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RNA@core: “Molecular mechanisms in RNA biology”

Javier Martinez Fernandez (ORCID: 0000-0001-9152-7323)
  • Grant DOI 10.55776/DOC177
  • Funding program doc.funds
  • Status ongoing
  • Start July 1, 2023
  • End June 30, 2027
  • Funding amount € 2,059,173
  • Project website

Disciplines

Biology (100%)

Keywords

  • Structural Biology,
  • Science Communication,
  • RNA biology,
  • Industry,
  • Biochemistry,
  • New Technologies
Abstract

RNA@core is a new Doctoral School funded by FWF that focuses on emerging biological and biochemical aspects of RNA molecules, multifunctional players in a living cell. RNA@core builds on a 12-year-long RNA Biology Doctoral School and aims to educate candidate PhD students recruited through the International PhD programs at the Vienna BioCenter and the Medical University of Vienna. Ground-breaking technologies in molecular biology and genetics have recently enabled great mechanistic discoveries and revolutionary therapies with RNA. To maintain this progress, it is imperative to educate the RNA biologists of tomorrow. Therefore, we have created RNA@core to fully equip PhD candidates at theoretical, practical, and communicational levels; we aim to educate PhD candidates to think critically and independently, design experiments and manage their own projects. RNA@core brings together twelve research groups, led by Junior and Senior scientists, to translate excellent research in RNA biochemistry and biology into a cutting-edge PhD training and create a dynamic and interdisciplinary network for the benefit of the students. The curriculum of RNA@core introduces key innovations such as short lab exchanges and professional coaching to learn to present projects conceptually as chalk talks and to deliver classical, slide-based presentations to an international scientific audience. RNA@core will also offer an advanced theoretical course in RNA molecular biology, a structural biology workshop focusing on enzymology in disease, and a series of short workshops dedicated to critical technologies for RNA research. To gain insights into alternatives to academic career paths, RNA@core will provide candidate PhD students with the possibility to enjoy short internships in three RNA-focused companies at the Vienna BioCenter. This initiative will allow PhD candidates to make more informed decisions for their future careers in Academia, Industry, or alternative directions. In summary, the Faculty of RNA@core expects to create a vibrant PhD training program where our students will acquire robust and interdisciplinary knowledge in RNA biology but also in transferable communication skills to tackle any challenge that may arise in their careers.

Consortium
  • Boris Görke, Universität Wien
    consortium member (01.07.2023 -)
  • Clemens Plaschka, Institut für Molekulare Pathologie - IMP
    consortium member (01.07.2023 -)
  • Elisa Vilardo, Medizinische Universität Wien
    consortium member (01.07.2023 -)
  • Gülsün Elif Karagöz, Medizinische Universität Wien
    consortium member (01.07.2023 -)
  • Isabella Moll, Universität Wien
    consortium member (01.07.2023 -)
  • Javier Martinez Fernandez, Medizinische Universität Wien
    consortium member (01.07.2023 -)
  • Julius Brennecke, IMBA – Institut für Molekulare Biotechnologie GmbH
    consortium member (01.07.2023 -)
  • Matthias R. Schaefer, Medizinische Universität Wien
    consortium member (01.07.2023 -)
  • Sebastian Falk, Universität Wien
    consortium member (01.07.2023 -)
  • Stefan L. Ameres, IMBA – Institut für Molekulare Biotechnologie GmbH
    consortium member (01.07.2023 -)
Research institution(s)
  • Medizinische Universität Wien

Research Output

  • 407 Citations
  • 51 Publications
  • 2 Methods & Materials
  • 1 Disseminations
  • 1 Fundings
Publications
  • 2026
    Title Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity.
    DOI 10.1038/s41467-026-68420-5
    Type Journal Article
    Author Budroni V
    Journal Nature communications
  • 2023
    Title piRNA processing by a trimeric Schlafen-domain nuclease
    DOI 10.1038/s41586-023-06588-2
    Type Journal Article
    Author Podvalnaya N
    Journal Nature
    Pages 402-409
    Link Publication
  • 2023
    Title Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells
    DOI 10.1261/rna.079714.123
    Type Journal Article
    Author Anisimova A
    Journal RNA
    Pages 1818-1836
    Link Publication
  • 2023
    Title Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex
    DOI 10.1261/rna.079732.123
    Type Journal Article
    Author Jaksch D
    Journal RNA
    Pages 1856-1869
    Link Publication
  • 2023
    Title Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex
    DOI 10.1101/2023.05.26.542437
    Type Preprint
    Author Jaksch D
    Pages 2023.05.26.542437
    Link Publication
  • 2023
    Title Role of the 5' end phosphorylation state for small RNA stability and target RNA regulation in bacteria
    DOI 10.1093/nar/gkad226
    Type Journal Article
    Author Schilder A
    Journal Nucleic Acids Research
    Pages 5125-5143
    Link Publication
  • 2025
    Title Lessons from RatA: Why the Basics in Molecular Biology Are Still Crucial!
    DOI 10.3390/ijms26073100
    Type Journal Article
    Author Fasnacht M
    Journal International Journal of Molecular Sciences
    Pages 3100
    Link Publication
  • 2025
    Title Direct cell-to-cell transmission of retrotransposons
    DOI 10.1101/2025.03.14.642691
    Type Preprint
    Author Voichek M
    Pages 2025.03.14.642691
    Link Publication
  • 2025
    Title HaloPROTAC3 treatment activates the unfolded protein response of the endoplasmic reticulum in nonengineered mammalian cell lines
    DOI 10.1091/mbc.e24-08-0342
    Type Journal Article
    Author Anisimova A
    Journal Molecular Biology of the Cell
    Link Publication
  • 2025
    Title Mechanistic basis for PYROXD1-mediated protection of the human tRNA ligase complex against oxidative inactivation
    DOI 10.1038/s41594-025-01516-6
    Type Journal Article
    Author Loeff L
    Journal Nature Structural & Molecular Biology
    Pages 1205-1212
    Link Publication
  • 2025
    Title In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET
    DOI 10.1016/j.cell.2025.02.003
    Type Journal Article
    Author Klumpe S
    Journal Cell
    Link Publication
  • 2025
    Title Ampicillin treatment in persister cell studies may cause non-physiological artifacts
    DOI 10.15698/mic2025.03.845
    Type Journal Article
    Author Fasnacht M
    Journal Microbial Cell
    Pages 53
    Link Publication
  • 2024
    Title Author Correction: piRNA processing by a trimeric Schlafen-domain nuclease.
    DOI 10.1038/s41586-024-07938-4
    Type Journal Article
    Author Bronkhorst Aw
    Journal Nature
  • 2024
    Title Selfish conflict underlies RNA-mediated parent-of-origin effects
    DOI 10.1038/s41586-024-07155-z
    Type Journal Article
    Author Marvanova H
    Journal Nature
  • 2024
    Title Genome-wide profiling of DNA repair proteins in single cells
    DOI 10.1038/s41467-024-54159-4
    Type Journal Article
    Author Rullens P
    Journal Nature Communications
  • 2024
    Title Multiple regulatory inputs including cell envelope stress orchestrate expression of the Escherichia coli rpoN operon.
    DOI 10.1111/mmi.15280
    Type Journal Article
    Author Budja Lvp
    Journal Molecular microbiology
    Pages 11-28
  • 2024
    Title Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
    DOI 10.1038/s44318-024-00102-8
    Type Journal Article
    Author Mandlbauer A
    Journal The EMBO Journal
    Pages 2506-2525
    Link Publication
  • 2024
    Title Rnalib: a Python library for custom transcriptomics analyses
    DOI 10.1093/bioinformatics/btae751
    Type Journal Article
    Author Popitsch N
    Journal Bioinformatics
    Link Publication
  • 2024
    Title Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
    DOI 10.1186/s13059-024-03313-8
    Type Journal Article
    Author Popitsch N
    Journal Genome Biology
    Pages 166
    Link Publication
  • 2024
    Title Mechanism for the initiation of spliceosome disassembly
    DOI 10.1038/s41586-024-07741-1
    Type Journal Article
    Author Vorländer M
    Journal Nature
    Pages 443-450
    Link Publication
  • 2024
    Title Endoplasmic reticulum: Monitoring and maintaining protein and membrane homeostasis in the endoplasmic reticulum by the unfolded protein response
    DOI 10.1016/j.biocel.2024.106598
    Type Journal Article
    Author Kettel P
    Journal The International Journal of Biochemistry & Cell Biology
    Pages 106598
    Link Publication
  • 2024
    Title MUT-7 exoribonuclease activity and localization are mediated by an ancient domain
    DOI 10.1093/nar/gkae610
    Type Journal Article
    Author Busetto V
    Journal Nucleic Acids Research
    Pages 9076-9091
    Link Publication
  • 2024
    Title Proteome-scale tagging and functional screening in mammalian cells by ORFtag
    DOI 10.1038/s41592-024-02339-x
    Type Journal Article
    Author Nemcko F
    Journal Nature Methods
    Pages 1668-1673
    Link Publication
  • 2024
    Title Multi-scale Simulations of MUT-16 Scaffold Protein Phase Separation and Client Recognition
    DOI 10.1101/2024.04.13.589337
    Type Preprint
    Author Gaurav K
    Pages 2024.04.13.589337
    Link Publication
  • 2024
    Title Evaluation of 5'-End Phosphorylation for Small RNA Stability and Target Regulation In Vivo
    DOI 10.1007/978-1-0716-3565-0_14
    Type Book Chapter
    Author Schilder A
    Publisher Springer Nature
    Pages 255-272
  • 2024
    Title Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals
    DOI 10.7554/elife.93194
    Type Journal Article
    Author Baumgartner L
    Journal eLife
    Link Publication
  • 2023
    Title SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis
    DOI 10.1016/j.celrep.2023.112070
    Type Journal Article
    Author Bhat P
    Journal Cell Reports
    Pages 112070
    Link Publication
  • 2023
    Title Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy
    DOI 10.15252/embj.2022112053
    Type Journal Article
    Author Picchianti L
    Journal The EMBO Journal
    Link Publication
  • 2024
    Title Structural basis of human U5 snRNP late biogenesis and recycling
    DOI 10.1038/s41594-024-01243-4
    Type Journal Article
    Author Riabov Bassat D
    Journal Nature Structural & Molecular Biology
    Pages 747-751
    Link Publication
  • 2024
    Title IGF2BP1 phosphorylation in the disordered linkers regulates ribonucleoprotein condensate formation and RNA metabolism
    DOI 10.1038/s41467-024-53400-4
    Type Journal Article
    Author Hornegger H
    Journal Nature Communications
    Pages 9054
    Link Publication
  • 2024
    Title Disordered regions in the IRE1a ER lumenal domain mediate its stress-induced clustering
    DOI 10.1038/s44318-024-00207-0
    Type Journal Article
    Author Kettel P
    Journal The EMBO Journal
    Pages 4668-4698
    Link Publication
  • 2025
    Title Sugar caps protect mRNAs from decay
    DOI 10.1073/pnas.2527312122
    Type Journal Article
    Author Forbes R
    Journal Proceedings of the National Academy of Sciences
    Link Publication
  • 2025
    Title RNA decay via the nuclear exosome is essential for Piwi-mediated transposon silencing
    DOI 10.64898/2025.12.16.694471
    Type Preprint
    Author Yu C
    Pages 2025.12.16.694471
    Link Publication
  • 2025
    Title The unfolded protein response in progeria arteries originates from non-endothelial cell types
    DOI 10.26508/lsa.202503485
    Type Journal Article
    Author Silva R
    Journal Life Science Alliance
    Link Publication
  • 2025
    Title Multi-tissue characterization of the constitutive heterochromatin proteome in Drosophila identifies a link between satellite DNA organization and transposon repression
    DOI 10.1371/journal.pbio.3002984
    Type Journal Article
    Author Chavan A
    Journal PLOS Biology
  • 2025
    Title Mechanisms of Messenger RNA Packaging and Export.
    DOI 10.1146/annurev-cellbio-101123-045256
    Type Journal Article
    Author Faraway R
    Journal Annual review of cell and developmental biology
    Pages 479-504
  • 2025
    Title An ATP-gated molecular switch orchestrates human mRNA export
    DOI 10.1038/s41586-025-09832-z
    Type Journal Article
    Author Hohmann U
    Journal Nature
    Pages 1042-1050
    Link Publication
  • 2025
    Title Hierarchical assembly and functional resilience of the mammalian RNA exosome
    DOI 10.1101/2025.03.14.643291
    Type Preprint
    Author Navalayeu T
    Pages 2025.03.14.643291
    Link Publication
  • 2025
    Title Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses
    DOI 10.1038/s44318-025-00471-8
    Type Journal Article
    Author Senti K
    Journal The EMBO Journal
    Pages 1889-1908
    Link Publication
  • 2025
    Title ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA
    DOI 10.1093/nar/gkaf545
    Type Journal Article
    Author Soderholm A
    Journal Nucleic Acids Research
    Link Publication
  • 2025
    Title Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance
    DOI 10.1101/2025.09.09.675111
    Type Preprint
    Author Shang R
    Pages 2025.09.09.675111
    Link Publication
  • 2025
    Title Collective homeostasis of condensation-prone proteins via their mRNAs
    DOI 10.1038/s41586-025-09568-w
    Type Journal Article
    Author Faraway R
    Journal Nature
    Pages 798-808
    Link Publication
  • 2025
    Title Multi-scale simulations of MUT-16 scaffold protein phase separation and client recognition
    DOI 10.1016/j.bpj.2025.08.001
    Type Journal Article
    Author Gaurav K
    Journal Biophysical Journal
    Pages 3987-4004
    Link Publication
  • 2025
    Title Target RNA recognition drives PIWI complex assembly for transposon silencing
    DOI 10.1016/j.molcel.2025.08.007
    Type Journal Article
    Author Portell-Montserrat J
    Journal Molecular Cell
  • 2023
    Title Epigenetic Manipulation of Transposable and Repetitive Elements.
    DOI 10.1007/978-1-0716-2883-6_16
    Type Journal Article
    Author Jachowicz Jw
    Journal Methods in molecular biology (Clifton, N.J.)
    Pages 355-368
  • 2023
    Title ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers.
    DOI 10.1038/s41556-022-01051-2
    Type Journal Article
    Author Stecher K
    Journal Nature cell biology
    Pages 42-55
  • 2023
    Title mRNA recognition and packaging by the human transcription-export complex.
    DOI 10.1038/s41586-023-05904-0
    Type Journal Article
    Author Pacheco-Fiallos B
    Journal Nature
    Pages 828-835
  • 2023
    Title A fine balancing act: how epitranscriptome regulates dosage compensation in mammals.
    DOI 10.1038/s41594-023-01055-y
    Type Journal Article
    Author Jachowicz Jw
    Journal Nature structural & molecular biology
    Pages 1057-1059
  • 2023
    Title MUT-7 exoribonuclease activity and localisation are mediated by an ancient domain
    DOI 10.1101/2023.12.20.572533
    Type Preprint
    Author Busetto V
    Pages 2023.12.20.572533
    Link Publication
  • 0
    Title See above
    Type PhD Thesis
    Author All Doctoral Theses Are Ongoing; None Has Been Finished. We Report This Here Because We Do Not Find A Proper Field To Indicate This.
  • 0
    DOI 10.2210/pdb8q7w/pdb
    Type Other
Methods & Materials
  • 2024 Link
    Title ORFtag
    DOI 10.1038/s41592-024-02339-x
    Type Technology assay or reagent
    Public Access
    Link Link
  • 0
    Title HA-tagged RBPs mESC lines
    Type Cell line
    Public Access
Disseminations
  • 2024
    Title "Dark genome and beginning of life" at the IMBA Family Day
    Type Participation in an open day or visit at my research institution
Fundings
  • 2024
    Title Determinants of mRNA Lifetime and Translation Efficiency
    Type Research grant (including intramural programme)
    Start of Funding 2024
    Funder Vienna Science and Technology Fund

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