Project description:Validation of DNA ImmunoPrecipitation with microarray analysis (DIP-chip) technique using the Leu3 DNA binding domain. Keywords: DIP-chip, Leu3
Project description:Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (validation)
Project description:Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (different concentrations)
Project description:H3 ChIP and input DNA were hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and accounts for some of the correlation between occupancy patterns of nucleosomes assembled in vivo and in vitro. Using an improved method for measuring nucleosome occupancy in vivo that does not involve MNase, we confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions, nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nucleosome occupancy at terminators is strongly affected by growth conditions, indicating that it is not primarily determined by intrinsic histone-DNA interactions. Rapid removal of RNA polymerase II (Pol II) causes increased nucleosome occupancy at terminators, strongly suggesting a transcription-based mechanism of nucleosome depletion. However, the distinct behavior of terminator regions and their corresponding coding regions suggests that nucleosome depletion at terminators is not simply associated with passage of Pol II, but rather involves a distinct mechanism linked to 3’ end formation.
Project description:Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
Project description:RNA-seq data of chemostat conditions was collected in triplicate to get accurate genome-wide transcript levels that could be integrated with ChIP data from transcription factor binding to understand transcriptional regulation.
