RNA structural ensemble dynamics
RNA is a single-stranded molecule, able to fold back on itself to form intricate secondary and tertiary structures.
An n nucleotide-long RNA can virtually assume up to 1.8n different conformations, but only a tiny subset of such structures is actually sampled in vivo.
Their formation is governed by the crosstalk between a plethora of factors, such as ions, macromolecular crowding, RNA binding proteins (RBPs) and chaperones, post-transcriptional modifications (PTMs), etcetera.
These structures are crucial to the ability of RNA to perform complex biological functions such as catalysis, regulation of gene expression, and macromolecular scaffolding, making the understanding of how it folds a key need.
The main aim of our lab is to decipher the rules underlying RNA structure formation and to dissect the role of the individual players (RBPs, PTMs, etc.), by means of NGS-based and computational approaches, in order to tackle the complexity of the in vivo RNA structurome.
We are interested in:
▪ Understanding the mechanistic aspects of RNA folding
▪ Investigating the crosstalk between RNA structure, PTMs and RBPs
▪ Characterizing the biological function of key RNA structure elements
Exploiting traditional molecular genetics and biochemistry techniques to study the formation, the regulation and the biological impact of RNA structure
Devising novel NGS methods to query RNA structure and post-transcriptional modifications (e.g. CIRS-seq, SPET-seq, 2Ome-seq)
Developing computational tools and analysis methods for improved RNA structure inference (e.g. RNA Framework)
If you are highly-motivated and really enthusiastic about RNA biology, and if you are interested in tackling biological problems at 360° (wet-lab and bioinformatics),
this is the place for you!
We have several positions available at all levels. Please submit an informal inquiry if you are interested!
Several short-term (3 months) and long-term (6 months) projects are available for Master students from the University of Gronigen.
To enquire, please send an email to:
d.incarnato [at] rug.nl
Chinese Council Scholarship (CSC)
for Chinese students only
The CSC scholarship will be topped-up so all bursary PhD students have a monthly income of ~1,700 €.
All PhD candidates need to fulfil the English language proficiency requirement
If you have an idea for a new exciting RNA-related project, we can apply to several funding bodies:
▪ Marie Skłodowska-Curie Actions
▪ EMBO fellowships
▪ Human Frontier Science Program (HFSP)
Structural and biophysical dissection of RNA conformational ensembles
SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data
Probing the dynamic RNA structurome and its functions
SHAPE-guided RNA structure homology search and motif discovery
Genome-scale deconvolution of RNA structure ensembles
A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy
Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements
University of Groningen
GBB Institute - Zernike Campus
Nijenborgh 7
9747 AG Groningen
The Netherlands
