Over the recent years, several fascinating discoveries have revealed an implication of RNA molecules in the regulation of chromatin condensation and transcription. Inversely, we have shown that chromatin and chromatin remodeling complexes can influence the maturation of messenger RNAs during the process known as alternative splicing (Batsché et al., NSMB, 2006). A connection between RNAs and factors regulating transcription and chromatin is not surprising as RNA is by definition an integer component of the transcription machinery. However, our knowledge of this connection is still very restricted and there is a clear need of a more comprehensive characterization of the crosstalk between the transcription machinery and the RNAs that this machinery produces. The objective of our group is to investigate this crosstalk, defining the proteins, the RNAs and the mechanisms involved, in an attempt to achieve an overview on its impact on transcriptional regulation in a broad sense.

We focus on both long and short RNAs:

Long RNAs: Control of alternative splicing by chromatin regulating factors ?

Alternative splicing is a major source of diversity for the proteome. It is regulated by the very complex spliceosomes but also by several factors involved in transcription. These factors can affect maturation of the transcripts because splicing is initiated while transcription is still ongoing. In the slipstream of our pioneering study on the implication of the SWI/SNF chromatin-remodeling complex in the regulation of alternative splicing, we now show that inclusion of alternative exons is also controlled by methylation of histone H3 on lysine 9 and the subsequent binding of the chromatin protein HP1γ. Our observations further suggest that HP1 proteins participate in linking the chromatin with the proteins chaperoning the nascent pre-mRNA with consequences on the elongation rate of the RNAPII (Saint-André et al., NSMB, in press). To further characterize the impact of chromatin on the regulation of alternative splicing, a siRNA screen is currently carried out to identify chromatin and transcription regulators able to modify the exon content of mature messenger RNAs.

Short RNAs: A role for aborted transcripts in the recruitment of the HP1 chromatin regulators ?

Many inducible promoters recruit the RNAPII while they are still inactive. Much recent data suggest that these pre-recruited RNAPII are engaged in the transcription of short (aborted) transcripts. The HIV1 LTR is a prototype of such promoters and it has been known for decades that in phase of viral latency, this promoter recruits a non-elongating RNAPII engaged in the transcription of the short RNA TAR. Using this model, we have shown that HP1 proteins participate in the control of RNAPII elongation and that the recruitment of these factors to the idle promoter is dependent on the transcriptional activity of the RNAPII (Mateescu et al, EMBO rep, 2008). A similar phenomenon is observed on several cellular promoters involved in immune defense. This study further show that HP1 protein can benefit from SWI/SNF chromatin remodeling to access and bind sites internal to the nucleosome (Lavigne, PloS Genet, 2009). Currently, we are further exploring the implication of short RNAs produced by non-elongating RNAPII in the recruitment of factors involved in transcriptional repression.

Finally, in a model for multiple sclerosis (MS), we show that defective HP1-mediated repression can result in re-activation of both pro-inflammatory genes and endogenous retrovirus, phenomenon frequently observed in MS patients (Sharma et al, in preparation).

Keywords: Transcription, chromatin, RNA, splicing, HP1, immune genes, AIDS

Lavigne M, Eskeland R, Azebi S, Saint-André V, Jang SM, Batsché E, Fan HY, Kingston R, Imhof A, Muchardt C (2009) Interaction of HP1 and Brg1/Brm with the globular of histone H3 is required for HP1-mediated repression. PloS genetics, 5 (12) : e1000769.

Boukarabila H, Saurin AJ, Batsché E, Mossadegh N, van Lohuizen M, Otte AP, Pradel J, Muchardt C, Sieweke M, Duprez E (2009) The PRC1 Polycomb group complex interacts with PLZF/RARA to mediate leukemic transformation. Genes & development 23: 1195-1206

Mateescu B, Bourachot B, Rachez C, Ogryzko V, Muchardt C. (2008) Regulation of an inducible promoter by an HP1beta-HP1gamma switch. EMBO Rep. (3):267-72.

Arbibe L, Kim DW, Batsché E, Pedron T, Mateescu B, Muchardt C, Parsot C, Sansonetti PJ. (2007) An injected bacterial effector targets chromatin access for transcription factor NF-kappaB to alter transcription of host genes involved in immune responses. Nat Immunol. (1):47-56.