Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function [RNA-Seq]
Protein-DNA interactions are dynamic and these dynamics are an important aspect of chromatin-associated processes such as transcription or replication. Due to a lack of methods to study on- and off-rates across entire genomes, protein-DNA interaction dynamics have not been studied extensively. Here we determine in vivo off-rates for the Saccharomyces cerevisiae chromatin organizing factor Abf1, at 191 sites simultaneously across the yeast genome. Average Abf1 residence times span a wide-range, varying between 4.5 and 37 minutes. Sites with different off-rates are associated with different functional characteristics. This includes their transcriptional dependency on Abf1, nucleosome positioning and the size of the nucleosome-free region, as well as the ability to roadblock RNA polymerase II for termination. The results show how off-rates contribute to transcription factor function and that DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing) is a meaningful way of investigating protein-DNA binding dynamics genome-wide. Overall design: Nascent RNA was labelled and measured using 4tU-seq before (0 min) and at 10 time points (5, 10, 15, 20, 30, 40, 50, 60, 75, 90 min) during depletion from the nucleus using anchor-away, in triplicate. A non-tagged WT control was taken along at the first (0 min) and last (90 min) time point.