Deciphering the Epitranscriptome: analysis of tRNA and mRNA modifications
RNA is a central player in life and to fulfil its various functions it is heavily modified. Modifications in all RNAs, including mRNA and tRNA, have a substantial impact on cellular homeostasis and a modification imbalance is connected to a plethora of human diseases, called modopathies.
The summer school will focus on RNA modifications found in human mRNA and tRNA. During this 3 day course, participants will have the opportunity to learn how to isolate RNA from stable isotope-labeled cells, purify tRNA isoacceptors and mRNA. Participants will also learn how to analyze LC-MS/MS data of RNA hydrolysates and NAIL-MS experiments for modification quantification.
This course will include hands-on practical classes on standard and state-of-the-art RNA biology techniques, lectures from internationally renowned scientists, discussions, workshops and social activities in the wonderful city of Aveiro, Portugal.
Speakers
Stefanie Kaiser
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany
Pascal Giehr
Department of Organic Chemistry, LMU Munich, Germany
Matthias Schäfer
Center for Anatomy & Cell Biology, Medical University of Vienna, Austri
Robert Schneider
Institute of Functional Epigenetics (IFE), Helmholtz Munich, Germany
Programme
Day 1 | Monday, 4th September 2023
NAIL-MS and tRNA isoacceptor isolation
| 09h00 – 09h30 | Registration |
| 09h30 – 10h00 | Course Introduction |
| 10h00 – 10h45 | Introduction to RNA modifications Stefanie Kaiser |
| 10h45 – 11h00 | Coffee Break |
| 11h00 – 12h00 | Finding new RNA methyltransferases and their function Robert Schneider |
| 12h00 – 13h00 | Lunch |
| 13h00 – 13h15 | Introduction Practical Session I Gregor Ammann |
| 13h15 – 15h45 | Practical Session I |
| 15h45 – 16h00 | Coffee Break |
| 16h00 – 18h30 | Practical Session I |
| 18h30 – 20h30 | Get together |
Day 2 | Tuesday, 5th September 2023
MS data analysis and harvesting of RNA
| 09h00 – 10h00 | Introduction to Nanopore sequencing Pascal Giehr |
| 10h00 – 10h15 | Introduction Practical Session II Max Berg |
| 10h15 – 11h15 | Practical Session II |
| 11h15 – 11h30 | Coffee Break |
| 11h30 – 12h30 | TBA Pascal Giehr |
| 12h30 – 13h30 | Lunch |
| 13h30 – 14h30 | Introduction to MS of RNA modifications Stefanie Kaiser |
| 14h30 – 14h45 | Break |
| 14h45 – 15h00 | Introduction Practical Session III Nur Yesiltac |
| 15h00 – 16h30 | Practical Session III |
| 16h30 – 16h45 | Coffee Break |
| 16h45 – 19h00 | Practical Session III |
| 19h00 – 23h00 | Dinner & Pub Quiz |
Day 3 | Wednesday, 6th September 2023
mRNA preparation
| 09h00 – 10h00 | ‘Can a Biologist (Really) Fix a Radio?‘: a Persistent Problem Impacting RNA Modification Research Matthias Schäfer |
| 10h00 – 10h15 | Introduction Practical Session IV Alexandre Vicente |
| 10h15 – 11h15 | Practical Session IV |
| 11h15 – 11h30 | Coffee Break |
| 11h30 – 12h30 | tRNA-Derived Small RNAs (tsRNAs): Numbers, Molecular Interactions and Use of a ‘Waste Product’ Matthias Schäfer |
| 12h30 – 13h30 | Lunch |
| 13h30 – 13h45 | Introduction Practical Session V Alexandre Vicente & Jannick Schicktanz |
| 13h45 – 14h15 | Practical Session V |
| 14h15 – 14h45 | Introduction Practical Session VI Hagen Wesseling |
| 14h45 – 16h00 | Practical Session VI |
| 16h00 – 16h15 | Coffee Break |
| 16h15 – 18h30 | Practical Session V |
| 18h30 – 19h30 | Final Discussion |
| 19h30 – 21h30 | Dinner |
Course Coordination
The course will be coordinated by Prof. Stefanie Kaiser from the Laboratory of Analytical Chemistry, Institute of Pharmaceutical Chemistry of Goethe University Frankfurt (GUF) in Germany. Prof. Kaiser is an international renowned RNA mass spectrometrist working on the forefront of RNA modification discovery, charaterization and absolute quantification.
Scientific Organization
Stefanie Kaiser
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany
Ana Soares
Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro
Organizing Committee
Max Berg
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany
Felix Dalwigk
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany
Gregor Ammann
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany
Nur Yesiltac
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Germany
Daniela Ribeiro
Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro
Ana Rita Ferreira
Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro
Registration
Registration deadline: August 15th 2023
Participants requirements
This Summer School is directed to MSc or PhD students, as well as early stage post-doctoral scientists who are interested in the topic. Basic background in molecular biology, biochemistry, cell biology or related fields is required. Applicants should provide a CV, a background on the study or research they are (or intend to be) engaged in, a motivation letter and a letter of recommendation from their current/past supervisor. There is a maximum of 16 people accepted to enroll the hands-on practical course. Additional participants can join the theoretical program in person (with a maximum of 30 participants in total)
Fees
*The fee includes coffee breaks, lunches, 2 dinners and course materials
- Pratical and theoretical course: 85€
- Pratical and theoretical course for UA student & ECIU members: 50€
- Theoretical course (on-site): 50€
- Theoretical course (on-site) for UA students & ECIU members: 25€
Venue
iBiMED – Institute of Biomedicine
Department of Medical Sciences
Campus Universitário de Santiago,
Agra do Crasto – Edifício 30
3810-193 Aveiro
Portugal
The University of Aveiro was founded in 1973 and is one of the most innovative universities in Portugal, recognized by the quality of its teaching and research and its cooperation with regional and national business. Map of the University Campus
Travel Information
Flying to Portugal:
The closest airport is Francisco Sá Carneiro International Airport in Oporto, located some 80 km to the north of Aveiro.
Travel to Aveiro from Oporto Airport:
- Public transport
- Hire a car (driving time to Aveiro 1 hour)
- Taxi (~ 60€)
Oporto Airport to Aveiro by Public Transport
Airporto to train station:
At the airport you can catch a TAXI to the train station (Porto-Campanhã). It costs approximately 20€ and takes about 25 minutes.
or
At the airport, you can catch the METRO (subway) to the city centre (Line E – Trindade; Ticket Z4 ~2.60€).
At Porto-Trindade, validate the same ticket and change to any of the following lines to reach the train station “Porto-Campanhã” Subway Map and Timetables:
Line A and B to “Estádio do Dragão”
Line C to “Campanhã”
Line F to “Fânzeres”
Exit at Campanhã stop and reach the Porto-Campanhã train station after a short walk (~5min).
or
More information can be found on Public Transportation | Porto Airport (aeroportoporto.pt)
Porto-Campanhã to Aveiro:
Trains to Aveiro run regularly throughout the day (one every hour). The ticket costs 3.55€ and the trip takes 50min to 1h10min.
Faster trains (Alpha or Intercidades) are also available.
Please consult the website www.cp.pt for more information.
Aveiro train station to University Campus
Aveiro railway station is located about 30 minutes walking distance.
The Aveiro Bus Line 11 departs from the bus terminal “Terminal Rodoviário“, which is located next to the train station and stops at the venue “Universidade – Crasto” (it is not listed in the schedule but it is the stop between Universidade – Santiago A and ISCAUA A).
The ride takes approximately 15 min and the ticket costs 2.05€ (you can buy the ticket in the bus). Schedule information – Aveiro Bus.
or
Taxi or uber ride takes about 5 minutes (~3€ -6€).
or
Go by bike – Buga2
Accomodation
