Abstract
Competition ChIP is an experimental method that allows transcription factor (TF) chromatin turnover dynamics to be measured across a genome. We develop and apply a physical model of TF-chromatin competitive binding using chemical reaction rate theory and are able to derive the physical half-life or residence time for TATA-binding protein (TBP) across the yeast genome from competition ChIP data. Using our physical modeling approach where we explicitly include the induction profile of the competitor in the model, we are able to estimate yeast TBP-chromatin residence times as short as 1.3 minutes, demonstrating that competition ChIP is a relatively high temporal-resolution approach. Strikingly, we find a median value of ~5 TBP-chromatin binding events associated with the synthesis of one RNA molecule across Pol II genes, suggesting multiple rounds of pre-initiation complex assembly and disassembly before productive elongation of Pol II is achieved at most genes in the yeast genome.
Highlights
Cellular processes including transcription are inherently dynamic
Comparing TATA-binding protein (TBP)-chromatin residence times with nascent RNA transcription rates[18], we found that a median value of ~5 TBP binding events were associated with productive RNA synthesis across Pol II genes
We developed and applied a physical model of competitive binding using chemical kinetic theory to TBP competition chromatin immunoprecipitation (ChIP)-chip data and derived TBP-chromatin residence times genome-wide in yeast
Summary
Cellular processes including transcription are inherently dynamic. Currently, the dynamics of transcription and other molecular processes in the cell are poorly understood[1] because of a lack of methods that measure fundamental kinetic parameters in vivo. We developed and applied a physical modeling approach using chemical kinetic theory that directly estimates the physical half-life or residence time of TATA-binding protein (TBP)—the general transcription factor which initiates PIC formation17—on chromatin across the yeast genome from TBP competition ChIP data[16]. We are capable of estimating TBP-chromatin residence times as short as 1.3 minutes and as long as 53 minutes, demonstrating that competition ChIP is a relatively high temporal resolution method. An advantage of estimating the physical residence time as opposed to relative turnover is that comparison of physical residence times to other physical timescales including nascent RNA transcription rates inform qualitative and quantitative models of the efficiency or stochasticity of PIC formation and transcription[1]. Our findings point to the dynamics and occupancy of factors that regulate the late stages of transcription initiation including Pol II elongation associating more strongly with nascent RNA transcription rates than that of factors regulating early stages including PIC formation such as TBP and Rap[1]
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