Project description:The presence of Set2-mediated methylation of H3K36 (K36me) correlates with transcription frequency throughout the yeast genome. K36me targets the Rpd3S complex to deacetylate transcribed regions and suppress cryptic transcription initiation at certain genes. Here, using a genome-wide approach, we report that the Set2-Rpd3S pathway is generally required for controlling acetylation at coding regions. When using acetylation as a functional read-out for this pathway, we discovered that longer genes and, surprisingly, genes transcribed at lower frequency exhibit a stronger dependency. Moreover, a systematic screen using high resolution tiling microarrays allowed us to identify a group of genes that rely on Set2-Rpd3S to suppress spurious transcripts. Interestingly, most of these genes are within the group that depend the same pathway to maintain a hypo-acetylated state at coding regions. These data highlight the importance of using the functional readout of histone codes to define the roles of specific pathways.
Project description:Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in an isw1 chd1 mutant yeast strain. Two color experiment. Mutant/WT. Biological replicates=3. Hybridisation of same samples to strand-specific gene expression arrays.
Project description:Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in K36A, K56R and K36AK56R mutant yeast strain compared to wildtype. Two color experiment. Mutant/WT. Biological replicates=3. Hybridisation of same samples to strand-specific gene expression arrays.
Project description:Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in K36A, K56R and K36AK56R mutant yeast strain compared to wildtype. Two color experiment. Mutant/WT. Biological replicates=3. Hybridisation of same samples to strand-specific gene expression arrays.
Project description:Comparison of mouse macrophage responses to 12-o-tetradecanoylphorbol-13-acetate (TPA), lipopolysaccharide (LPS), and LPS plus dexamethasone between wild-type and NCoR-/- mice.
Project description:Comparison of mouse macrophage responses to lipopolysaccharide (LPS) and 12-o-tetradecanoylphorbol-13-acetate (TPA) between wild-type and NcoR-/- mice.
Project description:Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel zinc-binding motif that is conserved among dicers in yeast. Although the C-terminal domain of Dcr1 still binds nucleic acids, this property is dispensable for proper functioning of Dcr1. In contrast, disruption of zinc coordination renders Dcr1 mainly cytoplasmic and leads to remarkable changes in gene expression and loss of heterochromatin assembly. In summary, our results reveal novel insights into the mechanism of nuclear retention of Dcr1 and raise the possibility that this new class of dsRBDs might generally function in nucleo-cytoplasmic trafficking and not substrate binding. The C-terminal domain of Dcr1 constitutes a novel regulatory module that might represent a potential target for therapeutic intervention with fungal diseases. 12 chips representing 4 different strains. Every condition is represented by three biological replicates