Time series data of chromatin occupancy and transcription under cadmium stress
Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists in a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins---including histones, transcription factors (TFs), and polymerases---interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. While gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state is modified and how those modifications connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA binding factors. Overall design: Time course of cadmium treated yeast for T=0 min (prior to cadmium addition), 7.5 min, 15 min, 30 min, 60 min, and 120 min. 12 samples of MNase chromatin (2 technical replicates) and 6 samples of RNA