Projet SMART
PRRI SMART Project: An innovative technology in the field of « Epitranscriptome ».
After decades of near-dormancy, the field of « RNA modifications » is undergoing an unprecedented scientific breakthrough. This revival is the direct consequence of recent technological advances, allowing not only the fine and quantitative detection of these modifications, but also their « mapping» within RNA species.
The potential of the emerging field of « Epitranscriptome » is enhanced by a number of factors :
- More than 170 RNA modifications have been identified up to now.
- Recent studies on a handful of them have revealed the existence of an « invisible code », affecting gene expression and major biological functions in a physiological and pathological context.
- Most RNA modifications are conserved in all living organisms.
- Its potential for the discovery of new biomarkers for diagnosis, prognosis and therapeutic monitoring (Cancer, Neurobiology).
The SMART project (2019-2021), led by the University of Montpellier and the CHU, co-directed by Prof. C. Hirtz (UM/CHU) and Dr. Alexandre David (IGF), was financed by the Occitanie region (PRRI) with European funds for regional development (ERDF funding) to the amount of 981 433€. This project includes a project leader for 3 years (Mrs. Aurore Attina) and a TQ mass spectrometer dedicated to the realization of the analyses.
This PPC-SMART project therefore aims to develop methods for the detection and quantification by mass spectrometry of RNA modifications – a unique service in France – from samples of various origins (human, animal and plant).
Currently, we detect 4 nucleosides and 26 modified nucleosides in a 30-minute LC-MRM analysis. And we continue to enhance this method with further modifications as required.
|
Acronyms |
Name |
Known location (1) |
Phylogeny (1) |
|
A |
Adenosine |
all |
Archaea, Eubacteria, Eukaryota |
|
Am |
2′-O-methyladenosine |
rRNA, snRNA, snoRNA, tRNA |
Eubacteria, Eukaryota |
|
m6A |
N6-methyladenosine |
mRNA, rRNA, snRNA, tRNA |
Eubacteria, Eukaryota |
|
m6Am |
N6-2′-O-dimethyladenosine |
snRNA |
NA |
|
m1A |
N1-methyladenosine |
rRNA, tRNA |
Archaea, Eubacteria, Eukaryota |
|
m6,6A |
N6, N6-dimethyladenosine |
rRNA |
Eubacteria, Eukaryota |
|
m6,6Am |
N6, N6, 2′-O-trimethyladenosine |
NA |
NA |
|
I |
Inosine |
tRNA |
Eubacteria, Eukaryota |
|
C |
Cytidine |
all |
Archaea, Eubacteria, Eukaryota |
|
Cm |
2′-O-methylcytidine |
rRNA, snRNA, tRNA |
Eubacteria, Eukaryota |
|
m3C |
3-methylcytidine |
tRNA |
Eukaryota |
|
m5C |
5-methylcytidine |
mRNA, other, pre-tRNA, rRNA, tRNA |
Eubacteria, Eukaryota |
|
hm5C |
5-hydroxymethylcytidine |
NA |
NA |
|
ac4C |
4-acetylcytidine |
rRNA, tRNA |
Eubacteria, Eukaryota |
|
G |
Guanosine |
all |
Archaea, Eubacteria, Eukaryota |
|
Gm |
2′-O-methylguanosine |
rRNA, snRNA, tRNA |
Eubacteria, Eukaryota |
|
m1G |
N1-methylguanosine |
rRNA, tRNA |
Archaea, Eubacteria, Eukaryota |
|
m7G |
N7-methylguanosine |
rRNA, tRNA |
Eubacteria, Eukaryota |
|
m2,7G |
N2,7-dimethylguanosine |
NA |
Eukaryota |
|
m2,2,7G |
N2,N2,7-dimethylguanosine |
NA |
Eukaryota |
|
oxo8G |
8-oxoguanosine |
NA |
NA |
|
U |
Uridine |
rRNA, tRNA |
Archaea, Eubacteria, Eukaryota |
|
Um |
2′-O-methyluridine |
rRNA, snRNA, snoRNA, tRNA |
Archaea, Eubacteria, Eukaryota |
|
m3Um |
3,2′-O-dimethyluridine |
NA |
NA |
|
ncm5U |
5-carbamoylmethyluridine |
tRNA |
Eukaryota |
|
mcm5U |
5-methoxycarbonylmethyluridine |
tRNA |
Eukaryota |
|
mcm5s2U |
5-methoxycarbonylmethyl-2-thiouridine |
tRNA |
Eukaryota |
|
Ψ |
Pseudouridine |
rRNA, snRNA, snoRNA, tRNA |
Archaea, Eubacteria, Eukaryota |
|
q |
Queuine |
NA |
NA |
|
Q |
Queuosine |
tRNA |
Eubacteria, Eukaryota |
(1) MODOMICS: a database of RNA modification pathways. 2017 update
A new PhD student
A few weeks ago, Amandine Amalric has joined our team in order to perform a thesis in collaboration with IGH (Institute of Functional Genomics) as part of the SMART project (Mass Spectrometry of Total RNAs Modifications). Her thesis project is the identification of...
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Aurore Attina
MASS SPECTROMETRY ENGINEER - SMART PROJECT MANAGER
“Hello everyone, I’m a mass spectrometry engineer and I joined PPC as the SMART project manager. My role is the development and implementation of methods for the detection and quantification of RNA changes.”
Amandine Amalric
PhD student
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