E-MTAB-1950 - MNase-seq of budding yeast cells to determine nucleosome modelling over a Msn2-activation time-course

Released on 12 October 2013, last updated on 9 September 2014
Saccharomyces cerevisiae
Samples (6)
Protocols (7)
The aim of this experiment was to determine, using MNAse-Seq, how nucleosomes get remodeled during an Msn2 activation timecourse genome-wide. Diploid strain EY2807/ASH79 with genotype TPK1M164G TPK2M147G TPK3M165G msn4::TRP1/LEU2 MSN2-mCherry NHP6a-iRFP::kanMX was used. This strain is PKAas, so upon addition of the inhibitor 1-NM-PP1, Msn2 translocates to the nucleus and activates gene expression. In this experiment, the diploid strain was exposed to 3 uM 1-NM-PP1 for 0, 5, 10, 20 and 40 min and nucleosome positions determined using by crosslinking, MNAse treatment, nucleosomal DNA purification and paired-end high-throughput sequencing (Illumina). Results from transcriptional profiling of yeast with or without Msn2 expression were also deposited at ArrayExpress under accession number E-MTAB-1945 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1945/ ).
Experiment types
DNA-seq, ex vivo, time series
Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Anders S. Hansen, Erin K. O'Shea.
Exp. designProtocolsVariablesProcessedSeq. reads