INCARNATO lab

for RNA folding dynamics research

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What We Do

Dissecting the in vivo RNA structurome to decipher RNA folding rules

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

Molecular genetics & biochemistry

Exploiting traditional molecular genetics and biochemistry techniques to study the formation, the regulation and the biological impact of RNA structure

Next Generation Sequencing

Devising novel NGS methods to query RNA structure and post-transcriptional modifications (e.g. CIRS-seq, SPET-seq, 2Ome-seq)

Bioinformatics

Developing computational tools and analysis methods for improved RNA structure inference (e.g. RNA Framework)

Lab Members

Meet the lab

Danny Incarnato

Assistant Professor @ RUG

Principal Investigator

Principal Investigator

Tycho Marinus

PhD student @ RUG

PhD student

PhD student

Ilaria Manfredonia

PhD student @ RUG

PhD student

PhD student

Phillip Yesley

Undergraduate @ RUG

Undergraduate

Undergraduate

Marta Santos Cardoso

Undergraduate @ RUG

Undergraduate

Undergraduate

Work with us

Join our team!

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 currently no vacancies open but unsolicited applications are always welcome. Also, consider the following possibilities.

Undergraduates

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

PhD students

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

Post-docs

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)

Latest publications

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements

A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications

In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

Where We Are

University of Groningen
GBB Institute - Zernike Campus
Nijenborgh 7
9747 AG Groningen
The Netherlands