101
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Identification of genetic variants controlling RNA editing and their effect on RNA structure stabilization. Eur J Hum Genet 2020; 28:1753-1762. [PMID: 32651550 DOI: 10.1038/s41431-020-0688-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/31/2020] [Accepted: 06/11/2020] [Indexed: 12/31/2022] Open
Abstract
Post-transcriptional modification of RNA (RNA editing, RNAe) results in differences between the RNA transcript and the genomic DNA sequence (RDD). Enzymatic modification of adenosine to inosine (A2I) by ADAR is the most studied type of RNAe. However, few genetic association studies with A2I RNAe events have been conducted. Some studies have analyzed the inter-population RNAe-QTL diversity in humans, but the sample size of these studies was limited. Other types of RNA and DNA differences have been reported but are largely understudied. Here, we report a comprehensive analysis of all types of RDD, based on two independent datasets. We found that A2I was by far the most observed type of RDD. Moreover, manual curation suggests that A2I is likely the only enzymatically driven RNAe type observed in blood derived DNA, all other non-A2I RDD could either be attributed to sequencing and processing artifacts, or are a result of somatic DNA rearrangements. We then conducted an in-cis genetic association study and identified 472 genetic associations (RNAe-QTL), that were replicated in both datasets. We confirm the potential effect of the RNAe-QTL on RNA structure by showing that allele specific RNAe occurs in heterozygotes. Although the generally assumed function of RNAe is to destabilize double stranded RNA structure, we found clear evidence for the potential additional involvement of RNAe in maintaining RNA hairpin that has been altered by the RNAe-QTL. Our study confirms, in two independent datasets, the potential role of RNAe in maintaining RNA structure in the presence of genetic variation.
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102
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Schaffer AA, Kopel E, Hendel A, Picardi E, Levanon E, Eisenberg E. The cell line A-to-I RNA editing catalogue. Nucleic Acids Res 2020; 48:5849-5858. [PMID: 32383740 PMCID: PMC7293008 DOI: 10.1093/nar/gkaa305] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/30/2020] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular diseases as well as cancer. In addition, the endogenous A-to-I editing machinery has been recently harnessed for RNA engineering. The study of RNA editing in humans relies heavily on the usage of cell lines as an important and commonly-used research tool. In particular, manipulations of the editing enzymes and their targets are often developed using cell line platforms. However, RNA editing in cell lines behaves very differently than in normal and diseased tissues, and most cell lines exhibit low editing levels, requiring over-expression of the enzymes. Here, we explore the A-to-I RNA editing landscape across over 1000 human cell lines types and show that for almost every editing target of interest a suitable cell line that mimics normal tissue condition may be found. We provide CLAIRE, a searchable catalogue of RNA editing levels across cell lines available at http://srv00.recas.ba.infn.it/atlas/claire.html, to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing.
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Affiliation(s)
- Amos A Schaffer
- 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
| | - Ayal Hendel
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, I-70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, I-70126 Bari, Italy
| | - 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 6997801, Israel
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103
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Di Giorgio S, Martignano F, Torcia MG, Mattiuz G, Conticello SG. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2. SCIENCE ADVANCES 2020; 6:eabb5813. [PMID: 32596474 PMCID: PMC7299625 DOI: 10.1126/sciadv.abb5813] [Citation(s) in RCA: 244] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/05/2020] [Indexed: 05/13/2023]
Abstract
The COVID-19 outbreak has become a global health risk, and understanding the response of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host deaminases is an innate restriction process to counter virus infection, but it is not yet known whether this process operates against coronaviruses. Here, we analyze RNA sequences from bronchoalveolar lavage fluids obtained from coronavirus-infected patients. We identify nucleotide changes that may be signatures of RNA editing: adenosine-to-inosine changes from ADAR deaminases and cytosine-to-uracil changes from APOBEC deaminases. Mutational analysis of genomes from different strains of Coronaviridae from human hosts reveals mutational patterns consistent with those observed in the transcriptomic data. However, the reduced ADAR signature in these data raises the possibility that ADARs might be more effective than APOBECs in restricting viral propagation. Our results thus suggest that both APOBECs and ADARs are involved in coronavirus genome editing, a process that may shape the fate of both virus and patient.
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Affiliation(s)
- Salvatore Di Giorgio
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Filippo Martignano
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Maria Gabriella Torcia
- Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy
| | - Giorgio Mattiuz
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy
| | - Silvestro G. Conticello
- Core Research Laboratory, ISPRO, Firenze 50139, Italy
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
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104
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An O, Tan KT, Li Y, Li J, Wu CS, Zhang B, Chen L, Yang H. CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. Int J Mol Sci 2020; 21:ijms21113828. [PMID: 32481589 PMCID: PMC7312552 DOI: 10.3390/ijms21113828] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in FASTQ format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus.edu.sg/csingsportal.
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Affiliation(s)
- Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
- Correspondence: (O.A.); (H.Y.); Tel.: +65-8452-1766 (O.A.); +65-6601-1533 (H.Y.)
| | - Kar-Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; (K.-T.T.); (Y.L.); (J.L.); (C.-S.W.); (B.Z.); (L.C.)
- Correspondence: (O.A.); (H.Y.); Tel.: +65-8452-1766 (O.A.); +65-6601-1533 (H.Y.)
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105
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Lo Giudice C, Silvestris DA, Roth SH, Eisenberg E, Pesole G, Gallo A, Picardi E. Quantifying RNA Editing in Deep Transcriptome Datasets. Front Genet 2020; 11:194. [PMID: 32211029 PMCID: PMC7069340 DOI: 10.3389/fgene.2020.00194] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/18/2020] [Indexed: 12/20/2022] Open
Abstract
Massive transcriptome sequencing through the RNAseq technology has enabled quantitative transcriptome-wide investigation of co-/post-transcriptional mechanisms such as alternative splicing and RNA editing. The latter is abundant in human transcriptomes in which million adenosines are deaminated into inosines by the ADAR enzymes. RNA editing modulates the innate immune response and its deregulation has been associated with different human diseases including autoimmune and inflammatory pathologies, neurodegenerative and psychiatric disorders, and tumors. Accurate profiling of RNA editing using deep transcriptome data is still a challenge, and the results depend strongly on processing and alignment steps taken. Accurate calling of the inosinome repertoire, however, is required to reliably quantify RNA editing and, in turn, investigate its biological and functional role across multiple samples. Using real RNAseq data, we demonstrate the impact of different bioinformatics steps on RNA editing detection and describe the main metrics to quantify its level of activity.
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Affiliation(s)
- Claudio Lo Giudice
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy
| | | | - Shalom Hillel Roth
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
| | - Angela Gallo
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù," Rome, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
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106
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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] [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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