The functional relationship between the chromatin remodeler dMi-2 and RNA

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Gene expression in eukaryotic cells involves the generation of a conducive chromatin structure, transcription of the DNA template into RNA, co-transcriptional RNA processing, transport into the cytoplasm and translation of the mRNA into protein. Modulation of chromatin structure on the one hand and RNA production and processing on the other have long been viewed as largely separate steps of gene expression. However, recent research suggests the existence of many functional connections but the molecular principles of this interplay are just beginning to emerge. Drosophila Mi-2 is an ATP-dependent nucleosome remodeler with important functions in gene regulation during differentiation. We have recently demonstrated that dMi-2 associates with mRNA in vivo and that this interaction impacts its chromatin binding and nucleosome remodeling activities. We have now found that dMi-2 modulates alternative mRNA splicing. This identifies an unexpected reciprocal relationship between a classical chromatin remodeller and RNA. In this project we will identify the molecular mechanisms underlying the (1) formation and impact of dMi-2:RNA complexes and (2) the modulation of alternative splicing by dMi-2 by using complementary structural, biochemical, genetic and genomic approaches. In the first part of the project we will define the protein and RNA determinants of dMi-2:RNA complex formation, analyse the contributions of dMi-2-associated and RNA bound proteins and define the impact of dMi-2:RNA complexes on transcriptome and chromatin landscape. In the second part of the project we will define the mechanisms by which dMi-2 modulates alternative splicing by determining the contributions of altered RNA polymerase II elongation rate, splicing-associated chromatin modifications, the interplay with splicing factors and dMi2:RNA binding itself. Given the conservation of dMi-2/CHD4 functions and the important roles that dMi-2/CHD4 plays in development and disease we expect our findings to have far reaching implications.