PhD PROPOSAL FOR THE PASTEUR-PARIS UNIVERSITY INTERNATIONAL PROGRAM

 

Deadline for full application: December 15th, 2013

 

Interviews: March, 2014

Start of the Ph.D.: October 1st, 2014

 

 

Department: Génomes et Gènètique

Title of the PhD project: Regulation of alternative polyadenylation in Cryptococcus neoformans

Name of the lab: Unité Biologie et Pathogénicité Fongiques

Head of the lab: Christophe d’Enfert

PhD advisor: Guilhem Janbon

Email address: janbon@pasteur.fr

Web site address of the lab:

Doctoral school affiliation and University: B3MI

 

 

Presentation of the laboratory and its research topics:

The group lead by Guilhem Janbon is located in the Unité Biologie et Pathogénicité Fongiques lead by C. d’Enfert. Although the unit is mostly focused on the study of Candida albicans, the research projects of Guilhem Janbon’s group are aimed to study the complexity of the RNA metabolism in the pathogenic basidiomycetous yeast Cryptococcus neoformans. We are analyzing how variations in transcriptome structure and RNA metabolism can regulate the biology and the virulence of this eukaryotic pathogen.

 

 

Description of the project:

Fungi are widespread organisms that can be isolated from a wide range of environments. Sometimes considered as useful partners in the industry, they can however be severe pathogens. As plants and animals, fungi are exposed to diverse alteration of their environment. They adapt their biology and gene expression to cope with different sources of external stresses. Messenger RNA level measurements have been widely used as a mean to study gene expression. However, more recently, it has become obvious that RNA processing is a major player influencing the dynamic of gene regulation. Actually, in addition to alternative splicing and RNA editing, regulation of the mRNA 3’end by alternative polyadenylation (APA) has been recently recognized as major way to regulate gene expression as well as a main source of RNA diversity in eukaryotes. The very recent application of progresses in sequencing technologies to global analysis of APA in metazoans has revealed unexpected complexity. This field of research is quickly moving but strikingly, very little is known concerning this matter in eukaryotic micro-organisms and more specifically in fungi.

Our recent re-annotation of the C. neoformans genome using RNA-Seq data revealed an extensive complexity and flexibility of its transcriptome structure (1). Indeed 99% of the genes contain introns and most of them are regulated through alternative splicing. We also showed that these introns are necessary for gene expression (2). Interestingly, the annotation of polyadenylation sites in this organism revealed that APA is not rare and that it can also be regulated through alternative splicing. Finally, we identified a new motif associated with the polyadenylation site. C. neoformans seems to be a very promising organism for such an analysis. In the present project, global genome wide approached together with more adapted sequencing technologies will be used to understand how APA is regulated when cells are exposed to stressful conditions and at different stages of the cell cycle. This work will be performed in collaboration with a sequencing platform. More specific strategies using model genes to analyze APA will be also used. Thus, a genetic screen aimed to identify genes and pathways regulating APA will be set up. In addition, candidate genes potentially regulating APA will be studied. We will here apply the strength of the yeast genetics to explore a still obscure side of eukaryotic gene expression regulation.

C. neoformans is a opportunistic human pathogen living in the environment. As such the diversity of signals to which it can be exposed in the human body or in soil for example is huge. This organism has to cope with a large number of different stresses and probably needs a very flexible metabolism. It is tempting to hypothesize that its complex RNA metabolism provides a mechanism to achieve such flexibility. This project will also aim to understand how APA can alter the expression of different virulence factors of this yeast so as the pathophysiology of the infection.

 

References:

Goebels C., Thonn A., Gonsalez-Hilarion S., Rolland O., Moyrand F., Beilharz, T. H. & Janbon, G. (2013) Introns regulate gene expression in Cryptococcus neoformans in a Pab2p dependent pathway. PLoS Genet 9: e1003686.

Janbon G., Ormerod K.L., Paulet D. Byrnes III E.J., Chatterjee G, Yadav V., Hon C.C., Billmyre R.B., Brunel F., Bahn Y.S., Chen W. , Chen Y., Chow E.W.L., Coppée J.Y., Floyd-Averette A., Gaillardin C., Gerik K.J., Goebels C., Goldberg J., Gonzalez-Hilarion S., Gujja S., Hamlin J.L., Hsueh Y.P., Ianiri G., Jones S., Kodira C.D., Lam W., Marra M., Mesner L.D., Mieczkowski P.A., Moyrand F., Nielsen K., Proux C., Rossignol T., Schein J.E., Sun S., Wood I.A., Zeng Q., Neuvéglise C., Newlon C.S., Perfect J.R., Lodge J.K., Idnurm A., Stajich J.E., Kronstad J.W., Sanyal K., Heitman J., Fraser J.A., Cuomo C.A. & Dietrich F.S. (2013) The genome sequence of Cryptococcus neoformans var. grubii reveals complex mechanisms of RNA expression and virulence plasticity (submitted)

 

Keywords:

Cryptococcus neoformans; RNA; Intron; Splicing; Alternative polyadenylation; yeast; RNA-Seq

 

Expected profile of the candidate (optional):

The candidate should be interested in genetics and molecular biology. An interest in bioinformatics would be a plus.

 

Contact:

Guilhem Janbon

Unité Biologie et Pathogénicité Fongiques

25 rue du Dr Roux

75015

Paris

janbon@pasteur.fr

33 1 45 68 83 56

 

Mis à jour le 16/09/2013