The Chemical Basis of RNA Epigenetics

Publications

Active turnover of genomic methylcytosine in pluripotent cells

Author(s): Fabio Spada, Sarah Schiffers, Angie Kirchner, Yingqian Zhang, Gautier Arista, Olesea Kosmatchev, Eva Korytiakova, René Rahimoff, Charlotte Ebert, Thomas Carell
Published in: Nature Chemical Biology, Issue 16/12, 2020, Page(s) 1411-1419, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-020-0621-y

A prebiotically plausible scenario of an RNA–peptide world

Author(s): Felix Müller, Luis Escobar, Felix Xu, Ewa Wegrzyn, Milda Nainyte, Tynchtyk Amatov, Chun-Yin Chan, Alexander Pichler, Thomas Carell
Published in: Nature, Issue 605, 2022, Page(s) 279-284, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-04676-3

Amino Acid Modified RNA Bases as Building Blocks of an Early Earth RNA-Peptide World.

Author(s): Milda Nainytė; Felix Müller; Giacomo Ganazzoli; Chun-Yin Chan; Antony Crisp; Daniel Globisch; Thomas Carell
Published in: Chemistry, A European Journal, Issue 26(65), 2020, Page(s) 14856-14860, ISSN 1521-3765
Publisher: Wiley-VCH GmbH
DOI: 10.1002/chem.202002929

Human TRMT2A methylates tRNA and contributes to translation fidelity

Author(s): Monika Witzenberger, Sandra Burczyk, David Settele, Wieland Mayer, Luisa M Welp, Matthias Heiss, Mirko Wagner, Thomas Monecke, Robert Janowski, Thomas Carell, Henning Urlaub, Stefanie M Hauck, Aaron Voigt, and Dierk Niessing
Published in: Nucleic Acids Research, Issue 51(16), 2023, Page(s) 8691-8710, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad565

1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives

Author(s): Romeo C.A. Dubini, Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, Petra Rovó
Published in: ACS Physical Chemistry Au, Issue 2(3), 2022, Page(s) 237-246, ISSN 2694-2445
Publisher: ACS Publications
DOI: 10.1021/acsphyschemau.1c00050

Synthesis and Structure Elucidation of Glutamyl-Queuosine

Author(s): Alexander Pichler, Markus Hillmeier, Matthias Heiss, Elsa Peev, Stylianos Xefteris, Barbara Steigenberger, Ines Thoma, Markus Müller, Marco Borsò, Axel Imhof, and Thomas Carell
Published in: Journal of the American Chemical Society, Issue 145(47), 2023, Page(s) 25528-25532, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c10075

Epigenetic Anti-Cancer Treatment With a Stabilized Carbocyclic Decitabine Analogue

Author(s): Franziska R. Traube, Natércia F. Brás, Dr. Wynand P. Roos, Corinna C. Sommermann, Tamara Diehl, Robert J. Mayer, Armin R. Ofial, Markus Müller, Hendrik Zipse, Thomas Carell
Published in: Chemistry - A European Journal, Issue Early View, 2022, Page(s) e202200640, ISSN 1521-3765
Publisher: Wiley-VCH
DOI: 10.1002/chem.202200640

Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine

Author(s): Markus Hillmeier, Mirko Wagner, Timm Ensfelder, Eva Korytiakova, Peter Thumbs, Markus Müller, Thomas Carell
Published in: Nature Communications, Issue 12, 2021, Page(s) 7123, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27371-9

5-Hydroxymethyl-, 5-Formyl- and 5-Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks

Author(s): Florian Schelter, Angie Kirchner, Franziska R. Traube, Markus Müller, Wolfgang Steglich, Thomas Carell
Published in: Chemistry - A European Journal, Issue 27, 2021, Page(s) 8100-8104, ISSN 1521-3765
Publisher: Wiley-VCH
DOI: 10.1002/chem.202100551

Isoxazole Nucleosides as Building Blocks for a Plausible Proto-RNA

Author(s): Felix Xu, Antony Crisp, Thea Schinkel, Romeo C.A. Dubini, Sarah Hübner, Sidney Becker, Florian Schelter, Petra Rovó, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 61(45), 2022, Page(s) e202211945, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202211945

A Unifying Concept for the Prebiotic Formation of RNA Pyrimidine Nucleosides

Author(s): Jonas Feldmann, Mads K. Skaanning, Marcus Lommel, Tobias Kernmayr, Peter Mayer, Thomas Carell
Published in: ChemistryEurope, Issue 1(1), 2023, Page(s) e202300013, ISSN 2751-4765
Publisher: Wiley-VCH
DOI: 10.1002/ceur.202300013

Suppression of SARS-CoV-2 Replication with Stabilized and Click-Chemistry Modified siRNAs

Author(s): Franziska R. Traube, Marcel Stern, Annika J. Tölke, Martina Rudelius, Ernesto Mejías-Pérez, Nada Raddaoui, Beate M. Kümmerer, Céline Douat, Filipp Streshnev, Manuel Albanese, Paul R. Wratil, Yasmin V. Gärtner, Milda Nainyte, Grazia Giorgio, Stylianos Michalakis, Sabine Schneider, Hendrik Streeck, Markus Müller, Oliver T. Keppler, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 61(38), 2022, Page(s) e202204556, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202204556

Intragenomic decarboxylation of 5-carboxy-2’-deoxycytidine

Author(s): Ewelina Kaminska; Eva Korytiaková; Andreas Reichl; Markus Müller; Thomas Carell
Published in: Angewandte Chemie (International Ed. in English), Issue 60, 2021, Page(s) 23207-23211, ISSN 1521-3773
Publisher: Wiley-VCH
DOI: 10.1002/anie.202109995

Loading of Amino Acids onto RNA in a Putative RNA-Peptide World

Author(s): Johannes N. Singer, Felix M. Müller, Ewa Węgrzyn, Christina Hölzl, Hans Hurmiz, Chuyi Liu, Luis Escobar, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 62(21), 2023, Page(s) e202302360, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202302360

Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons

Author(s): Franziska R. Traube, Dilara Özdemir, Hanife Sahin, Constanze Scheel, Andrea F. Glück, Anna S. Geserich, Sabine Oganesian, Sarantos Kostidis, Katharina Iwan, René Rahimoff, Grazia Giorgio, Markus Müller, Fabio Spada, Martin Biel, Jürgen Cox, Martin Giera, Stylianos Michalakis, Thomas Carell
Published in: Nature Communications, Issue 12, 2021, Page(s) 4100, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24353-9

Comparative nucleosomal reactivity of 5-formyl-uridine and 5-formyl-cytidine

Author(s): Leander Simon Runtsch; Michael Stadlmeier; Alexander Schön; Markus Müller; Thomas Carell
Published in: Chemistry (Weinheim an Der Bergstrasse, Germany), Issue 27, 2021, Page(s) 12747-12752, ISSN 1521-3765
Publisher: Wiley-VCH
DOI: 10.1002/chem.202102159

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

Author(s): Romeo C A Dubini, Alexander Schön, Markus Müller, Thomas Carell, and Petra Rovó
Published in: Nucleic Acids Research, Issue 48, 2020, Page(s) 8796-8807, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa589

Third-Generation Sequencing of Epigenetic DNA

Author(s): Bethany Searle, Markus Müller, Thomas Carell, Andrew Kellett
Published in: Angewandte Chemie International Edition, Issue 62(14), 2023, Page(s) e202215704, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202215704

Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis

Author(s): Sidney Becker, Christina Schneider, Hidenori Okamura, Antony Crisp, Tynchtyk Amatov, Milan Dejmek, Thomas Carell
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-02639-1

Noncanonical RNA Nucleosides as Molecular Fossils of an Early Earth-Generation by Prebiotic Methylations and Carbamoylations

Author(s): Christina Schneider, Sidney Becker, Hidenori Okamura, Antony Crisp, Tynchtyk Amatov, Michael Stadlmeier, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 57/20, 2018, Page(s) 5943-5946, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201801919

Non-canonical nucleosides and chemistry of the emergence of life

Author(s): Sidney Becker, Christina Schneider, Antony Crisp, Thomas Carell
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-07222-w

5-Formylcytosine to cytosine conversion by C–C bond cleavage in vivo

Author(s): Katharina Iwan, René Rahimoff, Angie Kirchner, Fabio Spada, Arne S Schröder, Olesea Kosmatchev, Shqiponja Ferizaj, Jessica Steinbacher, Edris Parsa, Markus Müller, Thomas Carell
Published in: Nature Chemical Biology, Issue 14/1, 2018, Page(s) 72-78, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/nchembio.2531

A one-pot, water compatible synthesis of pyrimidine nucleobases under plausible prebiotic conditions

Author(s): Hidenori Okamura, Sidney Becker, Niklas Tiede, Stefan Wiedemann, Jonas Feldmann, Thomas Carell
Published in: Chemical Communications, Issue 55/13, 2019, Page(s) 1939-1942, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8cc09435g

Super-sensitive multi-fluorophore RNA-FISH for early virus detection and flow-FISH using click chemistry

Author(s): Nada Raddaoui, Stefano Groce, Florian Geiger, Alexander Borodavka, Leonhard Möckl, Samuele Stazzoni, Bastien Viverge, Christoph Bräuchle, Thomas Frischmuth, Hanna Engelke, Thomas Carell
Published in: ChemBioChem, Issue 18.03.2020, 2020, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000081

Synthesis and Incorporation of k 2 U into RNA

Author(s): Milda Nainyte, Thomas Carell
Published in: Helvetica Chimica Acta, Issue 103/3, 2020, ISSN 0018-019X
Publisher: Verlag Helvetica Chimica Acta
DOI: 10.1002/hlca.202000016

TLR8 Is a Sensor of RNase T2 Degradation Products

Author(s): Wilhelm Greulich, Mirko Wagner, Moritz M. Gaidt, Che Stafford, Yiming Cheng, Andreas Linder, Thomas Carell, Veit Hornung
Published in: Cell, Issue 179/6, 2019, Page(s) 1264-1275.e13, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.11.001

A Click‐Chemistry Linked 2′3′‐cGAMP Analogue

Author(s): Clemens Reto Dialer, Samuele Stazzoni, David Jan Drexler, Felix Moritz Müller, Simon Veth, Alexander Pichler, Hidenori Okamura, Gregor Witte, Karl‐Peter Hopfner, Thomas Carell
Published in: Chemistry – A European Journal, Issue 25/8, 2019, Page(s) 2089-2095, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201805409

Proto‐Urea‐RNA (Wöhler RNA) Containing Unusually Stable Urea Nucleosides

Author(s): Hidenori Okamura, Antony Crisp, Sarah Hübner, Sidney Becker, Petra Rovó, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 58/51, 2019, Page(s) 18691-18696, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201911746

A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

Author(s): Michael Stadlmeier, Leander Simon Runtsch, Filipp Streshnev, Martin Wühr, Thomas Carell
Published in: ChemBioChem, Issue 21/1-2, 2019, Page(s) 103-107, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.201900611

Influencing Epigenetic Information with a Hydrolytically Stable Carbocyclic 5‐Aza‐2′‐deoxycytidine

Author(s): Thomas M. Wildenhof, Sarah Schiffers, Franziska R. Traube, Peter Mayer, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 58/37, 2019, Page(s) 12984-12987, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201904794

ALKBH5-induced demethylation of mono- and dimethylated adenosine

Author(s): Timm T. Ensfelder, Matthias Q. Kurz, Katharina Iwan, Simon Geiger, Sarah Matheisl, Markus Müller, Roland Beckmann, Thomas Carell
Published in: Chemical Communications, Issue 54/62, 2018, Page(s) 8591-8593, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8cc03980a

Synthesis of an acp 3 U phosphoramidite and incorporation of the hypermodified base into RNA

Author(s): Milda Nainytė, Tynchtyk Amatov, Thomas Carell
Published in: Chemical Communications, Issue 55/81, 2019, Page(s) 12216-12218, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9cc06314e

Synthesis of galactosyl‐queuosine and distribution of hypermodified Q‐nucleosides in mouse tissues

Author(s): Peter Thumbs, Timm T. Ensfelder, Markus Hillmeier, Mirko Wagner, Matthias Heiss, Constanze Scheel, Alexander Schön, Markus Müller, Stylianos Michalakis, Stefanie Kellner, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 11.03.2020, 2020, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202002295

Analysis of an Active Deformylation Mechanism of 5‐Formyl‐deoxycytidine (fdC) in Stem Cells

Author(s): Alexander Schön, Ewelina Kaminska, Florian Schelter, Eveliina Ponkkonen, Eva Korytiaková, Sarah Schiffers, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 59/14, 2020, Page(s) 5591-5594, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202000414

Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides

Author(s): Sidney Becker, Jonas Feldmann, Stefan Wiedemann, Hidenori Okamura, Christina Schneider, Katharina Iwan, Antony Crisp, Martin Rossa, Tynchtyk Amatov, Thomas Carell
Published in: Science, Issue 366/6461, 2019, Page(s) 76-82, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aax2747

Novel Poxin Stable cGAMP-Derivatives Are Remarkable STING Agonists

Author(s): Samuele Stazzoni, Daniel F.R. Böhmer, Fabian Hernichel, Dilara Özdemir, Aikaterini Pappa, David Drexler, Stefan Bauernfeind, Gregor Witte, Mirko Wagner, Simon Veth, Karl-Peter Hopfner, Veit Hornung, Lars M. König, Thomas Carell
Published in: Angewandte Chemie International Edition, Issue 61(40), 2022, Page(s) e202207175, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202207175

Intercellular cGAMP transmission induces innate immune activation and tissue inflammation in Trex1 deficiency.

Author(s): Bianca B. Jütte; Calvin Krollmann; Kevin Cieslak; Ruth-Miriam Koerber; Peter Boor; Claus Moritz Graef; Eva Bartok; Eva Bartok; Mirko Wagner; Thomas Carell; Jennifer Landsberg; Pia Aymans; Jörg Wenzel; Peter Brossart; Lino L. Teichmann
Published in: iScience, Issue 24(8), 2021, Page(s) 102833, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2021.102833

An Aminoisoxazole-Based Proto-RNA

Author(s): Felix Xu, Stefan Wiedemann, Jonas Feldmann, Sidney Becker, Thomas Carell
Published in: ChemistryEurope, Issue 1(3), 2023, Page(s) e202300057, ISSN 2751-4765
Publisher: Wiley-VCH
DOI: 10.1002/ceur.202300057

DNA hydroxymethylation is associated with disease severity and persists at enhancers of oncogenic regions in multiple myeloma

Author(s): J. B. Alberge, F. Magrangeas, M. Wagner, S. Denié, C. Guérin-Charbonnel, L. Campion, M. Attal, H. Avet-Loiseau, T. Carell, P. Moreau, S. Minvielle, A. A. Sérandour
Published in: Clinical Epigenetics, Issue 12(1), 2020, Page(s) 163, ISSN 1868-7083
Publisher: Springer Nature
DOI: 10.1186/s13148-020-00953-y

Deformylation of 5-Formylcytidine in Different Cell Types.

Author(s): Eva Korytiaková; Ewelina Kaminska; Markus Müller; Thomas Carell
Published in: Angewandte Chemie (International Ed. in English), Issue 60, 2021, Page(s) 16869-16873, ISSN 1521-3773
Publisher: Wiley-VCH
DOI: 10.1002/anie.202107089

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