RNAi machinery cooperates with SWI/SNF complexes in nucleosome positioning at Transcriptional Start Sites

In Eukaryotes, Argonaute (AGO) proteins have a well-established role in the cytoplasm in post-transcriptional regulation of gene expression in association with different classes of small non-coding RNAs (sRNAs). In plants and yeast, it has been demonstrated that AGO proteins exert a role in the epigenetic regulation of chromatin modifications. Furthermore, AGO2 protein acts also in the nuclei of human cell lines and emerging literature reports that upon the transfection of sRNAs complementary to non-coding promoter transcripts, AGO2 is recruited on target promoters. Previous results in our laboratory demonstrated that AGO2 and SWI/SNF have a physical interaction, which is independent of RNA or DNA, in human cell lines. As SWI/SNF is the major chromatin-remodelling complex in human, these data suggest that AGO2 might participate in the regulation of chromatin plasticity. In eukaryotes, the proper organization of chromatin is essential for the control of gene expression and is achieved through the concerted activity of histone modifications, DNA methylation and nucleosome positioning. The focus of the present thesis has been the development of relevant bioinformatics pipelines for data processing, analysis and visualization, all aiming at dissection of the functional significance of the AGO2-SWI/SNF interaction. Interestingly, this bioinformatics pipeline allowed me to identify a novel class of nuclear AGO2-bound sRNAs arising from genomic regions 150 nt around the Transcription Start Sites (TSS) bound by SWI/SNF (swiRNAs). Furthermore, swiRNAs present a Dicer-dependent processing and show an involvement in nucleosome occupancy at nucleosome +1. These data represent the first description of a molecular mechanism through which AGO2 is involved in nucleosome positioning in mammalian cells.