The general objective of the lab is to explore the crosstalk between the transcription machinery, the coding and non-coding RNA it produces, and the chromatin in the context of cancer and multiple sclerosis.
Currently, we are focusing on chromatin factors best known for their role in long-term transcriptional repression (Silencing). We study the function these factors may have in regulating gene-expression and alternative splicing in response to inflammatory cues, and how they may use non-coding RNAs for their targeting to chromatin.
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Stabilize chromatin for the management of diseases with inflammatory components
The advent of protocols allowing generation of induced pluripotent stem cells has revealed that genes turned off during cell differentiation are stably but not definitively repressed, and that the “silencing” machineries involved in this repression share mechanisms and properties with the more transient repression detected at inducible promoters.
H3K9 trimethylation (H3K9me3) are among the histone marks that function in both stable “silencing” of repeat rich regions and transient repression of euchromatic genes. Consistent with this, HP1 proteins that bind this histone modification are enriched at interspersed repeats, while they also function as very general regulators of inducible genes involved in development, cell differentiation, cell cycle, and immune response.
Consistent with the role of HP1 proteins in the transcriptional control of both inducible genes and repeated DNA sequences, we have shown that in patients with Multiple Sclerosis a defect in HP1-mediated silencing causes reactivation of both pro-inflammatory cytokines and human endogenous retroviruses (HERVs). In a subset of the patients, this reactivation is correlated with increased activity of the peptidyl arginine deiminase PADI4 that interferes with the binding of HP1 proteins to H3K9me3 by converting the neighbouring arginine 8 into a citrulline.
Currently, we are further exploring anomalies in the chromatin structure of patients with Multiple Sclerosis with a special interest for the impact of transcripts encoded by interspersed DNA repeats. We are also investigating additional mechanisms regulating the interaction of HP1 proteins with chromatin. In this context, we find that increased activity of the DYRK1A kinase causes decreased HP1-mediated repression of cytokine genes in Down’s syndrome associated megakaryoblastic leukemia.
Finally, we are screening for small molecules allowing for a chemical control of HP1-mediated silencing, with a special interest for molecules able to facilitate induction of pluripotent stem cells.
Regulation of alternative splicing by RNAi and non-coding RNAs
Alternative splicing is a major source of diversity for the proteome. A few years ago, our laboratory provided pioneering data showing that chromatin and chromatin factors play a role the regulation of this alternative splicing.
Along this track, we have now shown in collaboration with the laboratory of A. Harel-Bellan (CEA, Saclay) that alternative splicing is affected by a novel machinery combining nuclear proteins involved in RNAi and splicing factor.
Within this machinery, Argonaute 1 and 2 (AGO1 and AGO2) participate in the recruitment to intragenic chromatin of both chromatin-structuring factors (HP1 and histone methylases) and components of the spliceosome in response to activation of the MAP kinase pathway.
Altogether, our data suggests that this machinery facilitates inclusion of alternative exons by locally assisting the rapid assembly of a functional spliceosome and by generating chromatin structures interfering with the elongation rate of the RNA polymerase II.
Currently, we are exploring the mechanism allowing for the targeted recruitment of the machinery inside the coding region of actively transcribed genes with a special interest for the nature and the origin of the small RNAs associated with AGO1 and AGO2 in the nucleus.
In parallel, we have elaborated an in vitro transcription-splicing system on chromatinized templates that allows us to biochemically explore the connections between chromatin and splicing. This system has now provided the first in vitro evidence for an impact of chromatin on the efficiency of splicing.
Finally, with a reversed approach, we have shown that the activity of several enzymes catalysing histone modifications is affected by alternative splicing events. This represents an additional layer of complexity in the crosstalk between chromatin and splicing.
Alternative splicing affects the activity of Silencing proteins
We have investigated how alternative splicing affects the function of two human histone methyltransferases (HMTase): G9A and SUV39H2. We show that a wide range of tissues express multiple isoforms of these proteins, each displaying activity, stability, or sub-nuclear localization.
Bacterial effector targets HP1 and reveals their role in gut tissue regeneration
In collaboration with the team of Laurence Arbibe in the Unit of Philippe Sansonetti, we show that S. flexneri takes over transcriptional regulation of cellular defense genes by interacting with HP1. This study uncovered a role for HP1g in the dampening of the innate immune response and in increased tissue regeneration within the gut epithelium.