SRA

Epigenetic mechanisms contribute to gene regulation by altering the accessibility of the chromatin, resulting in transcription factor (TF) and nucleosome occupancy changes throughout the genome. A major challenge is defining and dissecting this complex chromatin-mediated code to model transcriptional regulation and predict gene expression. We address this by employing a factor-agnostic, reverse-genetics approach to capture TF and nucleosome occupancies genome-wide in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae using MNase-seq, totalling nearly 1,000,000 possible mutant-gene interactions. We developed a powerful, novel approach to quantify and identify chromatin changes genome-wide. Compared with existing gene expression data, well-established pathways were recapitulated solely by observing differences in TF and nucleosome occupancy, and we found distinct chromatin signatures associated with the upregulation/downregulation of genes. Finally, we demonstrated that these chromatin features are predictive of transcriptional activity, and leveraged these features to reconstruct transcriptional regulatory networks, resolving direct vs. indirect interactions and predicting the transcriptional activity of putative targets based on their chromatin dynamics. Overall, this demonstrates the powerful approach of combining a genetic perturbation with high-resolution epigenomic profiling that enables a closer examination of the interplay between TFs and nucleosomes genome-wide, providing a deeper, mechanistic understanding into the complex relationship between chromatin organization and transcription. Overall design: 201 yeast knockout strains each with an individual gene deletion are profiled using MNase-seq. RNA-seq data for GAL80 knockout yeast strains and wild-type yeast with galactose/dextrose induction