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Measuring Chromatin Interaction Dynamics on the Second Time Scale at Single-Copy Genes

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Science  18 Oct 2013:
Vol. 342, Issue 6156, pp. 369-372
DOI: 10.1126/science.1242369

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Capturing Binding Location and Speed

Transcription factor–binding sites in chromatin can be mapped by the chromatin immunoprecipitation (ChIP) assay, which analyzes formaldehyde-fixed chromatin fragments obtained from cells. However, the standard ChIP assay does not provide information about how stable the inter-actions are. Other approaches, including live-cell imaging, can reveal aspects of the dynamic behavior of transcription factors but are limited either in location precision or time resolution. Poorey et al. (p. 369, published online 3 October) developed a model to explain how the ChIP signal relates to formaldehyde cross-linking time, and they developed a method to measure chromatin site–specific binding dynamics with high temporal resolution.

Abstract

The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins, but it is unknown how stable most native interactions are. Although live-cell imaging suggests short-lived interactions at tandem gene arrays, current methods cannot measure rapid binding dynamics at single-copy genes. We show, by using a modified ChIP assay with subsecond temporal resolution, that the time dependence of formaldehyde cross-linking can be used to extract in vivo on and off rates for site-specific chromatin interactions varying over a ~100-fold dynamic range. By using the method, we show that a regulatory process can shift weakly bound TATA-binding protein to stable promoter interactions, thereby facilitating transcription complex formation. This assay provides an approach for systematic, quantitative analyses of chromatin binding dynamics in vivo.

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