211 PMCID: PMC10897195 DOI: 10.1038/s41525-024-00397-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
The majority of human genetic diseases are caused by single nucleotide variants (SNVs) in the genome sequence. Excitingly, new genomic techniques known as base editing have opened efficient pathways to correct erroneous nucleotides. Due to reliance on deaminases, which have the capability to convert A to I(G) and C to U, the direct applicability of base editing might seem constrained in terms of the range of mutations that can be reverted. In this evaluation, we assess the potential of DNA and RNA base editing methods for treating human genetic diseases. Our findings indicate that 62% of pathogenic SNVs found within genes can be amended by base editing; 30% are G>A and T>C SNVs that can be corrected by DNA base editing, and most of them by RNA base editing as well, and 29% are C>T and A>G SNVs that can be corrected by DNA base editing directed to the complementary strand. For each, we also present several factors that affect applicability such as bystander and off-target occurrences. For cases where editing the mismatched nucleotide is not feasible, we introduce an approach that calculates the optimal substitution of the deleterious amino acid with a new amino acid, further expanding the scope of applicability. As personalized therapy is rapidly advancing, our demonstration that most SNVs can be treated by base editing is of high importance. The data provided will serve as a comprehensive resource for those seeking to design therapeutic base editors and study their potential in curing genetic diseases.
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Affiliation(s)
- Ariel Dadush
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Rona Merdler-Rabinowicz
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Gorelik
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Ariel Feiglin
- Skip Therapeutics Ltd, 2 Ilan Ramon St, Ness Ziona, Israel
| | | | - Lipika R Pal
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shay Ben-Aroya
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel.
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4
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Knebel UE, Peleg S, Dai C, Cohen-Fultheim R, Jonsson S, Poznyak K, Israeli M, Zamashanski L, Glaser B, Levanon EY, Powers AC, Klochendler A, Dor Y. Disrupted RNA editing in beta cells mimics early-stage type 1 diabetes. Cell Metab 2024; 36:48-61.e6. [PMID: 38128529 PMCID: PMC10843671 DOI: 10.1016/j.cmet.2023.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/18/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
A major hypothesis for the etiology of type 1 diabetes (T1D) postulates initiation by viral infection, leading to double-stranded RNA (dsRNA)-mediated interferon response and inflammation; however, a causal virus has not been identified. Here, we use a mouse model, corroborated with human islet data, to demonstrate that endogenous dsRNA in beta cells can lead to a diabetogenic immune response, thus identifying a virus-independent mechanism for T1D initiation. We found that disruption of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) in beta cells triggers a massive interferon response, islet inflammation, and beta cell failure and destruction, with features bearing striking similarity to early-stage human T1D. Glycolysis via calcium enhances the interferon response, suggesting an actionable vicious cycle of inflammation and increased beta cell workload.
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Affiliation(s)
- Udi Ehud Knebel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Military Medicine and "Tzameret", Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel, and Medical Corps, Israel Defense Forces, Israel
| | - Shani Peleg
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chunhua Dai
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Roni Cohen-Fultheim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Sara Jonsson
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Karin Poznyak
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maya Israeli
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Liza Zamashanski
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Alvin C Powers
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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5
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Zambrano-Mila MS, Witzenberger M, Rosenwasser Z, Uzonyi A, Nir R, Ben-Aroya S, Levanon EY, Schwartz S. Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2. Nat Commun 2023; 14:8212. [PMID: 38081817 PMCID: PMC10713624 DOI: 10.1038/s41467-023-43633-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Millions of adenosines are deaminated throughout the transcriptome by ADAR1 and/or ADAR2 at varying levels, raising the question of what are the determinants guiding substrate specificity and how these differ between the two enzymes. We monitor how secondary structure modulates ADAR2 vs ADAR1 substrate selectivity, on the basis of systematic probing of thousands of synthetic sequences transfected into cell lines expressing exclusively ADAR1 or ADAR2. Both enzymes induce symmetric, strand-specific editing, yet with distinct offsets with respect to structural disruptions: -26 nt for ADAR2 and -35 nt for ADAR1. We unravel the basis for these differences in offsets through mutants, domain-swaps, and ADAR homologs, and find it to be encoded by the differential RNA binding domain (RBD) architecture. Finally, we demonstrate that this offset-enhanced editing can allow an improved design of ADAR2-recruiting therapeutics, with proof-of-concept experiments demonstrating increased on-target and potentially decreased off-target editing.
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Affiliation(s)
- Marlon S Zambrano-Mila
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Monika Witzenberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Zohar Rosenwasser
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Shay Ben-Aroya
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Erez Y Levanon
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel.
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6
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Astre G, Atlan T, Goshtchevsky U, Oron-Gottesman A, Smirnov M, Shapira K, Velan A, Deelen J, Levy T, Levanon EY, Harel I. Genetic perturbation of AMP biosynthesis extends lifespan and restores metabolic health in a naturally short-lived vertebrate. Dev Cell 2023; 58:1350-1364.e10. [PMID: 37321215 DOI: 10.1016/j.devcel.2023.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
During aging, the loss of metabolic homeostasis drives a myriad of pathologies. A central regulator of cellular energy, the AMP-activated protein kinase (AMPK), orchestrates organismal metabolism. However, direct genetic manipulations of the AMPK complex in mice have, so far, produced detrimental phenotypes. Here, as an alternative approach, we alter energy homeostasis by manipulating the upstream nucleotide pool. Using the turquoise killifish, we mutate APRT, a key enzyme in AMP biosynthesis, and extend the lifespan of heterozygous males. Next, we apply an integrated omics approach to show that metabolic functions are rejuvenated in old mutants, which also display a fasting-like metabolic profile and resistance to high-fat diet. At the cellular level, heterozygous cells exhibit enhanced nutrient sensitivity, reduced ATP levels, and AMPK activation. Finally, lifelong intermittent fasting abolishes the longevity benefits. Our findings suggest that perturbing AMP biosynthesis may modulate vertebrate lifespan and propose APRT as a promising target for promoting metabolic health.
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Affiliation(s)
- Gwendoline Astre
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Tehila Atlan
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Uri Goshtchevsky
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Adi Oron-Gottesman
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Margarita Smirnov
- Central Fish Health Laboratory, Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir David 10803, Israel
| | - Kobi Shapira
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ariel Velan
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Joris Deelen
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Tomer Levy
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Itamar Harel
- Department of Genetics, the Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel.
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7
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Jbara A, Lin KT, Stossel C, Siegfried Z, Shqerat H, Amar-Schwartz A, Elyada E, Mogilevsky M, Raitses-Gurevich M, Johnson JL, Yaron TM, Ovadia O, Jang GH, Danan-Gotthold M, Cantley LC, Levanon EY, Gallinger S, Krainer AR, Golan T, Karni R. RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature 2023; 617:147-153. [PMID: 36949200 PMCID: PMC10156590 DOI: 10.1038/s41586-023-05820-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is characterized by aggressive local invasion and metastatic spread, leading to high lethality. Although driver gene mutations during PDA progression are conserved, no specific mutation is correlated with the dissemination of metastases1-3. Here we analysed RNA splicing data of a large cohort of primary and metastatic PDA tumours to identify differentially spliced events that correlate with PDA progression. De novo motif analysis of these events detected enrichment of motifs with high similarity to the RBFOX2 motif. Overexpression of RBFOX2 in a patient-derived xenograft (PDX) metastatic PDA cell line drastically reduced the metastatic potential of these cells in vitro and in vivo, whereas depletion of RBFOX2 in primary pancreatic tumour cell lines increased the metastatic potential of these cells. These findings support the role of RBFOX2 as a potent metastatic suppressor in PDA. RNA-sequencing and splicing analysis of RBFOX2 target genes revealed enrichment of genes in the RHO GTPase pathways, suggesting a role of RBFOX2 splicing activity in cytoskeletal organization and focal adhesion formation. Modulation of RBFOX2-regulated splicing events, such as via myosin phosphatase RHO-interacting protein (MPRIP), is associated with PDA metastases, altered cytoskeletal organization and the induction of focal adhesion formation. Our results implicate the splicing-regulatory function of RBFOX2 as a tumour suppressor in PDA and suggest a therapeutic approach for metastatic PDA.
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Affiliation(s)
- Amina Jbara
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chani Stossel
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Haya Shqerat
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ela Elyada
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maxim Mogilevsky
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ofek Ovadia
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gun Ho Jang
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Steven Gallinger
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | | | - Talia Golan
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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8
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Mann TD, Kopel E, Eisenberg E, Levanon EY. Increased A-to-I RNA editing in atherosclerosis and cardiomyopathies. PLoS Comput Biol 2023; 19:e1010923. [PMID: 37036839 PMCID: PMC10085048 DOI: 10.1371/journal.pcbi.1010923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/05/2023] [Indexed: 04/11/2023] Open
Abstract
Adenosine-to-inosine RNA editing is essential to prevent undesired immune activation. This diverse process alters the genetic content of the RNA and may recode proteins, change splice sites and miRNA targets, and mimic genomic mutations. Recent studies have associated or implicated aberrant editing with pathological conditions, including cancer, autoimmune diseases, and neurological and psychiatric conditions. RNA editing patterns in cardiovascular tissues have not been investigated systematically so far, and little is known about its potential role in cardiac diseases. Some hints suggest robust editing in this system, including the fact that ADARB1 (ADAR2), the main coding-sequence editor, is most highly expressed in these tissues. Here we characterized RNA editing in the heart and arteries and examined a contributory role to the development of atherosclerosis and two structural heart diseases -Ischemic and Dilated Cardiomyopathies. Analyzing hundreds of RNA-seq samples taken from the heart and arteries of cardiac patients and controls, we find that global editing, alongside inflammatory gene expression, is increased in patients with atherosclerosis, cardiomyopathies, and heart failure. We describe a single recoding editing site and suggest it as a target for focused research. This recoding editing site in the IGFBP7 gene is one of the only evolutionary conserved sites between mammals, and we found it exhibits consistently increased levels of editing in these patients. Our findings reveal that RNA editing is abundant in arteries and is elevated in several key cardiovascular conditions. They thus provide a roadmap for basic and translational research of RNA as a mediator of atherosclerosis and non-genetic cardiomyopathies.
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Affiliation(s)
- Tomer D Mann
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eli Kopel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv, University, Tel Aviv, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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9
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Avram-Shperling A, Kopel E, Twersky I, Gabay O, Ben-David A, Karako-Lampert S, Rosenthal JJC, Levanon EY, Eisenberg E, Ben-Aroya S. Identification of exceptionally potent adenosine deaminases RNA editors from high body temperature organisms. PLoS Genet 2023; 19:e1010661. [PMID: 36877730 PMCID: PMC10019624 DOI: 10.1371/journal.pgen.1010661] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/16/2023] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
The most abundant form of RNA editing in metazoa is the deamination of adenosines into inosines (A-to-I), catalyzed by ADAR enzymes. Inosines are read as guanosines by the translation machinery, and thus A-to-I may lead to protein recoding. The ability of ADARs to recode at the mRNA level makes them attractive therapeutic tools. Several approaches for Site-Directed RNA Editing (SDRE) are currently under development. A major challenge in this field is achieving high on-target editing efficiency, and thus it is of much interest to identify highly potent ADARs. To address this, we used the baker yeast Saccharomyces cerevisiae as an editing-naïve system. We exogenously expressed a range of heterologous ADARs and identified the hummingbird and primarily mallard-duck ADARs, which evolved at 40-42°C, as two exceptionally potent editors. ADARs bind to double-stranded RNA structures (dsRNAs), which in turn are temperature sensitive. Our results indicate that species evolved to live with higher core body temperatures have developed ADAR enzymes that target weaker dsRNA structures and would therefore be more effective than other ADARs. Further studies may use this approach to isolate additional ADARs with an editing profile of choice to meet specific requirements, thus broadening the applicability of SDRE.
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Affiliation(s)
- Adi Avram-Shperling
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Kopel
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orshay Gabay
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Amit Ben-David
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Joshua J. C. Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Erez Y. Levanon
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EE); (SB-A)
| | - Shay Ben-Aroya
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail: (EE); (SB-A)
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10
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Karmon M, Kopel E, Barzilai A, Geva P, Eisenberg E, Levanon EY, Greenberger S. Altered RNA Editing in Atopic Dermatitis Highlights the Role of Double-Stranded RNA for Immune Surveillance. J Invest Dermatol 2022; 143:933-943.e8. [PMID: 36502941 DOI: 10.1016/j.jid.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/03/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Atopic dermatitis (AD) is associated with dysregulated type 1 IFN‒mediated responses, in parallel with the dominant type 2 inflammation. However, the pathophysiology of this dysregulation is largely unknown. Adenosine-to-inosine RNA editing plays a critical role in immune regulation by preventing double-stranded RNA recognition by MDA5 and IFN activation. We studied global adenosine-to-inosine editing in AD to elucidate the role played by altered editing in the pathophysiology of this disease. Analysis of three RNA-sequencing datasets of AD skin samples revealed reduced levels of adenosine-to-inosine RNA editing in AD. This reduction was seen globally throughout Alu repeats as well as in coding genes and in specific pre-mRNA loci expected to create long double-stranded RNA, the main substrate of MDA5 leading to type I IFN activation. Consistently, IFN signature genes were upregulated. In contrast, global editing was not altered in systemic lupus erythematosus and systemic sclerosis, despite IFN activation. Our results indicate that altered editing leading to impairment of the innate immune response may be involved in the pathogenesis of AD. Possibly, it may be relevant for additional autoimmune and inflammatory diseases.
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Affiliation(s)
- Miriam Karmon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Aviv Barzilai
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Polina Geva
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel
| | - Eli Eisenberg
- Raymond & Beverly Sackler School of Physics & Astronomy, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shoshana Greenberger
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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11
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Gabay O, Shoshan Y, Kopel E, Ben-Zvi U, Mann TD, Bressler N, Cohen-Fultheim R, Schaffer AA, Roth SH, Tzur Z, Levanon EY, Eisenberg E. Landscape of adenosine-to-inosine RNA recoding across human tissues. Nat Commun 2022; 13:1184. [PMID: 35246538 PMCID: PMC8897444 DOI: 10.1038/s41467-022-28841-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 01/27/2022] [Indexed: 12/18/2022] Open
Abstract
RNA editing by adenosine deaminases changes the information encoded in the mRNA from its genomic blueprint. Editing of protein-coding sequences can introduce novel, functionally distinct, protein isoforms and diversify the proteome. The functional importance of a few recoding sites has been appreciated for decades. However, systematic methods to uncover these sites perform poorly, and the full repertoire of recoding in human and other mammals is unknown. Here we present a new detection approach, and analyze 9125 GTEx RNA-seq samples, to produce a highly-accurate atlas of 1517 editing sites within the coding region and their editing levels across human tissues. Single-cell RNA-seq data shows protein recoding contributes to the variability across cell subpopulations. Most highly edited sites are evolutionary conserved in non-primate mammals, attesting for adaptation. This comprehensive set can facilitate understanding of the role of recoding in human physiology and diseases. Gabay et al. provide a highly-accurate atlas of recoding by A-to-I RNA editing in human, profiled across tissues and cell subpopulations. Most highly edited sites are evolutionary conserved in non-primate mammals, attesting for adaptation.
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Affiliation(s)
- Orshay Gabay
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yoav Shoshan
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Udi Ben-Zvi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Tomer D Mann
- Tel Aviv Sourasky Medical Center and Sackler school of medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Bressler
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Roni Cohen-Fultheim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Amos A Schaffer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Ziv Tzur
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel. .,The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel.
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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12
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Buchumenski I, Roth SH, Kopel E, Katsman E, Feiglin A, Levanon EY, Eisenberg E. Global quantification exposes abundant low-level off-target activity by base editors. Genome Res 2021; 31:2354-2361. [PMID: 34667118 PMCID: PMC8647836 DOI: 10.1101/gr.275770.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/14/2021] [Indexed: 12/26/2022]
Abstract
Base editors are dedicated engineered deaminases that enable directed conversion of specific bases in the genome or transcriptome in a precise and efficient manner, and hold promise for correcting pathogenic mutations. A major concern limiting application of this powerful approach is the issue of off-target edits. Several recent studies have shown substantial off-target RNA activity induced by base editors and demonstrated that off-target mutations may be suppressed by improved deaminases versions or optimized guide RNAs. Here, we describe a new class of off-target events that are invisible to the established methods for detection of genomic variations and were thus far overlooked. We show that nonspecific, seemingly stochastic, off-target events affect a large number of sites throughout the genome or the transcriptome, and account for the majority of off-target activity. We develop and employ a different, complementary approach that is sensitive to the stochastic off-target activity and use it to quantify the abundant off-target RNA mutations due to current, optimized deaminase editors. We provide a computational tool to quantify global off-target activity, which can be used to optimize future base editors. Engineered base editors enable directed manipulation of the genome or transcriptome at single-base resolution. We believe that implementation of this computational approach would facilitate design of more specific base editors.
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Affiliation(s)
- Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Kopel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Efrat Katsman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ariel Feiglin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 69978, Israel
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13
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Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
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Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
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14
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Buchumenski I, Holler K, Appelbaum L, Eisenberg E, Junker JP, Levanon EY. Systematic identification of A-to-I RNA editing in zebrafish development and adult organs. Nucleic Acids Res 2021; 49:4325-4337. [PMID: 33872356 PMCID: PMC8096273 DOI: 10.1093/nar/gkab247] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022] Open
Abstract
A-to-I RNA editing is a common post transcriptional mechanism, mediated by the Adenosine deaminase that acts on RNA (ADAR) enzymes, that increases transcript and protein diversity. The study of RNA editing is limited by the absence of editing maps for most model organisms, hindering the understanding of its impact on various physiological conditions. Here, we mapped the vertebrate developmental landscape of A-to-I RNA editing, and generated the first comprehensive atlas of editing sites in zebrafish. Tens of thousands unique editing events and 149 coding sites were identified with high-accuracy. Some of these edited sites are conserved between zebrafish and humans. Sequence analysis of RNA over seven developmental stages revealed high levels of editing activity in early stages of embryogenesis, when embryos rely on maternal mRNAs and proteins. In contrast to the other organisms studied so far, the highest levels of editing were detected in the zebrafish ovary and testes. This resource can serve as the basis for understanding of the role of editing during zebrafish development and maturity.
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Affiliation(s)
- Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Karoline Holler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Lior Appelbaum
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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15
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Gold A, Levanon EY, Eisenberg E. The New RNA-Editing Era - Ethical Considerations. Trends Genet 2021; 37:685-687. [PMID: 33975753 DOI: 10.1016/j.tig.2021.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/18/2022]
Abstract
The characteristics of RNA editing, including the lower risk compared with genome editing, may loosen the ethical barriers that are currently imposed on genetic engineering, thus opening new possibilities for research, therapy, and human enhancement. We should start considering the future ethical and social implications of this new and promising technology.
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Affiliation(s)
- Azgad Gold
- Forensic Psychiatry Unit, Beer Yaakov Mental Health Center, Beer Yaakov, 7032102, Israel.
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
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16
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Uzonyi A, Nir R, Shliefer O, Stern-Ginossar N, Antebi Y, Stelzer Y, Levanon EY, Schwartz S. Deciphering the principles of the RNA editing code via large-scale systematic probing. Mol Cell 2021; 81:2374-2387.e3. [PMID: 33905683 DOI: 10.1016/j.molcel.2021.03.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/31/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Adenosine-to-inosine editing is catalyzed by ADAR1 at thousands of sites transcriptome-wide. Despite intense interest in ADAR1 from physiological, bioengineering, and therapeutic perspectives, the rules of ADAR1 substrate selection are poorly understood. Here, we used large-scale systematic probing of ∼2,000 synthetic constructs to explore the structure and sequence context determining editability. We uncover two structural layers determining the formation and propagation of A-to-I editing, independent of sequence. First, editing is robustly induced at fixed intervals of 35 bp upstream and 30 bp downstream of structural disruptions. Second, editing is symmetrically introduced on opposite sites on a double-stranded structure. Our findings suggest a recursive model for RNA editing, whereby the structural alteration induced by the editing at one site iteratively gives rise to the formation of an additional editing site at a fixed periodicity, serving as a basis for the propagation of editing along and across both strands of double-stranded RNA structures.
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Affiliation(s)
- Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ofir Shliefer
- Faculty of Life Sciences, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yaron Antebi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yonatan Stelzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Erez Y Levanon
- Faculty of Life Sciences, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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17
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Abstract
Alu elements are repetitive short interspersed elements prevalent in the primate genome. These repeats account for over 10% of the genome with more than a million highly similar copies. A direct outcome of this is an enrichment in long structures of stable dsRNA, which are the target of adenosine deaminases acting on RNAs (ADARs), the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, despite the radical increase in ADAR targets brought on by the introduction of Alu elements, the few evolutionary conserved editing sites manage to retain their editing levels. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which possibly contributed to accelerating primate evolution.
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Affiliation(s)
- Amos A Schaffer
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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18
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Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen-Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. EMBO Mol Med 2020; 12:e13551. [PMID: 33438831 DOI: 10.15252/emmm.202013551] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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19
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Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen‐Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. EMBO Mol Med 2020; 12:e11942. [PMID: 32715657 PMCID: PMC7507321 DOI: 10.15252/emmm.201911942] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) are brain-abundant RNAs of mostly unknown functions. To seek their roles in Parkinson's disease (PD), we generated an RNA sequencing resource of several brain region tissues from dozens of PD and control donors. In the healthy substantia nigra (SN), circRNAs accumulate in an age-dependent manner, but in the PD SN this correlation is lost and the total number of circRNAs reduced. In contrast, the levels of circRNAs are increased in the other studied brain regions of PD patients. We also found circSLC8A1 to increase in the SN of PD individuals. CircSLC8A1 carries 7 binding sites for miR-128 and is strongly bound to the microRNA effector protein Ago2. Indeed, RNA targets of miR-128 are also increased in PD individuals, suggesting that circSLC8A1 regulates miR-128 function and/or activity. CircSLC8A1 levels also increased in cultured cells exposed to the oxidative stress-inducing agent paraquat but were decreased in cells treated with the neuroprotective antioxidant regulator drug Simvastatin. Together, our work links circSLC8A1 to oxidative stress-related Parkinsonism and suggests further exploration of its molecular function in PD.
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Affiliation(s)
- Mor Hanan
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Alon Simchovitz
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Nadav Yayon
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Shani Vaknine
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Roni Cohen‐Fultheim
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Miriam Karmon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Nimrod Madrer
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Talia Miriam Rohrlich
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Moria Maman
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Estelle R Bennett
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - David S Greenberg
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Eran Meshorer
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Hermona Soreq
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Sebastian Kadener
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Biology DepartmentBrandeis UniversityWalthamMAUSA
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20
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Barak M, Porath HT, Finkelstein G, Knisbacher BA, Buchumenski I, Roth SH, Levanon EY, Eisenberg E. Purifying selection of long dsRNA is the first line of defense against false activation of innate immunity. Genome Biol 2020; 21:26. [PMID: 32028986 PMCID: PMC7006430 DOI: 10.1186/s13059-020-1937-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Mobile elements comprise a large fraction of metazoan genomes. Accumulation of mobile elements is bound to produce multiple putative double-stranded RNA (dsRNA) structures within the transcriptome. These endogenous dsRNA structures resemble viral RNA and may trigger false activation of the innate immune response, leading to severe damage to the host cell. Adenosine to inosine (A-to-I) RNA editing is a common post-transcriptional modification, abundant within repetitive elements of all metazoans. It was recently shown that a key function of A-to-I RNA editing by ADAR1 is to suppress the immunogenic response by endogenous dsRNAs. RESULTS Here, we analyze the transcriptomes of dozens of species across the Metazoa and identify a strong genomic selection against endogenous dsRNAs, resulting in their purification from the canonical transcriptome. This purifying selection is especially strong for long and nearly perfect dsRNAs. These are almost absent from mRNAs, but not pre-mRNAs, supporting the notion of selection due to cytoplasmic processes. The few long and nearly perfect structures found in human transcripts are weakly expressed and often heavily edited. CONCLUSION Purifying selection of long dsRNA is an important defense mechanism against false activation of innate immunity. This newly identified principle governs the integration of mobile elements into the genome, a major driving force of genome evolution. Furthermore, we find that most ADAR1 activity is not required to prevent an immune response to endogenous dsRNAs. The critical targets of ADAR1 editing are, likely, to be found mostly in non-canonical transcripts.
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Affiliation(s)
- Michal Barak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Gilad Finkelstein
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel.
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 69978, Israel.
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21
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Roth SH, Levanon EY, Eisenberg E. Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity. Nat Methods 2019; 16:1131-1138. [PMID: 31636457 DOI: 10.1038/s41592-019-0610-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing by the adenosine deaminase that acts on RNA (ADAR) enzymes is a common RNA modification, preventing false activation of the innate immune system by endogenous double-stranded RNAs. Methods for quantification of ADAR activity are sought after, due to an increasing interest in the role of ADARs in cancer and autoimmune disorders, as well as attempts to harness the ADAR enzymes for RNA engineering. Here, we present the Alu editing index (AEI), a robust and simple-to-use computational tool devised for this purpose. We describe its properties and demonstrate its superiority to current quantification methods of ADAR activity. The AEI is used to map global editing across a large dataset of healthy human samples and identify putative regulators of ADAR, as well as previously unknown factors affecting the observed Alu editing levels. These should be taken into account in future comparative studies of ADAR activity. The AEI tool is available at https://github.com/a2iEditing/RNAEditingIndexer.
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Affiliation(s)
- Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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22
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Pinto Y, Buchumenski I, Levanon EY, Eisenberg E. Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets. Nucleic Acids Res 2019; 46:71-82. [PMID: 29165639 PMCID: PMC5758889 DOI: 10.1093/nar/gkx1176] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/13/2017] [Indexed: 12/17/2022] Open
Abstract
A-to-I RNA editing is an important post-transcriptional modification, known to be altered in tumors. It targets dozens of sites within miRNAs, some of which impact miRNA biogenesis and function, as well as many miRNA recognition sites. However, the full extent of the effect of editing on regulation by miRNAs and its behavior in human cancers is still unknown. Here we systematically characterized miRNA editing in 10 593 human samples across 32 cancer types and normal controls. We find that the majority of previously reported sites show little to no evidence for editing in this dataset, compile a list of 58 reliable miRNA editing sites, and study them across normal and cancer samples. Edited miRNA versions tend to suppress expression of known oncogenes, and, consistently, we observe a clear global tendency for hypo-editing in tumors, in strike contrast to the behavior for mRNA editing, allowing an accurate classification of normal/tumor samples based on their miRNA editing profile. In many cancers this profile correlates with patients' survival. Finally, thousands of miRNA binding sites are differentially edited in cancer. Our study thus establishes the important effect of RNA editing on miRNA-regulation in the tumor cell, with prospects for diagnostic and prognostic applications.
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Affiliation(s)
- Yishay Pinto
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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23
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Denichenko P, Mogilevsky M, Cléry A, Welte T, Biran J, Shimshon O, Barnabas GD, Danan-Gotthold M, Kumar S, Yavin E, Levanon EY, Allain FH, Geiger T, Levkowitz G, Karni R. Specific inhibition of splicing factor activity by decoy RNA oligonucleotides. Nat Commun 2019; 10:1590. [PMID: 30962446 PMCID: PMC6453957 DOI: 10.1038/s41467-019-09523-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/12/2019] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing, a fundamental step in gene expression, is deregulated in many diseases. Splicing factors (SFs), which regulate this process, are up- or down regulated or mutated in several diseases including cancer. To date, there are no inhibitors that directly inhibit the activity of SFs. We designed decoy oligonucleotides, composed of several repeats of a RNA motif, which is recognized by a single SF. Here we show that decoy oligonucleotides targeting splicing factors RBFOX1/2, SRSF1 and PTBP1, can specifically bind to their respective SFs and inhibit their splicing and biological activities both in vitro and in vivo. These decoy oligonucleotides present an approach to specifically downregulate SF activity in conditions where SFs are either up-regulated or hyperactive. Alternative splicing, critical for gene expression, is deregulated in many diseases. Here the authors develop decoy oligonucleotides to specifically downregulate splicing factors activity.
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Affiliation(s)
- Polina Denichenko
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Maxim Mogilevsky
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, ETH Zurich, Hönggerbergring 64, 8093, Zurich, Switzerland
| | - Thomas Welte
- Dynamic Biosensors, GmbH, Lochhamer Strasse 15, 82152, Martinsried/Planegg, Germany
| | - Jakob Biran
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Odelia Shimshon
- Department of Medicinal Chemistry, Institute for Drug Research, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Miri Danan-Gotthold
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Saran Kumar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Eylon Yavin
- Department of Medicinal Chemistry, Institute for Drug Research, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Frédéric H Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, Hönggerbergring 64, 8093, Zurich, Switzerland
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gil Levkowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
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24
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Dick ALW, Khermesh K, Paul E, Stamp F, Levanon EY, Chen A. Adenosine-to-Inosine RNA Editing Within Corticolimbic Brain Regions Is Regulated in Response to Chronic Social Defeat Stress in Mice. Front Psychiatry 2019; 10:277. [PMID: 31133890 PMCID: PMC6512728 DOI: 10.3389/fpsyt.2019.00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/10/2019] [Indexed: 11/13/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a co-/posttranscriptional modification of double-stranded RNA, catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes, which results in recognition of inosine as guanosine by translational and splicing machinery causing potential recoding events in amino acid sequences. A-to-I editing is prominent within brain-specific transcripts, and dysregulation of editing at several well-studied loci (e.g., Gria2, Htr2c) has been implicated in acute and chronic stress in rodents as well as neurological (e.g., Alzheimer's) and psychopathological disorders such as schizophrenia and major depressive disorder. However, only a small fraction of recoding sites has been investigated within the brain following stress, and our understanding of the role of RNA editing in transcriptome regulation following environmental stimuli remains poorly understood. Thus, we aimed to investigate A-to-I editing at hundreds of loci following chronic social defeat stress (CSDS) in mice within corticolimbic regions responsive to chronic stress regulation. Adult male mice were subjected to CSDS or control conditions for 21 days and dynamic regulation of A-to-I editing was investigated 2 and 8 days following the final defeat within both the medial prefrontal cortex (mPFC) and basolateral amygdala (BLA). Employing a targeted resequencing approach, which utilizes microfluidics-based multiplex polymerase chain reaction (PCR) coupled with next-generation sequencing, we analyzed A-to-I editing at ∼100 high-confidence editing sites within the mouse brain. CSDS resulted in acute regulation of transcripts encoding several ADAR enzymes, which normalized 8 days following the final defeat and was specific for susceptible mice. In contrast, sequencing analysis revealed modest and dynamic regulation of A-to-I editing within numerous transcripts in both the mPFC and BLA of resilient and susceptible mice at both 2 and 8 days following CSDS with minimal overlap between regions and time points. Editing within the Htr2c transcript and relative abundance of Htr2c messenger RNA (mRNA)variants were also observed within the BLA of susceptible mice 2 days following CSDS. These results indicate dynamic RNA editing within discrete brain regions following CSDS in mice, further implicating A-to-I editing as a stress-sensitive molecular mechanism within the brain of potential relevance to resiliency and susceptibility to CSDS.
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Affiliation(s)
- Alec L W Dick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | | | - Evan Paul
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Fabian Stamp
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of LifeSciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany.,Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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25
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Jain M, Mann TD, Stulić M, Rao SP, Kirsch A, Pullirsch D, Strobl X, Rath C, Reissig L, Moreth K, Klein-Rodewald T, Bekeredjian R, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Pablik E, Cimatti L, Martin D, Zinnanti J, Graier WF, Sibilia M, Frank S, Levanon EY, Jantsch MF. RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure. EMBO J 2018; 37:e94813. [PMID: 30087110 PMCID: PMC6166124 DOI: 10.15252/embj.201694813] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/25/2018] [Accepted: 06/27/2018] [Indexed: 12/26/2022] Open
Abstract
Epitranscriptomic events such as adenosine-to-inosine (A-to-I) RNA editing by ADAR can recode mRNAs to translate novel proteins. Editing of the mRNA that encodes actin crosslinking protein Filamin A (FLNA) mediates a Q-to-R transition in the interactive C-terminal region. While FLNA editing is conserved among vertebrates, its physiological function remains unclear. Here, we show that cardiovascular tissues in humans and mice show massive editing and that FLNA RNA is the most prominent substrate. Patient-derived RNA-Seq data demonstrate a significant drop in FLNA editing associated with cardiovascular diseases. Using mice with only impaired FLNA editing, we observed increased vascular contraction and diastolic hypertension accompanied by increased myosin light chain phosphorylation, arterial remodeling, and left ventricular wall thickening, which eventually causes cardiac remodeling and reduced systolic output. These results demonstrate a causal relationship between RNA editing and the development of cardiovascular disease indicating that a single epitranscriptomic RNA modification can maintain cardiovascular health.
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Affiliation(s)
- Mamta Jain
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Tomer D Mann
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Maja Stulić
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Shailaja P Rao
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Andrijana Kirsch
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dieter Pullirsch
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Xué Strobl
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Claus Rath
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Lukas Reissig
- Division of Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Kristin Moreth
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tanja Klein-Rodewald
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Raffi Bekeredjian
- Department of Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Eleonore Pablik
- Section for Medical Statistics, CeMSIIS, Medical University of Vienna, Vienna, Austria
| | - Laura Cimatti
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - David Martin
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | | | - Wolfgang F Graier
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Maria Sibilia
- Department of Medicine I, Comprehensive Cancer Center, Institute for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Saša Frank
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Michael F Jantsch
- Division of Cell Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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26
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Shallev L, Kopel E, Feiglin A, Leichner GS, Avni D, Sidi Y, Eisenberg E, Barzilai A, Levanon EY, Greenberger S. Decreased A-to-I RNA editing as a source of keratinocytes' dsRNA in psoriasis. RNA 2018; 24:828-840. [PMID: 29592874 PMCID: PMC5959251 DOI: 10.1261/rna.064659.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/26/2018] [Indexed: 05/30/2023]
Abstract
Recognition of dsRNA molecules activates the MDA5-MAVS pathway and plays a critical role in stimulating type-I interferon responses in psoriasis. However, the source of the dsRNA accumulation in psoriatic keratinocytes remains largely unknown. A-to-I RNA editing is a common co- or post-transcriptional modification that diversifies adenosine in dsRNA, and leads to unwinding of dsRNA structures. Thus, impaired RNA editing activity can result in an increased load of endogenous dsRNAs. Here we provide a transcriptome-wide analysis of RNA editing across dozens of psoriasis patients, and we demonstrate a global editing reduction in psoriatic lesions. In addition to the global alteration, we also detect editing changes in functional recoding sites located in the IGFBP7, COPA, and FLNA genes. Accretion of dsRNA activates autoimmune responses, and therefore the results presented here, linking for the first time an autoimmune disease to reduction in global editing level, are relevant to a wide range of autoimmune diseases.
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Affiliation(s)
- Lea Shallev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Kopel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ariel Feiglin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gil S Leichner
- The Department of Dermatology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dror Avni
- Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Yechezkel Sidi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Medicine C, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Aviv Barzilai
- The Department of Dermatology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shoshana Greenberger
- The Department of Dermatology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Talpiot Medical Leadership Program, Sheba Medical Center, Tel Hashomer 52621, Israel
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27
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Abstract
RNA editing is a source of transcriptomic diversity, mainly in non-coding regions, and is found to be altered in cancer. In this issue of Cancer Cell, Peng et al. show that RNA editing events are manifested at the proteomic levels and are a source of cancer protein heterogeneity.
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Affiliation(s)
- Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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28
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Roth SH, Danan-Gotthold M, Ben-Izhak M, Rechavi G, Cohen CJ, Louzoun Y, Levanon EY. Increased RNA Editing May Provide a Source for Autoantigens in Systemic Lupus Erythematosus. Cell Rep 2018; 23:50-57. [PMID: 29617672 PMCID: PMC5905401 DOI: 10.1016/j.celrep.2018.03.036] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/21/2017] [Accepted: 03/09/2018] [Indexed: 12/12/2022] Open
Abstract
RNA-editing mechanisms, which induce nucleotide substitution in the RNA, increase transcript and protein diversities. Editing dysregulation has been shown to lead to grave outcomes, and transcriptome-wide aberrant RNA editing has been found in tumors. However, little is known about the involvement of editing in other diseases. Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease characterized by a loss of tolerance for autoantigens from various tissues and the production of multiple autoantibodies. Here, we show that blood samples from individuals with SLE have abnormally high levels of RNA editing, some of which affect proteins and potentially generate novel autoantigens. We suggest that elevated RNA editing, either by ADARs or APOBECs, may be involved in the pathophysiology of SLE, as well as in other autoimmune diseases, by generating or increasing the autoantigen load, a key requisite for the progression of autoimmunity.
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Affiliation(s)
- Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Meirav Ben-Izhak
- Department of Mathematics, Bar-Ilan University, Ramat Gan 5290002, Israel; The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Gideon Rechavi
- Cancer Research Center and the Wohl Institute for Translational Medicine, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Cyrille J Cohen
- Laboratory of Tumor Immunology and Immunotherapy, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan 5290002, Israel; The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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29
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Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biol 2018; 19:36. [PMID: 29548336 PMCID: PMC5857127 DOI: 10.1186/s13059-018-1403-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/02/2018] [Indexed: 11/22/2022] Open
Abstract
High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.
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Affiliation(s)
- Serghei Mangul
- Department of Computer Science, University of California, Los Angeles, CA, USA. .,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.
| | - Harry Taegyun Yang
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Nicolas Strauli
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Franziska Gruhl
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Kevin Hsieh
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Linus Chen
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Timothy Daley
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | | | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Prescott G Woodruff
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Esteban Burchard
- Schools of Pharmacy and Medicine, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Max A Seibold
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.,University of Colorado School of Medicine, Denver, CO, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Noah Zaitlen
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
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30
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Porath HT, Schaffer AA, Kaniewska P, Alon S, Eisenberg E, Rosenthal J, Levanon EY, Levy O. A-to-I RNA Editing in the Earliest-Diverging Eumetazoan Phyla. Mol Biol Evol 2018; 34:1890-1901. [PMID: 28453786 PMCID: PMC5850803 DOI: 10.1093/molbev/msx125] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.
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Affiliation(s)
- Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Amos A Schaffer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Paulina Kaniewska
- Global Change Institute, The University of Queensland, St Lucia, Australia
| | - Shahar Alon
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Joshua Rosenthal
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, The Marine Biological Laboratory, Woods Hole, MA
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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31
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Jacob-Hirsch J, Eyal E, Knisbacher BA, Roth J, Cesarkas K, Dor C, Farage-Barhom S, Kunik V, Simon AJ, Gal M, Yalon M, Moshitch-Moshkovitz S, Tearle R, Constantini S, Levanon EY, Amariglio N, Rechavi G. Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders. Cell Res 2018; 28:187-203. [PMID: 29327725 DOI: 10.1038/cr.2018.8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains. The majority of somatic brain retrotransposons integrate into pre-existing repetitive elements, preferentially A/T rich L1 sequences, resulting in nested insertions. Our findings document the fingerprints of encoded endonuclease independent mechanisms in the majority of L1 brain insertion events. The insertions are "non-classical" in that they are truncated at both ends, integrate in the same orientation as the host element, and their target sequences are enriched with a CCATT motif in contrast to the classical endonuclease motif of most other retrotranspositions. We show that L1Hs elements integrate preferentially into genes associated with neural functions and diseases. We propose that pre-existing retrotransposons act as "lightning rods" for novel insertions, which may give fine modulation of gene expression while safeguarding from deleterious events. Overwhelmingly uncontrolled retrotransposition may breach this safeguard mechanism and increase the risk of harmful mutagenesis in neurodevelopmental disorders.
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Affiliation(s)
- Jasmine Jacob-Hirsch
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Eran Eyal
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | | | - Jonathan Roth
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel Aviv Medical Center, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karen Cesarkas
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Chen Dor
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sarit Farage-Barhom
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Vered Kunik
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Amos J Simon
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Moran Gal
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Michal Yalon
- Department of Pediatric Hematology-Oncology, Edmond and Lily Safra Children's Hospital, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sharon Moshitch-Moshkovitz
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Rick Tearle
- Complete Genomics, 2071 Stierlin Court, Mountain View, CA 94043, USA
| | - Shlomi Constantini
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel Aviv Medical Center, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Ninette Amariglio
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Gideon Rechavi
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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32
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Abstract
Concentration is important and not only while driving; a new study indicates how an adjacent genomic element helps to increase the efficiency of a specific adenosine to inosine RNA editing reaction, by providing a means to increase the local concentration of the RNA editing enzyme ADAR.
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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
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel.
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33
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Porath HT, Knisbacher BA, Eisenberg E, Levanon EY. Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance. Genome Biol 2017; 18:185. [PMID: 28969707 PMCID: PMC5625713 DOI: 10.1186/s13059-017-1315-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/07/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Adenosine to inosine (A-to-I) RNA editing is a post-transcriptional modification catalyzed by the ADAR (adenosine deaminase that acts on RNA) enzymes, which are ubiquitously expressed among metazoans. Technical requirements have limited systematic mapping of editing sites to a small number of organisms. Thus, the extent of editing across the metazoan lineage is largely unknown. RESULTS Here, we apply a computational procedure to search for RNA-sequencing reads containing clusters of editing sites in 21 diverse organisms. Clusters of editing sites are abundant in repetitive genomic regions that putatively form double-stranded RNA (dsRNA) structures and are rarely seen in coding regions. The method reveals a considerable variation in hyper-editing levels across species, which is partly explained by differences in the potential of sequences to form dsRNA structures and the variability of ADAR proteins. Several commonly used model animals exhibit low editing levels and editing levels in primates is not exceptionally high, as previously suggested. CONCLUSIONS Editing by ADARs is highly prevalent across the Metazoa, mostly targeting dsRNA structures formed by genomic repeats. The degree to which the transcriptome of a given species undergoes hyper-editing is governed by the repertoire of repeats in the underlying genome. The strong association of RNA editing with the long dsRNA regions originating from non-coding repetitive elements is contrasted by the almost non-existing signal seen in coding regions. Hyper-edited regions are rarely expressed in a non-edited form. These results support the notion that the main role of ADAR is to suppress the cellular response to endogenous dsRNA structures.
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Affiliation(s)
- Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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34
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Levy O, Knisbacher BA, Levanon EY, Havlin S. Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes. Sci Adv 2017; 3:e1701256. [PMID: 29043294 PMCID: PMC5640379 DOI: 10.1126/sciadv.1701256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/20/2017] [Indexed: 05/28/2023]
Abstract
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements. We develop a computational framework based on network theory that tracks the path of RE proliferation throughout evolution. We analyze SVA (SINE-VNTR-Alu), the youngest RE family in human genomes, to understand RE dynamics across hominids. Integrating comparative genomics and network tools enables us to track the course of SVA proliferation, identify yet unknown active communities, and detect tentative "master REs" that played key roles in SVA propagation, providing strong support for the fundamental "master gene" model of RE proliferation. The method is generic and thus can be applied to REs of any of the thousands of available genomes to identify active RE communities and master REs that were pivotal in the evolution of their host genomes.
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Affiliation(s)
- Orr Levy
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Binyamin A. Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Erez Y. Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shlomo Havlin
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
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35
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Liscovitch-Brauer N, Alon S, Porath HT, Elstein B, Unger R, Ziv T, Admon A, Levanon EY, Rosenthal JJC, Eisenberg E. Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods. Cell 2017; 169:191-202.e11. [PMID: 28388405 DOI: 10.1016/j.cell.2017.03.025] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/02/2017] [Accepted: 03/16/2017] [Indexed: 12/29/2022]
Abstract
RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP.
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Affiliation(s)
- Noa Liscovitch-Brauer
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shahar Alon
- Media Lab and McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hagit T Porath
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Boaz Elstein
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ron Unger
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Tamar Ziv
- Smoler Proteomics Center and Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Arie Admon
- Smoler Proteomics Center and Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Joshua J C Rosenthal
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan 00901, Puerto Rico.
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
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36
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Gal-Mark N, Shallev L, Sweetat S, Barak M, Billy Li J, Levanon EY, Eisenberg E, Behar O. Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition. Sci Rep 2017; 7:43421. [PMID: 28266523 PMCID: PMC5339895 DOI: 10.1038/srep43421] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/24/2017] [Indexed: 11/10/2022] Open
Abstract
Adenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level. A-to-I RNA editing is abundant in the brain, and altered editing levels have been reported in various neurological pathologies and following spinal cord injury (SCI). The prevailing concept is that the RNA editing process itself is dysregulated by brain pathologies. Here we analyzed recent RNA-seq data, and found that, except for few mammalian conserved editing sites, editing is significantly higher in neurons than in other cell populations of the brain. We studied A-to-I RNA editing in stab wound injury (SWI) and SCI models and showed that the apparent under-editing observed after injury correlates with an approximately 20% reduction in the relative density of neurons, due to cell death and immune cell infiltration that may account for the observed under-editing. Studies of neuronal and astrocyte cultures and a computational analysis of SCI RNA-seq data further supported the possibility that a reduction in neuronal density is responsible for alterations in the tissue-wide editing patterns upon injury. Thus, our data suggest that the case for a mechanistic linkage between A-to-I RNA editing and brain pathologies should be revisited.
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Affiliation(s)
- Nurit Gal-Mark
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lea Shallev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Sahar Sweetat
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Michal Barak
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oded Behar
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
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Kipper S, Frolov L, Guy O, Pellach M, Glick Y, Malichi A, Knisbacher BA, Barbiro-Michaely E, Avrahami D, Yavets-Chen Y, Levanon EY, Gerber D. Control and automation of multilayered integrated microfluidic device fabrication. Lab Chip 2017; 17:557-566. [PMID: 28102868 DOI: 10.1039/c6lc01534d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Integrated microfluidics is a sophisticated three-dimensional (multi layer) solution for high complexity serial or parallel processes. Fabrication of integrated microfluidic devices requires soft lithography and the stacking of thin-patterned PDMS layers. Precise layer alignment and bonding is crucial. There are no previously reported standards for alignment of the layers, which is mostly performed using uncontrolled processes with very low alignment success. As a result, integrated microfluidics is mostly used in academia rather than in the many potential industrial applications. We have designed and manufactured a semiautomatic Microfluidic Device Assembly System (μDAS) for full device production. μDAS comprises an electrooptic mechanical system consisting of four main parts: optical system, smart media holder (for PDMS), a micropositioning xyzθ system and a macropositioning XY mechanism. The use of the μDAS yielded valuable information regarding PDMS as the material for device fabrication, revealed previously unidentified errors, and enabled optimization of a robust fabrication process. In addition, we have demonstrated the utilization of the μDAS technology for fabrication of a complex 3 layered device with over 12 000 micromechanical valves and an array of 64 × 64 DNA spots on a glass substrate with high yield and high accuracy. We increased fabrication yield from 25% to about 85% with an average layer alignment error of just ∼4 μm. It also increased our protein expression yields from 80% to over 90%, allowing us to investigate more proteins per experiment. The μDAS has great potential to become a valuable tool for both advancing integrated microfluidics in academia and producing and applying microfluidic devices in the industry.
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Affiliation(s)
- Sarit Kipper
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Ludmila Frolov
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Ortal Guy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Michal Pellach
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Yair Glick
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Asaf Malichi
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Binyamin A Knisbacher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Efrat Barbiro-Michaely
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Dorit Avrahami
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Yehuda Yavets-Chen
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
| | - Doron Gerber
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
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38
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Sapoznik S, Bahar-Shany K, Brand H, Pinto Y, Gabay O, Glick-Saar E, Dor C, Zadok O, Barshack I, Zundelevich A, Gal-Yam EN, Yung Y, Hourvitz A, Korach J, Beiner M, Jacob J, Levanon EY, Barak M, Aviel-Ronen S, Levanon K. Activation-Induced Cytidine Deaminase Links Ovulation-Induced Inflammation and Serous Carcinogenesis. Neoplasia 2016; 18:90-9. [PMID: 26936395 PMCID: PMC5005261 DOI: 10.1016/j.neo.2015.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 12/10/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022] Open
Abstract
In recent years, the notion that ovarian carcinoma results from ovulation-induced inflammation of the fallopian tube epithelial cells (FTECs) has gained evidence. However, the mechanistic pathway for this process has not been revealed yet. In the current study, we propose the mutator protein activation-induced cytidine deaminase (AID) as a link between ovulation-induced inflammation in FTECs and genotoxic damage leading to ovarian carcinogenesis. We show that AID, previously shown to be functional only in B lymphocytes, is expressed in FTECs under physiological conditions, and is induced in vitro upon ovulatory-like stimulation and in vivo in carcinoma-associated FTECs. We also report that AID activity results in epigenetic, genetic and genomic damage in FTECs. Overall, our data provides new insights into the etiology of ovarian carcinogenesis and may set the ground for innovative approaches aimed at prevention and early detection.
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Affiliation(s)
- Stav Sapoznik
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Keren Bahar-Shany
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Hadar Brand
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Israel
| | - Yishay Pinto
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Orshay Gabay
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Efrat Glick-Saar
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Chen Dor
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Oranit Zadok
- Department of Pathology, Chaim Sheba Medical Center, Ramat-Gan 52621, Israel
| | - Iris Barshack
- Department of Pathology, Chaim Sheba Medical Center, Ramat-Gan 52621, Israel
| | - Adi Zundelevich
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Einav Nili Gal-Yam
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel; The Talpiot Medical Leadership Program, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Yuval Yung
- IVF Unit and Reproduction Lab, Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Ramat-Gan, 52621, Israel
| | - Ariel Hourvitz
- IVF Unit and Reproduction Lab, Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Ramat-Gan, 52621, Israel
| | - Jacob Korach
- Department of Gynecologic Oncology, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Mario Beiner
- Department of Gynecologic Oncology, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Jasmine Jacob
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Michal Barak
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Sarit Aviel-Ronen
- Department of Pathology, Chaim Sheba Medical Center, Ramat-Gan 52621, Israel; The Talpiot Medical Leadership Program, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Keren Levanon
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Israel; The Talpiot Medical Leadership Program, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel.
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39
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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: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Gal M, Khermesh K, Barak M, Lin M, Lahat H, Reznik Wolf H, Lin M, Pras E, Levanon EY. Expanding preconception carrier screening for the Jewish population using high throughput microfluidics technology and next generation sequencing. BMC Med Genomics 2016; 9:24. [PMID: 27175728 PMCID: PMC4865987 DOI: 10.1186/s12920-016-0184-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/02/2016] [Indexed: 11/15/2022] Open
Abstract
Background Genetic screening to identify carriers of autosomal recessive diseases has become an integral part of routine prenatal care. In spite of the rapid growth of known mutations, most current screening programs include only a small subset of these mutations, and are performed using diverse molecular techniques, which are generally labor-intensive and time consuming. We examine the implementation of the combined high-throughput technologies of specific target amplification and next generation sequencing (NGS), for expanding the carrier screening program in the Israeli Jewish population as a test case. Methods We compiled a panel of 370 germline mutations, causing 120 disorders, previously identified in affected Jewish individuals from different ethnicities. This mutation panel was simultaneously captured in 48 samples using a multiplex PCR-based microfluidics approach followed by NGS, thereby performing 17,760 individual assays in a single experiment. Results The sensitivity (measured with depth of at least 50×) and specificity of the target capture was 98 and 95 % respectively, leaving minimal rate of inconclusive tests per sample tested. 97 % of the targeted mutations present in the samples were correctly identified and validated. Conclusion Our methodology was shown to successfully combine multiplexing of target specific primers, samples indexing and NGS technology for population genetic screens. Moreover, it’s relatively ease of use and flexibility of updating the targets screened, makes it highly suitable for clinical implementation. This protocol was demonstrated in pre-conceptional screening for pan-Jewish individuals, but can be applied to any other population or different sets of mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0184-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moran Gal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Khen Khermesh
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Michal Barak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Min Lin
- Fluidigm corporation, South San Francisco, California
| | - Hadas Lahat
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Haike Reznik Wolf
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Michael Lin
- Fluidigm corporation, South San Francisco, California
| | - Elon Pras
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel.
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Pinto Y, Gabay O, Arbiza L, Sams AJ, Keinan A, Levanon EY. Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. Genome Res 2016; 26:579-87. [PMID: 27056836 PMCID: PMC4864454 DOI: 10.1101/gr.199240.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/16/2016] [Indexed: 11/29/2022]
Abstract
The gradual accumulation of mutations by any of a number of mutational processes is a major driving force of divergence and evolution. Here, we investigate a potentially novel mutational process that is based on the activity of members of the AID/APOBEC family of deaminases. This gene family has been recently shown to introduce—in multiple types of cancer—enzyme-induced clusters of co-occurring somatic mutations caused by cytosine deamination. Going beyond somatic mutations, we hypothesized that APOBEC3—following its rapid expansion in primates—can introduce unique germline mutation clusters that can play a role in primate evolution. In this study, we tested this hypothesis by performing a comprehensive comparative genomic screen for APOBEC3-induced mutagenesis patterns across different hominids. We detected thousands of mutation clusters introduced along primate evolution which exhibit features that strongly fit the known patterns of APOBEC3G mutagenesis. These results suggest that APOBEC3G-induced mutations have contributed to the evolution of all genomes we studied. This is the first indication of site-directed, enzyme-induced genome evolution, which played a role in the evolution of both modern and archaic humans. This novel mutational mechanism exhibits several unique features, such as its higher tendency to mutate transcribed regions and regulatory elements and its ability to generate clusters of concurrent point mutations that all occur in a single generation. Our discovery demonstrates the exaptation of an anti-viral mechanism as a new source of genomic variation in hominids with a strong potential for functional consequences.
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Affiliation(s)
- Yishay Pinto
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Orshay Gabay
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Leonardo Arbiza
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Aaron J Sams
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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Gal M, Magen D, Zahran Y, Ravid S, Eran A, Khayat M, Gafni C, Levanon EY, Mandel H. A novel homozygous splice site mutation in NALCN identified in siblings with cachexia, strabismus, severe intellectual disability, epilepsy and abnormal respiratory rhythm. Eur J Med Genet 2016; 59:204-9. [PMID: 26923739 DOI: 10.1016/j.ejmg.2016.02.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 12/12/2022]
Abstract
We studied three siblings, born to consanguineous parents who presented with severe intellectual disability, cachexia, strabismus, seizures and episodes of abnormal respiratory rhythm. Whole exome sequencing led to identification of a novel homozygous splice site mutation, IVS29-1G > A in the NALCN gene, that resulted in aberrant transcript in the patients. NALCN encodes a voltage-independent cation channel, involved in regulation of neuronal excitability. Three homozygous mutations in the NALCN gene were previously identified in only eight patients with severe hypotonia, speech impairment, cognitive delay, constipation and Infantile-Neuroaxonal-dystrophy- like symptoms. Our patients broaden the clinical spectrum associated with recessive mutations in NALCN, featuring also disrupted respiratory rhythm mimicking homozygous Nalcn knockout mice.
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Affiliation(s)
- Moran Gal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan Israel.
| | - Daniella Magen
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel; Laboratory of Molecular Medicine, Rappaport School of Medicine, Technion, Haifa, Israel
| | - Younan Zahran
- Department of Pediatric Medicine, Clalit Health Services, Ibillin, Israel
| | - Sarit Ravid
- Pediatric Neurology Unit and Epilepsy Service, Meyer Children's Hospital, Rambam Health Care Campus, Haifa, Israel.
| | - Ayelet Eran
- Department of Radiology, Health Care Campus, Haifa, Israel
| | - Morad Khayat
- The Genetic Institute, Emek Medical Center, Afula, Israel
| | - Chen Gafni
- The Genetic Institute, Emek Medical Center, Afula, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan Israel
| | - Hanna Mandel
- Metabolic Unit, Rambam Health Care Center, Haifa, Israel; Rappaport School of Medicine, Technion, Haifa, Israel
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Khermesh K, D'Erchia AM, Barak M, Annese A, Wachtel C, Levanon EY, Picardi E, Eisenberg E. Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease. RNA 2016; 22:290-302. [PMID: 26655226 PMCID: PMC4712678 DOI: 10.1261/rna.054627.115] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/18/2015] [Indexed: 05/20/2023]
Abstract
Adenosine to inosine (A-to-I) RNA editing, catalyzed by the ADAR enzyme family, acts on dsRNA structures within pre-mRNA molecules. Editing of the coding part of the mRNA may lead to recoding, amino acid substitution in the resulting protein, possibly modifying its biochemical and biophysical properties. Altered RNA editing patterns have been observed in various neurological pathologies. Here, we present a comprehensive study of recoding by RNA editing in Alzheimer's disease (AD), the most common cause of irreversible dementia. We have used a targeted resequencing approach supplemented by a microfluidic-based high-throughput PCR coupled with next-generation sequencing to accurately quantify A-to-I RNA editing levels in a preselected set of target sites, mostly located within the coding sequence of synaptic genes. Overall, editing levels decreased in AD patients' brain tissues, mainly in the hippocampus and to a lesser degree in the temporal and frontal lobes. Differential RNA editing levels were observed in 35 target sites within 22 genes. These results may shed light on a possible association between the neurodegenerative processes typical for AD and deficient RNA editing.
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Affiliation(s)
- Khen Khermesh
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Anna Maria D'Erchia
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy Institute of Biomembranes and Bioenergetics, National Research Council, Bari, 70126, Italy
| | - Michal Barak
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Anita Annese
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy
| | - Chaim Wachtel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 59002, Israel
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, 70126, Italy Institute of Biomembranes and Bioenergetics, National Research Council, Bari, 70126, Italy
| | - Eli Eisenberg
- Sagol School of Neuroscience and Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, 69978, Israel
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Sapoznik S, Bahar-Shany K, Brand H, Pinto Y, Gabay O, Glick-Saar E, Dor C, Zadok O, Barshack I, Zundelevich A, Gal-Yam EN, Yung Y, Hourvitz A, Korach J, Beiner M, Jacob J, Levanon EY, Barak M, Aviel-Ronen S, Levanon K. Abstract A34: Activation-induced cytidine deaminase links ovulation-induced inflammation and serous carcinogenesis. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.ovca15-a34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In recent years, the notion that serous ovarian carcinoma results from ovulation-induced inflammation of the fallopian tube epithelial cells (FTECs) has gained evidence. However, the mechanistic pathway that leads to mutagenesis and genomic instability has not been revealed yet. The mutator enzyme activation-induced cytidine deaminase (AID), which is known to be involved in the process of immunoglobulin somatic hypermutations, has also been recently implicated in inflammation-induced epithelial malignancies. In the current study, we propose that AID is a mechanistic link between ovulation-induced inflammation in FTECs and the genotoxic damage that leads to serous carcinogenesis.
We tested at the expression of AID in human fallopian tube tissues from patients with various gynecological pathologies, as well as in cultured FTECs in an experimental model mimicking normal ovulation. We also looked at the functional effects of AID up regulation in vitro by analyzing double strand DNA breaks, abasic sites, hypomethylation and chromosomal rearrangements. We also performed a comprehensive bioinformatic analysis of somatic mutations patterns in publically available serous carcinoma sequencing data in search of AID mutational fingerprints.
We show that AID, previously shown to be functional only in B lymphocytes, is expressed in human FTECs under physiological conditions, is induced in vitro upon ovulatory-like stimulation and is elevated in vivo under carcinogenesis-associated circumstances. We also report that AID activity results in epigenetic, genetic and genomic damage in FTECs.
Overall, our data provides new insights on the etiology of serous ovarian carcinogenesis and may set the ground for innovative approaches aimed at prevention and early-detection.
Citation Format: Stav Sapoznik, Keren Bahar-Shany, Hadar Brand, Yishay Pinto, Orshay Gabay, Efrat Glick-Saar, Chen Dor, Oranit Zadok, Iris Barshack, Adi Zundelevich, Einav Nili Gal-Yam, Yuval Yung, Ariel Hourvitz, Jacob Korach, Mario Beiner, Jasmine Jacob, Erez Y. Levanon, Michal Barak, Sarit Aviel-Ronen, Keren Levanon. Activation-induced cytidine deaminase links ovulation-induced inflammation and serous carcinogenesis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A34.
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Affiliation(s)
| | | | - Hadar Brand
- 1Chaim Sheba Medical Center, Ramat Gan, Israel,
| | | | | | | | - Chen Dor
- 1Chaim Sheba Medical Center, Ramat Gan, Israel,
| | | | | | | | | | - Yuval Yung
- 1Chaim Sheba Medical Center, Ramat Gan, Israel,
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Knisbacher BA, Gerber D, Levanon EY. DNA Editing by APOBECs: A Genomic Preserver and Transformer. Trends Genet 2016; 32:16-28. [PMID: 26608778 DOI: 10.1016/j.tig.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Information warfare is not limited to the cyber world because it is waged within our cells as well. The unique AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family comprises proteins that alter DNA sequences by converting deoxycytidines to deoxyuridines through deamination. This C-to-U DNA editing enables them to inhibit parasitic viruses and retrotransposons by disrupting their genomic content. In addition to attacking genomic invaders, APOBECs can target their host genome, which can be beneficial by initiating processes that create antibody diversity needed for the immune system or by accelerating the rate of evolution. AID can also alter gene regulation by removing epigenetic modifications from genomic DNA. However, when uncontrolled, these powerful agents of change can threaten genome stability and eventually lead to cancer.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel.
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Shamay-Ramot A, Khermesh K, Porath HT, Barak M, Pinto Y, Wachtel C, Zilberberg A, Lerer-Goldshtein T, Efroni S, Levanon EY, Appelbaum L. Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish. PLoS Genet 2015; 11:e1005702. [PMID: 26637167 PMCID: PMC4670233 DOI: 10.1371/journal.pgen.1005702] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 11/04/2015] [Indexed: 01/03/2023] Open
Abstract
Fragile X syndrome (FXS) is the most frequent inherited form of mental retardation. The cause for this X-linked disorder is the silencing of the fragile X mental retardation 1 (fmr1) gene and the absence of the fragile X mental retardation protein (Fmrp). The RNA-binding protein Fmrp represses protein translation, particularly in synapses. In Drosophila, Fmrp interacts with the adenosine deaminase acting on RNA (Adar) enzymes. Adar enzymes convert adenosine to inosine (A-to-I) and modify the sequence of RNA transcripts. Utilizing the fmr1 zebrafish mutant (fmr1-/-), we studied Fmrp-dependent neuronal circuit formation, behavior, and Adar-mediated RNA editing. By combining behavior analyses and live imaging of single axons and synapses, we showed hyperlocomotor activity, as well as increased axonal branching and synaptic density, in fmr1-/- larvae. We identified thousands of clustered RNA editing sites in the zebrafish transcriptome and showed that Fmrp biochemically interacts with the Adar2a protein. The expression levels of the adar genes and Adar2 protein increased in fmr1-/- zebrafish. Microfluidic-based multiplex PCR coupled with deep sequencing showed a mild increase in A-to-I RNA editing levels in evolutionarily conserved neuronal and synaptic Adar-targets in fmr1-/- larvae. These findings suggest that loss of Fmrp results in increased Adar-mediated RNA editing activity on target-specific RNAs, which, in turn, might alter neuronal circuit formation and behavior in FXS. The most frequent inherited mental retardation disorder is fragile X syndrome, which is characterized by learning disabilities, cognitive impairment, anxiety, and hyperactive behavior. The genetic cause of this disorder is the silencing of the fmr1 gene, which encodes the RNA-binding protein Fmrp. This protein inhibits the production of various proteins in the brain and interacts with the Adar enzyme, which converts the nucleotide A into I in RNAs. However, it is unclear by which mechanism the loss of Fmrp affects the sequence of neuronal genes and, ultimately, brain function. Here, we used the fmr1 mutant zebrafish (fmr1-/-), which enables high-throughput genetics and live imaging experiments in a transparent and evolutionarily conserved brain. We found that loss of Fmrp altered neuronal circuit formation. Furthermore, similar to human patients, the fmr1-/- larvae were hyperactive. Biochemical assays showed that Fmrp interacts with the Adar2a protein, which is increased in fmr1-/- larvae. Thus, we characterized global RNA editing in the zebrafish transcriptome and used a microfluidic-based high-throughput technique to accurately quantify RNA editing levels. Loss of Fmrp resulted in a mild increase in RNA editing in the coding sequences of conserved synaptic genes. These findings propose that altered RNA editing levels may affect neuronal and behavioral deficiencies in FXS.
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Affiliation(s)
- Adi Shamay-Ramot
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Khen Khermesh
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Hagit T. Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michal Barak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yishay Pinto
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Chaim Wachtel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Tali Lerer-Goldshtein
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Erez Y. Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Lior Appelbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail:
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Abstract
Long terminal repeat retrotransposons (LTR) are widespread in vertebrates and their dynamism facilitates genome evolution. However, these endogenous retroviruses (ERVs) must be restricted to maintain genomic stability. The APOBECs, a protein family that can edit C-to-U in DNA, do so by interfering with reverse transcription and hypermutating retrotransposon DNA. In some cases, a retrotransposon may integrate into the genome despite being hypermutated. Such an event introduces a unique sequence into the genome, increasing retrotransposon diversity and the probability of developing new function at the locus of insertion. The prevalence of this phenomenon and its effects on vertebrate genomes are still unclear. In this study, we screened ERV sequences in the genomes of 123 diverse species and identified hundreds of thousands of edited sites in multiple vertebrate lineages, including placental mammals, marsupials, and birds. Numerous edited ERVs carry high mutation loads, some with greater than 350 edited sites, profoundly damaging their open-reading frames. For many of the species studied, this is the first evidence that APOBECs are active players in their innate immune system. Unexpectedly, some birds and especially zebra finch and medium ground-finch (one of Darwin’s finches) are exceptionally enriched in DNA editing. We demonstrate that edited retrotransposons may be preferentially retained in active genomic regions, as reflected from their enrichment in genes, exons, promoters, and transcription start sites, thereby raising the probability of their exaptation for novel function. In conclusion, DNA editing of retrotransposons by APOBECs has a substantial role in vertebrate innate immunity and may boost genome evolution.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Erez Y Levanon
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
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Liscovitch N, Bazak L, Levanon EY, Chechik G. Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain. RNA Biol 2015; 11:1447-56. [PMID: 25692240 DOI: 10.4161/15476286.2014.992286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A-to-I RNA editing by adenosine deaminases acting on RNA is a post-transcriptional modification that is crucial for normal life and development in vertebrates. RNA editing has been shown to be very abundant in the human transcriptome, specifically at the primate-specific Alu elements. The functional role of this wide-spread effect is still not clear; it is believed that editing of transcripts is a mechanism for their down-regulation via processes such as nuclear retention or RNA degradation. Here we combine 2 neural gene expression datasets with genome-level editing information to examine the relation between the expression of ADAR genes with the expression of their target genes. Specifically, we computed the spatial correlation across structures of post-mortem human brains between ADAR and a large set of targets that were found to be edited in their Alu repeats. Surprisingly, we found that a large fraction of the edited genes are positively correlated with ADAR, opposing the assumption that editing would reduce expression. When considering the correlations between ADAR and its targets over development, 2 gene subsets emerge, positively correlated and negatively correlated with ADAR expression. Specifically, in embryonic time points, ADAR is positively correlated with many genes related to RNA processing and regulation of gene expression. These findings imply that the suggested mechanism of regulation of expression by editing is probably not a global one; ADAR expression does not have a genome wide effect reducing the expression of editing targets. It is possible, however, that RNA editing by ADAR in non-coding regions of the gene might be a part of a more complex expression regulation mechanism.
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Affiliation(s)
- Noa Liscovitch
- a Gonda Multidisiplinary Brain Research Center ; Bar-Ilan University ; Ramat Gan , Israel
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49
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Paz-Yaacov N, Bazak L, Buchumenski I, Porath HT, Danan-Gotthold M, Knisbacher BA, Eisenberg E, Levanon EY. Elevated RNA Editing Activity Is a Major Contributor to Transcriptomic Diversity in Tumors. Cell Rep 2015; 13:267-76. [PMID: 26440895 DOI: 10.1016/j.celrep.2015.08.080] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/02/2015] [Accepted: 08/28/2015] [Indexed: 01/08/2023] Open
Abstract
Genomic mutations in key genes are known to drive tumorigenesis and have been the focus of much attention in recent years. However, genetic content also may change farther downstream. RNA editing alters the mRNA sequence from its genomic blueprint in a dynamic and flexible way. A few isolated cases of editing alterations in cancer have been reported previously. Here, we provide a transcriptome-wide characterization of RNA editing across hundreds of cancer samples from multiple cancer tissues, and we show that A-to-I editing and the enzymes mediating this modification are significantly altered, usually elevated, in most cancer types. Increased editing activity is found to be associated with patient survival. As is the case with somatic mutations in DNA, most of these newly introduced RNA mutations are likely passengers, but a few may serve as drivers that may be novel candidates for therapeutic and diagnostic purposes.
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Affiliation(s)
- Nurit Paz-Yaacov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lily Bazak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eli Eisenberg
- School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
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50
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Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, Huang Z, Gorbunova V, Zhang L, Zhao W, Wildman DE, Xiong Y, Gudkov A, Zheng Q, Rechavi G, Liu S, Bazak L, Chen J, Knisbacher BA, Lu Y, Shams I, Gajda K, Farré M, Kim J, Lewin HA, Ma J, Band M, Bicker A, Kranz A, Mattheus T, Schmidt H, Seluanov A, Azpurua J, McGowen MR, Ben Jacob E, Li K, Peng S, Zhu X, Liao X, Li S, Krogh A, Zhou X, Brodsky L, Wang J. Erratum: Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat Commun 2015; 6:8051. [DOI: 10.1038/ncomms9051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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