SFB 80: RNA-DECO
Decorating RNA
for a purpose

Chemical modifications of RNAs allow the dynamic adaptation of organisms to respond to developmental or environmental changes.

Mission

At SFB (F80), RNA-DECO 12 research groups in Austria comprising of biochemists, biologists and bioinformaticians jointly aim at understanding the impact of chemical modifications on:

Structure & Function of specific RNAs using different models.

RNA modifications affect

Participants

Scientific Advisory Board

News

October 05 2020

Os­mium is key to shed light on genome organi­zation

Researchers at the University of Innsbruck and the Vienna BioCenter have developed a new method that analyzes the spatial organization of chromatin in a cell. Their recent article in Nature demonstrates how the two replicated sister DNA molecules can be mapped in each chromosome using chemical labeling and nucleoside conversion.

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October 02 2020

1st Annual SFB RNA DECO Retreat

The 1st SFB RNA DECO annual retreat took place at Schlosshotel Mondsee in Salzburg on the 7th & 8th of September providing an overview of current research in the field of RNA especially chemical modifications of RNA.
20200908 115610

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July 10 2020

FWF establishes new specialist research area for RNA modifications

The Austrian Science Fund (FWF) is establishing a new specialist research area called RNA-DECO. Over the next four years, total funding of over €4 million will be provided to fund a total of 12 research groups, who will study the chemical modification of ribonucleic acid (RNA). Five of these research groups (Walter Rossmanith, Matthias Schäfer, Elisa Vilardo, Javier Martinez, Michael Jantsch) are based at MedUni Vienna. Overall project leader is Michael Jantsch, Head of MedUni Vienna’s Centre for Anatomy and Cell Biology.

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Publications

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 volume 586, pages139–144(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 , Ronald Micura

Angew Chem Int Ed Engl. 2020 Apr 20

Open Positions

Open PhD Position - Jantsch Lab • open since January 25 2021

PhD position on RNA modifications and innate immune sensing

Michael Jantsch
Medical University of Vienna
Center for Anatomy & Cell Biology
Schwarzpanierstrasse 17
1090 Vienna
Austria
Michael.Jantsch@meduniwien.ac.at

An EU-funded Ph.D. position is available in the lab of Michael Jantsch. The international training network (ITN) consists of a multinational team studying RNA modifications in a multidisciplinary approach. Secondments allow diverse training and research experiences at a competitive salary including family allowance.
The lab of Michael Jantsch studies adenosine deamination in mice which is one of the most abundant RNA modifications in mammals. Deamination of adenosines (A) leads to the formation of inosines (I). Inosines are interpreted as guanosines by most cellular machineries, including translation.
A to I editing is mediated by two enzymes, ADAR1 or ADAR2. While ADAR2 is mainly responsible for editing events that alter the coding of mRNAs or the function of small RNAs, ADAR1 acts as an antiviral protein. Interestingly, loss of ADAR1 leads to elevated interferon signaling and upregulation of the antiviral signals.
It will be the aim of this Ph.D. project to decipher the signals that trigger antiviral responses and to determine how the introduction of inosines prevents antiviral signaling (Fig 1).
MDA5 ADAR
Figure 1: Sensing of dsRNA by antiviral immune proteins. In the absence of A to I editing, dsRNA activates antiviral signaling by recruiting and activating the MDA5-MAVS signaling pathways. In the presence of inosines this pathway is suppressed. Currently, the underlying mechanisms are not well understood.

The Division of Cell & Developmental Biology provides a stimulating atmosphere for RNA research with five research groups working on RNA modifications. The team is tightly linked to other Austrian RNA researchers via an RNA research network. The Division of Cell & Developmental Biology is located near the center of historic Vienna.

Interested candidates, please send their application including a curriculum vitae, a letter of motivation and two contacts for references to
Michael.Jantsch@meduniwien.ac.at under the reference “ROPES
until March 30th 2021
For further information please visit:
ROPES: https://cordis.europa.eu/project/id/956810/de
https://www.rna-deco.org/
https://anatomieundzellbiologie.meduniwien.ac.at/group-jantsch

MASTER THESIS IN STRUCTURAL BIOLOGY DJINOVIC & JANTSCH LABs • open since January 25 2021

Understanding the consequences of RNA-editing at the structural level

The labs of Kristina Djinovic-Carugo and Michael Jantsch are teaming up to understand how RNA-editing induced recoding of the pre-mRNA encoding the actin crosslinking protein filamin A changes the structure of this protein. To achieve this, the protein structure of parts of the filamin A protein will be determined in their natural and “edited” state.

Background: Adenosine deaminases acting on RNA deaminate adenosines to inosines in structured regions of RNAs. The RNA-editing process occurs in millions of sites in the human transcriptome. As inosines are interpreted as guanosines during translation, this RNA-editing process can alter codons and therefore lead to the formation of proteins that are not encoded in the genome. A prominent adenosine to inosine deamination event is found in the mRNA encoding filamin A, an abundant actin crosslinking protein that links the cellular cortex and transmembrane proteins with the cytoskeleton. Changes in the editing pattern of the filamin A mRNA lead to the expression of altered filamin A which causes high blood pressure but also causes gastrointestinal inflammatory disorders. To understand the molecular consequences of the editing-induced amino acid exchange, the affected domain will be studied by structural and biophysical means.

Thesis description: We are looking for a highly motivated and dedicated student to use a combination of structural and molecular biophysics approaches to investigate the molecular consequences of RNA-editing of filamin A. The successful candidate will have the opportunity to (i) express and purify native and “edited” variants and perform a comparative molecular biophysics analysis (ii) X-ray crystallography to determine their structures at high resolution (iii) use biochemical and biophysical methods to validate the mechanistic model.

Requirements: background in biochemistry or molecular biology, studies of Molecular Biology, Biochemistry, Chemistry, Cell Biology or related fields.

Application Details: Interested students, please send
• A cover letter
• Your CV
• Contact details of two referees
To Michael Jantsch <michael.jantsch@meduniwien.ac.at> and Kristina Djinovic-Carugo <Kristina.Djinovic@univie.ac.at>
Duration of thesis: 12 months, salary: 440 € per month. Beginning: immediately.

Further Information:
https://anatomieundzellbiologie.meduniwien.ac.at/abteilungen-wissenschaft-forschung/abteilung-fuer-zell-u-entwicklungsbiologie/epigenetics-and-rna-biology/group-jantsch/
https://www.maxperutzlabs.ac.at/research/research-groups/djinovic

Relevant Publications:
https://doi.org/10.15252/embj.201694813
https://doi.org/10.1080/15476286.2018.1480252

Open PhD Position - Rossmanith lab • open since January 25 2021

The role of modifications in the ‘core’ of human mitochondrial tRNAs

Walter Rossmanith, Ph.D.
Medical University of Vienna
Center for Anatomy & Cell Biology
Währinger Straße 13
1090 Vienna
Austria

A Ph.D. position is available in the lab of Walter Rossmanith at the Medical University of Vienna, Center for Anatomy & Cell Biology. The research of the lab is focused on tRNA biogenesis in human mitochondria (www.meduniwien.ac.at/wrlab). The specific project aims to understand the biological significance and structural role of chemical modifications in the tRNA ‘core’ (i.e., modifications outside of the anticodon loop) using human mitochondrial tRNAs as a model system.

Prospective PhD students are required to have a solid background in molecular and cellular biology. Basic knowledge or some experience in bioinformatics will be considered a plus, but is not a prerequisite. The project will involve the genetic engineering of mammalian cells and various state-of-the-art methods in RNA biology, including specific RNA-Seq/NGS technologies. The applicants should have the ability to work effectively in a team. Payment will be according to the salary scheme of the Austrian Science Fund (FWF; www.fwf.ac.at/en/research-funding/personnel-costs/).

The Medical University of Vienna ranks among the best of all medical institutions in Europe and has a well-established PhD program in RNA biology.
The city of Vienna is consistently rated as one of the best places to live worldwide.

Interested applicants are invited to send an up-to-date CV, a motivation letter, and provide the contact details of two references, all preferably in a single PDF file, to Walter Rossmanith (walter.rossmanith@meduniwien.ac.at).