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bioRxiv · 10.1101/2020.05.03.074815

Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function

de Jonge, W. J.·Brok, M.·Lijnzaad, P.·Kemmeren, P.·Holstege, F. C. P.
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Abstract

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 organising 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.

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de Jonge, W. J., Brok, M., Lijnzaad, P., Kemmeren, P., Holstege, F. C. P.. 2020-05-03. Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function. https://doi.org/10.1101/2020.05.03.074815

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