1
|
Hertler J, Slama K, Schober B, Özrendeci Z, Marchand V, Motorin Y, Helm M. Synthesis of point-modified mRNA. Nucleic Acids Res 2022; 50:e115. [PMID: 36062567 PMCID: PMC9723659 DOI: 10.1093/nar/gkac719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/20/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022] Open
Abstract
Synthetic mRNA has recently moved into the focus of therapeutic and vaccination efforts. Incorporation of modified nucleotides during in vitro transcription can improve translation and attenuate immunogenicity, but is limited to triphosphate nucleotides which are accepted by RNA polymerases, and their incorporation is either random or complete. In contrast, site-specific modification, herein termed 'point modification' in analogy to point mutations, holds significant technical challenge. We developed fundamental techniques for isolation of long, translatable and internally point-modified mRNAs. Enabling concepts include three-way-one-pot splint ligations, and isolation of mRNA by real-time elution from agarose gels. The use of blue light permitted visualization of mRNA in pre-stained gels without the photochemical damage associated with the use of hard UV-radiation. This allowed visualization of the mRNA through its migration in the agarose gel, which in turn, was a prerequisite for its recovery by electroelution into precast troughs. Co-eluting agarose particles were quantified and found to not be detrimental to mRNA translation in vitro. Translation of EGFP-coding mRNA into functional protein was quantified by incorporation of 35S-labelled methionine and by in-gel EGFP fluorescence. This enabled the functional analysis of point modifications, specifically of ribose methylations in the middle of a 1371 nt long mRNA.
Collapse
Affiliation(s)
| | | | - Benedikt Schober
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Zeynep Özrendeci
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Virginie Marchand
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Yuri Motorin
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France,Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Mark Helm
- To whom correspondence should be addressed. Tel: +49 6131 392 5731; Fax: +49 6131 392 0373;
| |
Collapse
|
2
|
Richter F, Plehn JE, Bessler L, Hertler J, Jörg M, Cirzi C, Tuorto F, Friedland K, Helm M. RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis. Nucleic Acids Res 2022; 50:4201-4215. [PMID: 34850949 PMCID: PMC9071408 DOI: 10.1093/nar/gkab1150] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
The accurate definition of an epitranscriptome is endangered by artefacts resulting from RNA degradation after cell death, a ubiquitous yet little investigated process. By tracing RNA marker modifications through tissue preparation protocols, we identified a major blind spot from daily lab routine, that has massive impact on modification analysis in small RNAs. In particular, m6,6A and Am as co-varying rRNA marker modifications, appeared in small RNA fractions following rRNA degradation in vitro and in cellulo. Analysing mouse tissue at different time points post mortem, we tracked the progress of intracellular RNA degradation after cell death, and found it reflected in RNA modification patterns. Differences were dramatic between liver, where RNA degradation commenced immediately after death, and brain, yielding essentially undamaged RNA. RNA integrity correlated with low amounts of co-varying rRNA markers. Thus validated RNA preparations featured differentially modified tRNA populations whose information content allowed a distinction even among the related brain tissues cortex, cerebellum and hippocampus. Inversely, advanced cell death correlated with high rRNA marker content, and correspondingly little with the naïve state of living tissue. Therefore, unless RNA and tissue preparations are executed with utmost care, interpretation of modification patterns in tRNA and small RNA are prone to artefacts.
Collapse
Affiliation(s)
- Florian Richter
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Johanna E Plehn
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Larissa Bessler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Jasmin Hertler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Marko Jörg
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Cansu Cirzi
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ) 69120 Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg 69120 Heidelberg, Germany
| | - Francesca Tuorto
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance69120 Heidelberg, Germany
| | - Kristina Friedland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5 55128 Mainz, Germany
| |
Collapse
|
3
|
Marchand V, Ayadi L, Ernst FGM, Hertler J, Bourguignon‐Igel V, Galvanin A, Kotter A, Helm M, Lafontaine DLJ, Motorin Y. AlkAniline‐Seq: Profiling of m
7
G and m
3
C RNA Modifications at Single Nucleotide Resolution. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Lilia Ayadi
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Felix G. M. Ernst
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Jasmin Hertler
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Valérie Bourguignon‐Igel
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Denis L. J. Lafontaine
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Yuri Motorin
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| |
Collapse
|
4
|
Marchand V, Ayadi L, Ernst FGM, Hertler J, Bourguignon‐Igel V, Galvanin A, Kotter A, Helm M, Lafontaine DLJ, Motorin Y. AlkAniline‐Seq: Profiling of m
7
G and m
3
C RNA Modifications at Single Nucleotide Resolution. Angew Chem Int Ed Engl 2018; 57:16785-16790. [DOI: 10.1002/anie.201810946] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Lilia Ayadi
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Felix G. M. Ernst
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Jasmin Hertler
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Valérie Bourguignon‐Igel
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Denis L. J. Lafontaine
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Yuri Motorin
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| |
Collapse
|
5
|
Slama K, Galliot A, Weichmann F, Hertler J, Feederle R, Meister G, Helm M. Determination of enrichment factors for modified RNA in MeRIP experiments. Methods 2018; 156:102-109. [PMID: 30394295 DOI: 10.1016/j.ymeth.2018.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022] Open
Abstract
In the growing field of RNA modification, precipitation techniques using antibodies play an important role. However, little is known about their specificities and protocols are missing to assess their effectiveness. Here we present a method to assess enrichment factors after MeRIP-type pulldown experiments, here exemplified with a commercial antibody against N6-methyladenosine (m6A). Testing different pulldown and elution conditions, we measure enrichment factors of 4-5 using m6A-containing mRNAs against an unmodified control of identical sequence. Both types of mRNA carry 32P labels at different nucleotides, allowing their relative quantification in a mixture after digestion to nucleotides, separation by TLC and quantitative phosphorimaging of the labels.
Collapse
Affiliation(s)
- Kaouthar Slama
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Aurellia Galliot
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Franziska Weichmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Jasmin Hertler
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany
| | - Regina Feederle
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, Munich, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Germany.
| |
Collapse
|