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Control of gene expression by RNA helicases DDX5 and DDX17 - Cyril Bourgeois

Control of gene expression by RNA helicases DDX5 and DDX17

                    Project leader : Cyril BOURGEOIS (cyril.bourgeois@inserm.fr)


ResearcherID  E-6337-2010
ORCID             0000-0002-0756-5501
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Twitter              @C_Bourgeois_ENS

Curriculum vitae


 

DDX17 and DDX5 are two highly related DEAD box ATPases that play various molecular functions contributing to the control of gene expression. They are directly involved in several RNA processing mechanisms (pre-mRNA splicing, processing of microRNA precursors) and our work has highlighted their important role in alternative splicing regulation (1,2,4). DDX17 and DDX5 also control directly the binding and the activity of several transcription factors on chromatin, through unclear mechanisms (4,5). Thus, the multi-layered activity of those proteins allows a dynamic orchestration of gene expression that is crucial for some cell differentiation processes (1-4). For example, we have shown the essential role of DDX17 and DDX5 during myogenic differentiation or during epithelial-to-mesenchymal transition (EMT) (1), a cellular transformation occuring during embryogenesis but also during metastasis. More recently we have also uncovered an important function of DDX17 in the early stages of neuroblastoma cell differentiation (4).

We are interested in the DDX17/DDX5-involving chromatin mechanisms that control the overall transcriptional process (RNA Polymerase II-mediated transcription itself, but also co-transcriptional steps such as splicing and polyadenylation). We are investigating the role of DDX17/DDX5 in the spatial folding of genes, and the impact that chromatin looping can have on gene expression in human cells. Beside traditional techniques of molecular and cellular biology (cell transfection, analysis of RNA and protein expression…), we are using more exploratory approaches allowing to specifically modify the genome (CRISPR-Cas9) or to analyse the 3D structure of genes (3C/4C). Our research exploits various NGS datasets (RNA-seq, ChIP-seq…) through computational approaches that allow to look into these mechanisms from a wider perspective.

Our main model system to study those mechanisms is neuroblastoma, a pediatric cancer that is often uncurable in its most serious forms. An essential aspect of the development of neuroblastomas to more or less aggressive forms is the capacity of cancer cells, originating from the peripheral nervous system, to proliferate in an aberrant manner or to differentiate into benign neuronal cells, a process very difficult to control therapeutically. DDX17 and DDX5 play a major role in the differentiation of neuroblastoma cells (4), and their expression has a good prognostic value for this cancer. These results suggest that a reduced expression of these factors, which leads in cellulo to deep transcriptomic (non genomic) alterations, may contribute to the development of the most aggressive neuroblastomas, an hypothesis we are investigating.

 


regulation of 3' RNA processing by DDX5 and DDX17

Jessica VALAT (PhD student, UCBL)

Our results indicate that in absence of DDX17/DDX5 RNA helicases in neuroblastoma cells, many transcripts present an extension of their 3' end, a transcriptional readthrough which typically results from a default in termination. In some cases this phenomenon can lead to the production of aberrant chimeric transcripts, by cis-splicing between exons transcribed from tandem-oriented adjacent genes.

The main objective of my PhD project is to determine the molecular mechanism by which DDX17/DDX5 control the termination and 3' end processing of transcripts of protein coding genes. Based on the literature and on our results several hypotheses are explored, for example a possible involvement of CTCF or the formation of R-loops. I am interested more largely in the regulation of the coupling between transcription and RNA processing. Our results indicate that the 3D conformation of genes (chromatin loops) affects the dynamics of their transcription and the co-transcriptional processing of their transcripts  (alternative splicing and cleavage/polyadenylation).

Funding : PhD fellowship from the doctoral school BMIC and Ligue contre le Cancer (4th year)

 


Functional relationship between MYCN oncogene and helicases DDX17 and DDX5 in neuroblastoma

      Valentine CLERC (PhD student, ENS-Lyon)

My PhD project is focussed on the regulation of 3' end processing of mRNA by DDX17 and DDX5 in the context of neuroblastoma. We are exploring the hypothesis that a reduced expression of DDX17 and DDX5 in agressive neuroblastomas could be associated to an alteration of transcription fidelity and to an increase in the production of aberrant transcripts (like chimeric transcripts). I am also investigating the functional relationship between the expression of DDX17 and DDX6 and the oncogene MYCN in neuroblastoma cells.

Funding : PhD fellowship from Fondation pour la Recherche Médicale

 


References

1.  Dardenne E, Polay Espinoza M, Fattet L, Germann S, Lambert MP, Neil H, Zonta E, Mortada H, Gratadou L, Deygas M, Chakrama FZ, Samaan S, Desmet FO, Tranchevent LC, Dutertre M, Rimokh R, Bourgeois CF*, Auboeuf D* (2014). RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation.Cell Rep.7:1900-13 (*corresponding authors). PDF here

2.  Bourgeois CF, Mortreux F, Auboeuf D (2016).The multiple functions of RNA helicases as drivers and switchers of the genetic information flow. Nat. Rev. Mol. Cell. Biol.17:426-38. 

3.  Bourgeois CF, Auboeuf D (2017). The RNA helicase DDX5 is a reprogramming roadblock. Stem Cell Investig.4:79. PDF here

4.  Lambert MP, Terrone S, Giraud G, Benoit-Pilven C, Cluet D, Combaret V, Mortreux F, Auboeuf D, Bourgeois CF (2018). The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation. Nucleic Acids Res.46:686–7700. PDF here

5.  Giraud G, Terrone S., Bourgeois CF (2018). Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation. BMB Rep.51: 613-622. PDF here

 


People involved

Jessica VALAT (PhD student, arrived in 2017)

Valentine CLERC (PhD student, arrived in 2020)

Xavier GRAND, PhD (computational biologist, arrived in 2021, contract UCBL in co-supervision with Barbara Testoni, CRCL)

 


collaborations

Thomas SEXTON (IGBMC, Illkirch/Strasbourg, France)

Barbara TESTONI (CRCL, Lyon, France)

Geneviève GOURDON et Mario GOMES-PEREIRA (Institut de Myologie, Paris, France)

Julien COURCHET (INMG, Lyon, France)

Sarah ENNIS (University of Southampton, UK)

 


recent funding

2016-2020       ANR CHROTOPAS (ANR16 CE12-0009-01)

2018-2019       Ligue contre le Cancer (Comité de la Loire)

2018-2019       Fondation ARC

2019-2020       ANRS

2020-2021       Ligue contre le Cancer (Comité du Rhône)

2020-2021       Association Hubert Gouin, "Enfance et Cancer"

 


Main past members

Sophie TERRONE, PhD (doctorat, 2015-2019)

Guillaume GIRAUD, PhD (post-doc, 2017-2019)

Marie-Pierre LAMBERT, PhD (post-doc, 2013-2016)

Micaela POLAY-ESPINOZA, PhD (doctorat, 2011-2014)