Nuclear Regulation and Stress
Study of the expression of genes transcribed by RNA polymerase III in yeast in response to different stresses.
Characterization of the networks involved in the modulation of transcriptional activity.
Development of biochemical techniques allowing the exhaustive identification of proteins that interact with the transcriptional machinery. Study of the influence of transcription by RNA polymerase III on the integration of Ty1 retrotransposons.
The regulation of transcription by RNA polymerase III (Pol III) plays a major role in the adaptation of the growth rate of cells to physiological changes or to variations in their environment. Moreover, the level of RNA synthesized by Pol III is abnormally high in tumor cells. Consequently, our research focuses on the regulation, in response to different stresses, of the expression of genes transcribed by Pol III in yeast. We aim to decipher the networks (conserved from yeast to human) involved in the modulation of transcriptional activity, from signal perception to the components of the transcriptional machinery. On the other hand, many DNA-dependent processes occur at or near Pol III-transcribed genes and interact with the transcription machinery through Pol III. For example, the integration of retroviruses and retrotransposons at LTR is not random in vivo. Genomic analyses clearly show that Ty1 retrotransposons preferentially integrate upstream of Pol III transcribed genes in the yeast Saccharomyces cerevisiae. This is why we have recently started a new project in collaboration with the group of Dr Pascale Lesage (IUH, Paris Diderot) to characterize the role of Pol III transcription on Ty1 selective integration.
Conservation of the role of transcription for the integration of retroelements
A common mechanism between retroelements (LTR retrotransposons such as Ty1 and retroviruses): targeting of integration complexes to the cell genome by an interaction between the integrase of the retroelement and cellular proteins (in light blue in the figure) involved in gene transcription.
Pascale Lesage (IUH, Paris Diderot)
To obtain a global view of all the phenomena that occur on the genes transcribed by Pol III, we first plan to identify all the actors directly involved by developing innovative biochemical approaches. We have successfully developed our own tandem chromatin purification technique (TChAP) after in vivo cross-linking, to identify Pol III-associated proteins under normal growth conditions but also in response to stress.
We study programmed genome rearrangements in a model species: Paramecium tetraurelia, which carries a ~100 Mb germline genome. During MAC development, the genome undergoes multiple rounds of endoreplication. Concomitantly, massive programmed genome rearrangements eliminate 25 to 30 % of germline DNA: (i) repeated sequences (transposons, minisatellites) are removed, leading to chromosome fragmentation or heterogeneous internal deletions; (ii) ~ 45,000 short, single copy and noncoding sequences scattered throughout the genome (IES, or internal eliminated sequences) are excised precisely to reconstitute functional open reading frames. At least a fraction of Paramecium IESs are degenerated remnants of transposons related to the Tc/mariner family.
The different steps of TChAP purification.
Nguyen and al. Gene 2015
Another part of our projects is dedicated to the fine dissection of the molecular mechanisms that allow cells to adjust their transcription level to environmental conditions. Thus, we are currently analyzing the role of novel factors that we have identified through our TChAP approach, on transcription through Pol III, using genome-wide, genetic and in vitro analysis approaches.
Our research has been, or is being, supported by ARC and ANR.
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