Publications

Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons

Maria Kompatscher, Karolina Bartosik, Kevin Erharter, Raphael Plangger, Fabian Sebastian Juen, Christoph Kreutz, Ronald Micura, Eric Westhof, and Matthias Erlacher

Nucleic Acids Research 52 (3) 1374–1386 (2024)

Proteome-scale tagging and functional screening in mammalian cells by ORFtag

Filip Nemčko, Moritz Himmelsbach, Vincent Loubiere, Ramesh Yelagandula, Michaela Pagani, Nina Fasching, Julius Brennecke, Ulrich Elling, Alexander Stark, Stefan L. Ameres

bioRxiv (2024)

Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types

Ariane Mandlbauer, Qiong Sun, Niko Popitsch, Tanja Schwickert, Miroslava Spanova, Jingkui Wang, Stefan Ameres, Meinrad Busslinger, Luisa Cochella

Embo Journal (2024)

eIF4E1b is a non-canonical eIF4E required for maternal mRNA dormancy

Laura Lorenzo-Orts, Marcus Strobl, Benjamin Steinmetz, Friederike Leesch, Carina Pribitzer, Michael Schutzbier, Gerhard Dürnberger, Andrea Pauli

bioRxiv (2023)

Cleavage kinetics of human mitochondrial RNase P and contribution of its non-nuclease subunits

Elisa Vilardo, Ursula Toth, Enxhi Hazisllari, Roland K Hartmann, Walter Rossmanith

Nucleic Acids Research gkad713 (2023)

Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species

Samuel E. Ross, Javier Vázquez-Marín, Krista R.B. Gert, Álvaro González-Rajal, Marcel E. Dinger, Andrea Pauli, Juan Ramon Martínez-Morales, Ozren Bogdanovic

Nucleic Acids Research gkad695 (2023)

Divergent molecular signatures in fish Bouncer proteins define cross-ferIlizaIon boundaries.

Krista R. B. Gert, Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov & Andrea Pauli

Nature Communications 14, 3506 (2023)

Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment

Mariam R Farman, Denisa Petráčková, Dilip Kumar, Jakub Držmíšek, Argha Saha, Ivana Čurnová, Jan Čapek, Václava Hejnarová, Fabian Amman, Ivo Hofacker, Branislav Večerek

Emerging Microbes & Infections 12 (1) (2023)

Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability

Anna Uzonyi, David Dierks, Ronit Nir, Oh Sung Kwon, Ursula Toth, Isabelle Barbosa, Cindy Burel, Alexander Brandis, Walter Rossmanith, Hervé Le Hir, Boris Slobodin, Schraga Schwartz

Molecular Cell 83 (2) 237-251 (2023)

No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV and MLV viral RNA

Anming Huang, Lydia Rieper, Dietmar Rieder, Janine Kimpel, Alexandra Lusser

RNA 29 (6) 756-763 (2023)

Local RNA Folding Revisisted

Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K. Beckmann, Ivo L. Hofacker, Sarah Von Lohneysen, and Peter F. Stadler

Journal of Bioinformatics and Computational Biology (2023)

DrTransformer: Heuristic cotranscriptional RNA folding using the nearest neighbor energy model

Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker

Bioinformatics 39 (1) (2023)

Investigating RNA–RNA interactions through computational and biophysical analysis

Tyler Mrozowich, Sean M Park, Maria Waldl, Amy Henrickson, Scott Tersteeg, Corey R Nelson, Anneke De Klerk, Borries Demeler, Ivo L Hofacker, Michael T Wolfinger, Trushar R Patel

Nucleic Acids Research 51 (9) 22 4588–4601 (2023)

A molecular network of conserved factors keeps ribosomes dormant in the egg

Friederike Leesch, Laura Lorenzo-Orts, Carina Pribitzer, Irina Grishkovskaya, Josef Roehsner, Anastasia Chugunova, Manuel Matzinger, Elisabeth Roitinger, Katarina Belačić, Susanne Kandolf, Tzi-Yang Lin, Karl Mechtler, Anton Meinhart, David Haselbach & Andrea Pauli

Nature 613 712–720 (2023)

Identification of RNA helicases with unwinding activity on angiogenin-processed tRNAs

Aleksej Drino, Lisa König, Charlotte Capitanchik, Nasim Sanadgol, Eva Janisiw, Tom Rappol, Elisa Vilardo, Matthias R Schaefer

Nucleic Acids Research 51 (3) 1326–1352 (2023)

The ADAR1 editome reveals drivers of editing-specificity for ADAR1-isoforms

Renata Kleinova, Vinod Rajendra, Alina F Leuchtenberger, Claudio Lo Giudice, Cornelia Vesely, Utkarsh Kapoor, Andrea Tanzer, Sophia Derdak, Ernesto Picardi, Michael F Jantsch

Nucleic Acids Research 51 (9), 4191-4207 (2023)

Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli

Maximilian P. Kohl, Maria Kompatscher, Nina Clementi, Lena Holl and Matthias D. Erlacher

Nucleic Acids Research 51 (1): 271–289 (2023)

SLAMseq resolves the kinetics of maternal and zygotic gene expression in early zebrafish embryogenesis

Pooja Bhat, Luis E. Cabrera-Quio, Veronika A. Herzog, Nina Fasching, Andrea Pauli and Stefan L. Ameres

Cell reports 24 (2): 1-20 (2023)

Experimental paradigms revisited: oxidative stress-induced tRNA fragmentation does not correlate with stress granule formation but is associated with delayed cell death

Nasim Sanadgol, Lisa König, Aleksej Drino, Michaela Jovic, Matthias R Schaefer

Nucleic Acids Research 50 (12): 6919-6937 (2022)

Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

Devadatta Gosavi, Iwona Wower, Irene K Beckmann, Ivo L Hofacker, Jacek Wower, Michael T Wolfinger, Joanna Sztuba-Solinska

RNA biology 19 (1) 496-506 (2022)

Caveats to deep learning approaches to RNA secondary structure prediction

Christoph Flamm, Julia Wielach, Michael T. Wolfinger, Stefan Badelt, Ronny Lorenz and Ivo L. Hofacker

Frontiers in Bioinformatics 2 (2022)

The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans.

Julia L Daiß, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl, Florian B Heiss, Guillermo Abascal-Palacios, Ewan P Ramsay, Katarina Tlučková, Jean-Clement Mars, Torben Fürtges, Astrid Bruckmann, Till Rudack, Carrie Bernecky, Valérie Lamour, Konstantin Panov, Alessandro Vannini, Tom Moss, Christoph Engel

Life Science Alliance 5 (11) (2022)

Transcriptome-wide Profiling of RNA Stability.

Nina Fasching, Jan Petržílek, Niko Popitsch, Veronika A Herzog, Stefan L Ameres

Methods in Molecular Biology 2404 311-330 (2022)

Structural and functional basis of mammalian microRNA biogenesis by Dicer

David Zapletal, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, Marek Sebesta, Valeria Buccheri, Filip Horvat, Irena Jenickova, Michaela Prochazkova, Jan Prochazka, Matyas Pinkas, Jiri Novacek, Diego F Joseph, Radislav Sedlacek, Carrie Bernecky, Dónal O’Carroll, Richard Stefl, Petr Svoboda

Molecular Cell 82 (21) 4064-4079 (2022)

Sperm membrane proteins DCST1 and DCST2 are required for sperm-egg interaction in mice and fish

Taichi Noda, Andreas Blaha, Yoshitaka Fujihara, Krista R. Gert, Chihiro Emori, Victoria E. Deneke, Seiya Oura, Karin Panser, Yonggang Lu, Sara Berent, Mayo Kodani, Luis Enrique Cabrera-Quio, Andrea Pauli & Masahito Ikawa

Communications Biology 5, (332) (2022)

A self-generated Toddler gradient guides mesodermal cell migration

Jessica Stock, Tomas Kazmar, Friederike Schlumm, Edouard Hannezo and Andrea Pauli

Science Advances 8 (37) 2022

SCON—a Short Conditional intrON for conditional knockout with one-step zygote injection

Szu-Hsien Sam Wu, Heetak Lee, Réka Szép-Bakonyi, Gabriele Colozza, Ayse Boese, Krista R. Gert, Natalia Hallay, Ji-Hyun Lee, Jihoon Kim, Yi Zhu, Margot M. Linssen, Sandra Pilat-Carotta, Peter Hohenstein, Hans-Christian Theussl, Andrea Pauli & Bon-Kyoung Koo

Experimental & Molecular Medicine 54 2188–2199 (2022)

Rapid, Highly SensiIve and Open-Access SARS-CoV02 DetecIon Assay for Laboratory and Home TesIng.

Max J Kellner, James J Ross, Jakob Schnabl, Marcus P S Dekens, Martin Matl, Robert Heinen, Irina Grishkovskaya, Benedikt Bauer, Johannes Stadlmann, Luis Menéndez-Arias, Andrew D Straw, Robert Fritsche-Polanz, Marianna Traugott, Tamara Seitz, Alexander Zoufaly, Manuela Födinger, Christoph Wenisch, Johannes Zuber, Andrea Pauli, Julius Brennecke

Frontiers in Molecular Biosciences 9 (2022)

Sister chromatid–sensitive Hi-C to map the conformation of replicated genomes

Michael Mitter, Zsuzsanna Takacs, Thomas Köcher, Ronald Micura, Christoph C. H. Langer & Daniel W. Gerlich

Nature Protocols 17 1486–1517 (2022)

Synthesis of N4-acetylated 3-methylcytidine phosphoramidites for RNA solid-phase synthesis

Sarah Moreno, Laurin Flemmich, Ronald Micura

Monatshefte für Chemie 153 285 – 291 (2022)

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis

Raphael Bereiter, Eva Renard, Kathrin Breuker, Christoph Kreutz, Eric Ennifar, and Ronald Micura

Journal of the American Chemical Society 144 10344-10352 (2022)

Functional integration of a semi-synthetic azido-queuosine derivative into translation and a tRNA modification circuit

Larissa Bessler, Navpreet Kaur, Lea-Marie Vogt, Laurin Flemmich, Carmen Siebenaller, Marie-Luise Winz, Francesca Tuorto, Ronald Micura, Ann E Ehrenhofer-Murray, Mark Helm

Nucleic Acids Research 50 (18) 10785–10800 (2022)

A new route for the synthesis of 1-deazaguanine and 1-deazahypoxanthine

Raphael Bereiter, Marco Oberlechner and Ronald Micura

Beilstein Journal of Organic Chemistry 18, 1617–1624 (2022)

Robust synthesis of 2′-azido modified RNA from 2′-amino precursors by diazotransfer reaction

Sarah Moreno, José M. Ramos Pittol, Markus Hartl and Ronald Micura

Organic & Biomolecular Chemistry 20 7845-7850 (2022)

Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes

Michaela Egger, Raphael Bereiter, Stefan Mair, Ronald Micura

Angewandte Chemie 134 (41) (2022)

NMD is required for Imely cell fate transiIons by fine-tuning gene expression and regulaIng translaIon

Michelle Huth, Laura Santini, Elena Galimberti, Julia Ramesmayer, Fabian Titz-Teixeira, Robert Sehlke, Michael Oberhuemer, Sarah Stummer, Veronika Herzog, Marius Garmhausen, Merrit Romeike, Anastasia Chugunova, Friederike Leesch, Laurenz Holcik, Klara Weipoltshammer, Andreas Lackner, Christian Schoefer, Arndt von Haeseler, Christa Buecker, Andrea Pauli, Stefan L Ameres, Austin Smith, Andreas Beyer, Martin Leeb

Genes & development 36 (5-6) 348-367 (2022)

Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes

Anna Köferle, Andreas Schlattl, Alexandra Hörmann, Venu Thatikonda, Alexandra Popa, Fiona Spreitzer, Madhwesh C Ravichandran, Verena Supper, Sarah Oberndorfer, Teresa Puchner, Corinna Wieshofer, Maja Corcokovic, Christoph Reiser, Simon Wöhrle, Johannes Popow, Mark Pearson, Javier Martinez, Stefan Weitzer, Barbara Mair, Ralph A Neumüller

Cell Reports 39 2 (2022)

Hijacking of transcriptional condensates by endogenous retroviruses.

Vahid Asimi, Abhishek Sampath Kumar, Henri Niskanen, Christina Riemenschneider, Sara Hetzel, Julian Naderi, Nina Fasching, Niko Popitsch, Manyu Du, Helene Kretzmer, Zachary D. Smith, Raha Weigert, Maria Walther, Sainath Mamde, David Meierhofer, Lars Wittler, René Buschow, Bernd Timmermann, Ibrahim I. Cisse, Stefan L. Ameres, Alexander Meissner & Denes Hnisz

Nature Genetics 54, 1238–1247 (2022)

Regulation of sensory perception and motor abilities by brain-specific action of chromatin remodeling factor CHD1

Ines Schoberleitner, Birte Mertens, Ingo Bauer and Alexandra Lusser

Frontiers in Molecular Neuroscience 15 (2022)

Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase

Hamid R. Mansouri, Oriol Gracia Carmona, Julia Jodlbauer, Lorenz Schweiger, Michael J. Fink, Erik Breslmayr, Christophe Laurent, Saima Feroz, Leticia C. P. Goncalves, Daniela V. Rial, Marko D. Mihovilovic, Andreas S. Bommarius, Roland Ludwig, Chris Oostenbrink and Florian Rudroff

ACS Catalytics 12 (19) 11761–11766 (2022)

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Runxuan Zhang, Richard Kuo, Max Coulter, Cristiane P. G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, Linda Milne, Stefan Riegler, Akihiro Matsui, Maho Tanaka, Sarah Harvey, Yubang Gao, Theresa Wießner-Kroh, Alejandro Paniagua, Martin Crespi, Katherine Denby, Asa ben Hur, Enamul Huq, Michael Jantsch, Artur Jarmolowski, Tino Koester, Sascha Laubinger, Qingshun Quinn Li, Lianfeng Gu, Motoaki Seki, Dorothee Staiger, Ramanjulu Sunkar, Zofia Szweykowska-Kulinska, Shih-Long Tu, Andreas Wachter, Robbie Waugh, Liming Xiong, Xiao-Ning Zhang, Ana Conesa, Anireddy S. N. Reddy, Andrea Barta, Maria Kalyna & John W. S. Brown

Genome Biology 23 (149) (2022)

A-to-I RNA editing of Filamin A regulates cellular adhesion, migration and mechanical properties

Mamta Jain, Andreas Weber, Kathrin Maly, Greeshma Manjaly, Joanna Deek, Olena Tsvyetkova, Maja Stulić, José L. Toca-Herrera, Michael F. Jantsch

The FEBS Journal 289 (15) 4580-4601 (2022)

Filamin A pre-mRNA editing modulates vascularization and tumor growth

Mamta Jain, Greeshma Manjaly, Kathrin Maly, Margreet R. de Vries, Michael Janisiw, Lisa König, Anne Yaël Nossent, Michael F. Jantsch

Molecular Therapy – Nucleic Acids 30 522-534 (2022)

How RNA editing keeps an I on physiology

Marion Goldeck, Aiswarya Gopal, Michael F. Jantsch, Hamid Reza Mansouri Khosravi, Vinod Rajendra, and Cornelia Vesely

American Journal of Physiology-Cell Physiology 323 (5) C1496-C1511 (2022)

The Sperm Protein Spaca6 is Essential for Fertilization in Zebrafish

Mirjam I. Binner, Anna Kogan, Karin Panser, Alexander Schleiffer, Victoria E. Deneke and Andrea Pauli

Frontiers in Cell and Developmental Biology 9 (2022)

A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA

Nir, R., Hoernes, T. P., Muramatsu, H., Faserl, K., Karikó, K., Erlacher, M. D., Sas-Chen, A., Schwartz, S.

Nucleic Acids Research 50 (9): 4900-4916 (2022)

Time-resolved single-cell RNA-seq using metabolic RNA labelling

Florian Erhard, Antoine-Emmanuel Saliba, Alexandra Lusser, Christophe Toussaint, Thomas Hennig, Bhupesh K. Prusty, Daniel Kirschenbaum, Kathleen Abadie, Eric A. Miska, Caroline C. Friedel, Ido Amit, Ronald Micura and Lars Dölken

Nature Reviews Methods Primers 2, 77 (2022)

Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA

Stefan Mair, Kevin Erharter, Eva Renard, Karl Brillet, Melanie Brunner, Alexandra Lusser, Christoph Kreutz, Eric Ennifar, Ronald Micura

Nucleic Acids Research 50 (11), 6038–6051 (2022)

6-Thioguanosine Monophosphate Prodrugs Display Enhanced Performance against Thiopurine-Resistant Leukemia and Breast Cancer Cells

Sarah Moreno, Magdalena Fickl, Ingo Bauer, Melanie Brunner, Anna Rázková, Dietmar Rieder, Isabel Delazer, Ronald Micura and Alexandra Lusser

Journal of Medicinal Chemistry 65 (22), 15165–15173 (2022)

Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling

Sarah Moreno, Melanie Brunner, Isabel Delazer, Dietmar Rieder, Alexandra Lusser and Ronald Micura

RSC Chem. Biol. 3, 447-455 (2022)

Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol

Egor A. Syroegin, Laurin Flemmich, Dorota Klepacki, Nora Vazquez-Laslop, Ronald Micura and Yury S. Polikanov

Nat. Struct. Mol. Biol. 29, 152–161 (2022)

Chapter Ten - Systematic refinement of gene annotations by parsing mRNA 3′ end sequencing datasets

Pooja Bhat, Thomas R. Burkard, Veronika A. Herzog, Andrea Pauli, Stefan L. Ameres

Methods in Enzymology 655, 205-223 (2021)

Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition

Xiaochen Xu, Michaela Egger, Hao Chen, Karolina Bartosik, Ronald Micura and Aiming Ren

Nucleic Acids Research 49, 12, 7139–7153 (2021)

The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response

Igor Asanović Emilia Strandback Alena Kroupova Djurdja Pasajlic Anton Meinhart Pai Tsung-Pin Nemanja Djokovic Dorothea Anrather Thomas Schuetz Marcin Józef Suskiewicz Sirelin Sillamaa Thomas Köcher Rebecca Beveridge Katarina Nikolic Alexander Schleiffer Martin Jinek Markus Hartl Tim Clausen Josef Penninger Peter Macheroux Stefan Weitzer Javier Martinez

Molecular Cell 81 (12) 2520-2532 (2021)

Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations

Irit Hochberg, Leigh A M Demain, Julie Richer, Kyle Thompson, Jill E Urquhart, Alessandro Rea, Waheeda Pagarkar, Agustí Rodríguez-Palmero, Agatha Schlüter, Edgard Verdura, Aurora Pujol, Pilar Quijada-Fraile, Albert Amberger, Andrea J Deutschmann, Sandra Demetz, Meredith Gillespie, Inna A Belyantseva, Hugh J McMillan, Melanie Barzik, Glenda M Beaman, Reeya Motha, Kah Ying Ng, James O’Sullivan, Simon G Williams, Sanjeev S Bhaskar, Isabella R Lawrence, Emma M Jenkinson, Jessica L Zambonin, Zeev Blumenfeld, Sergey Yalonetsky, Stephanie Oerum, Walter Rossmanith; Genomics England Research Consortium; Wyatt W Yue, Johannes Zschocke, Kevin J Munro, Brendan J Battersby, Thomas B Friedman, Robert W Taylor, Raymond T O’Keefe, William G Newman

The American Journal of Human Genetics 108 (11) 2195-2204 (2021)

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Jeffrey Y Lee, Ni Shuai, Manuel Garcia-Moreno, Anna Andrejeva, Michael J Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael L Knight, Kathryn S Lilley, Javier Martinez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castello

Molecular Cell 81(13) 2851-2867 (2021)

Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing

Krista R. Gert, Luis Enrique Cabrera Quio, Maria Novatchkova, Yixuan Guo, Bradley R. Cairns, Andrea Pauli

bioRxiv (2021)

Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos

Yixuan Guo, Krista R. Gert, Svetlana Lebedeva, Magdalena E. Potok, Candice L. Wike, Edward J. Grow, René F. Ketting, Andrea Pauli, Bradley R. Cairns

bioRxiv (2021)

Impact of 3-deazapurine nucleobases on RNA properties

Raphael Bereiter, Maximilian Himmelstoß, Eva Renard, Elisabeth Mairhofer, Michaela Egger, Kathrin Breuker, Christoph Kreutz, Eric Ennifar and Ronald Micura

Nucleic Acids Research 49, 8, 4281–4293 (2021)

The Fertilization Enigma: How Sperm and Egg Fuse

Victoria E. Deneke and Andrea Pauli

Annual Review of Cell and Developmental Biology 37 (391-414) (2021)

A natural riboswitch scaffold with self-methylation activity

Laurin Flemmich, Sarah Heel, Sarah Moreno, Kathrin Breuker & Ronald Micura

Nature Communications 12:387 (2021)

Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics

Max J. Kellner, Martin Matl, James J. Ross, Jakob Schnabl, Dominik Handler, Robert Heinen, Justine Schaeffer, Peter Hufnagl, Alexander Indra, Marcus P.S. Dekens, Robert Fritsche-Polanz, Manuela Födinger, Johannes Zuber, Vienna Covid-19 Detection Initiative (VCDI), Franz Allerberger, Andrea Pauli, Julius Brennecke

medRxiv (2021)

The conserved fertility factor SPACA4/Bouncer has divergent modes of action in vertebrate fertilization

Yoshitaka Fujihara, Sarah Herberg, Andreas Blaha, Karin Panser, Kiyonori Kobayashi, Tamara Larasati, Maria Novatchkova, Hans-Christian Theussl, Olga Olszanska, Masahito Ikawa and Andrea Pauli

PNAS 118 (39) (2021)

Site-directed RNA editing: recent advances and open challenges

Hamid Mansouri Khosravi and Michael F. Jantsch

RNA Biology 18, S1, 41–50 (2021)

Molecular architecture of the human tRNA ligase complex

Alena Kroupova, Fabian Ackle, Igor Asanović, Stefan Weitzer, Franziska M Boneberg, Marco Faini, Alexander Leitner, Alessia Chui, Ruedi Aebersold, Javier Martinez, Martin Jinek

eLife 10 (2021)

Transportin-1: A Nuclear Import Receptor with Moonlighting Functions

Allegra Mboukou, Vinod Rajendra, Renata Kleinova, Carine Tisné, Michael F. Jantsch and Pierre Barraud

Front. Mol. Biosci. 8, 638149 (2021)

RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes

Gregor Entzian, Ivo L Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer

Bioinformatics 37 (15) 2126–2133 (2021)

CHD1 controls H3.3 incorporation in adult brain chromatin to maintain metabolic homeostasis and normal lifespan

Schoberleitner, I., Bauer, I., Huang, A., Andreyeva, E. N., Sebald, J., Pascher, K., Rieder, D., Brunner, M., Podhraski, V., Oemer, G., Cázarez-García, D., Rieder, L., Keller, M. A., Winkler, R., Fyodorov, D. V., Lusser, A.

Cell Reports 37, 109769 (2021)

Amine-to-Azide Conversion on Native RNA via Metal-Free Diazotransfer Opens New Avenues for RNA Manipulations

Olga A. Krasheninina, Julia Thaler, Matthias D. Erlacher and Ronald Micura

Angew. Chem. Int. Ed. 60 (13), 6970–6974 (2021)

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC

Lisa-Marie Appel, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, Martin G. Puchinger, Sebastian Kostrhon, Carmen Ebenwaldner, Marek Sebesta, Etienne Beltzung, Karl Mechtler, Gen Lin, Anna Vlasova, Martin Leeb, Rushad Pavri, Alexander Stark, Altuna Akalin, Richard Stefl, Carrie Bernecky, Kristina Djinovic-Carugo & Dea Slade

Nature Communications 12 (6078) (2021)

Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel

Sonja Zayni, Samar Damiati, Susana Moreno-Flores, Fabian Amman, Ivo Hofacker, David Jin, Eva-Kathrin Ehmoser

Membranes 11 (10) 741 (2021)

Synthesis of O6-alkylated preQ1 derivatives

Laurin Flemmich, Sarah Moreno and Ronald Micura

Beilstein Journal of Organic Chemistry 17 2295–2301 (2021)

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler and Andrea Pauli

PLoS Genet 17(2): e1009390 (2021)

An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing

Cornelia Vesely and Michael F. Jantsch

Genes 12, 1026 (2021)

CharacterizaIon of regulatory elements of L11 and L1 operons in thermophilic bacteria and archaea.

Alisa O Mikhaylina, Ekaterina Y Nikonova, Olga S Kostareva, Wolfgang Piendl, Matthias Erlacher, Svetlana V Tishchenko

Biochemistry (Mosc) 86 (4) 397-408 (2021)

Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia

Samoil Sekulovski, Pascal Devant, Silvia Panizza, Tasos Gogakos, Anda Pitiriciu, Katharina Heitmeier, Ewan Phillip Ramsay, Marie Barth, Carla Schmidt, Thomas Tuschl, Frank Baas, Stefan Weitzer, Javier Martinez, Simon Trowitzsch

Nature Communications 12 (1) 5610 (2021)

Transcriptional profiling of human macrophages during infection with Bordetella pertussis

Denisa Petráčková, Mariam R Farman, Fabian Amman, Irena Linhartová, Ana Dienstbier, Dilip Kumar, Jakub Držmíšek,* Ivo Hofacker*, Maria Eugenia Rodriguez, Branislav Večerek

RNA Biology 17 (5) 731-742 (2020)

The locality dilemma of Sankoff-like RNA alignments

Teresa Müller, Milad Miladi, Frank Hutter, Ivo Hofacker, Sebastian Will, Rolf Backofen

Bioinformatics 36, Issue Supplement 1 i242–i250 (2020)

Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding

Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker and Peter F. Stadler

Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies 3 23-31 (2020)

A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals

Niko Popitsch, Christian D. Huber, Ilana Buchumenski, Eli Eisenberg, Michael Jantsch, Arndt von Haeseler and Miguel Gallach

Genome Biol. Evol. 12(4), 345–357 (2020)

An internal deletion of ADAR rescued by MAVS deficiency leads to a minute phenotype

Prajakta Bajad, Florian Ebner, Fabian Amman, Brigitta Szabó, Utkarsh Kapoor, Greeshma Manjali, Alwine Hildebrandt, Michael P. Janisiw and Michael F. Jantsch

Nucleic Acids Research 48, 6, 3286–3303 (2020)

ADAR-deficiency perturbs the global splicing landscape in mouse tissues

Utkarsh Kapoor, Konstantin Licht, Fabian Amman, Tobias Jakobi, David Martin, Christoph Dieterich and Michael Jantsch

Genome Res. 30, 1107-1118 (2020)

Spt6 is a maintenance factor for centromeric CENP-A

Bobkov, G. O. M., Huang, A., van den Berg, S. J. W., Mitra, S., Anselm, E., Lazou, V., Schunter, S., Feederle, R., Imhof, A., Lusser, A., Jansen, L. E. T., Heun, P.

Nature Communications 11(1), 2919 (2020)

Conformation of sister chromatids in the replicated human genome

Michael Mitter, Catherina Gasser, Zsuzsanna Takacs, Christoph C. H. Langer, Wen Tang,
Gregor Jessberger, Charlie T. Beales, Eva Neuner, Stefan L. Ameres, Jan-Michael Peters,
Anton Goloborodko,* Ronald Micura*, Daniel W. Gerlich

Nature 586: 139 – 144 (2020)

Structure-function analysis of microRNA 3′-end trimming by Nibbler

Xie W, Sowemimo I, Hayashi R, Wang J, Burkard TR, Brennecke J, Ameres SL, Patel DJ

PNAS 117 (48) 30370-30379 (2020)

Thiouridine-to-Cytidine conversion sequencing (TUC-seq) to measure mRNA transcription and degradation rates

Lusser, A., Gasser, C., Trixl, L., Piatti, P., Delazer, I., Rieder, D., Bashin, J., Riml, C., Amort, T., and Micura, R

J. LaCava, and S. Vanacova, (eds.), The Eukaryotic RNA Exosome: Methods and Protocols, Methods in Molecular Biology (Clifton, NJ), 2062, 191–211 (2020)

Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B

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Nucleic Acids Research 48 (11) 6157-6169 (2020)

Conformation of sister chromatids in the replicated human genome

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Nature 586, 139–144 (2020)

Production and purification of endogenously modified tRNA-derived small RNAs

Aleksej Drino, Vera Oberbauer, Conor Troger, Eva Janisiw, Dorothea Anrather, Markus Hartl, Steffen Kaiser, Stefanie Kellner, Matthias R Schaefer

RNA Biology 17 (8) 1104-1115 (2020)

ANGEL2 is a member of the CCR4 family of deadenylases with 2',3'-cyclic phosphatase activity

Paola H Pinto, Alena Kroupova, Alexander Schleiffer, Karl Mechtler, Martin Jinek, Stefan Weitzer, Javier Martinez

Science 369 (6503) 524-530 (2020)

tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila

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Nucleic Acids Research 48 (4) 2050-2072 (2020)

Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding

Hao Chen, Michaela Egger, Xiaochen Xu, Laurin Flemmich, Olga Krasheninina, Aiai Sun, Ronald Micura, Aiming Ren

Nucleic Acids Research 48 (21), 12394–12406,(2020)

YBEY is an essential biogenesis factor for mitochondrial ribosomes

Sabrina Summer, Anna Smirnova, Alessandro Gabriele, Ursula Toth, Akinyemi Mandela Fasemore, Konrad U Förstner, Lauriane Kuhn, Johana Chicher, Philippe Hammann, Goran Mitulović, Nina Entelis, Ivan Tarassov, Walter Rossmanith, Alexandre Smirnov

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2′-O-Trifluoromethylated RNA – a powerful modification for RNA chemistry and NMR spectroscopy

Maximilian Himmelstoß, Kevin Erharter, Eva Renard, Eric Ennifar, Christoph Kreutz and Ronald Micura

Chemical Science 11 11322-11330 (2020)

Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL)

Catherina Gasser, Isabel Delazer , Eva Neuner , Katharina Pascher , Karl Brillet , Sarah Klotz , Lukas Trixl , Maximilian Himmelstoß , Eric Ennifar , Dietmar Rieder , Alexandra Lusser and Ronald Micura

Angew. Chem. Int. Ed. 59, 6881 – 6886 (2020)

Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

Ronald Micura and Claudia Höbartner

Chem. Soc. Rev. 49, 7331 (2020)

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing.

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Genome Res. 29(9), 1453–1463 (2019)

The Editor’s I on Disease Development

Mamta Jain, Michael F. Jantsch and Konstantin Licht

Trends in Genetics 35, 12 (2019)

Of funding and finches

Verena Jantsch and Michael Jantsch

Genome Biology 20, 176 (2019)

Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains

Marie Fablet, Angelo Jacquet, Rita Rebollo, Annabelle Haudry, Carine Rey, Judit Salces-Ortiz, Prajakta Bajad, Nelly Burlet, Michael F. Jantsch, Maria Pilar García Guerreiro and Cristina Vieira

G3: Genes, Genomes, Genetics 9, 3, 855 – 865 (2019)

“Mining the Epitranscriptome: Detection of RNA editing and RNA modifications”

Michael F. Jantsch and Matthias R. Schaefer

Methods 156, 1-4 (2019)

Inosine induces context-dependent recoding and translational stalling

Konstantin Licht, Markus Hartl, Fabian Amman, Dorothea Anrather, Michael P. Janisiw and Michael F. Jantsch

Nucleic Acids Research 47, 1, 3–14 (2019)