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Nat Methods. 2014 Jan;11(1):66-72. doi: 10.1038/nmeth.2713. Epub 2013 Nov 3.

Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.

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1
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
2
1] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington, USA.

Abstract

It is currently not possible to resolve the genome-wide relationship of transcription factors (TFs) and nucleosomes at the level of individual chromatin templates despite rapidly increasing data on TF and nucleosome occupancy in the human genome. Here we describe DNase I-released fragment-length analysis of hypersensitivity (DNase-FLASH), an approach that directly couples mapping of TF occupancy, via quantification of DNA microfragments released from individual TF recognition sites in regulatory DNA, to the surrounding nucleosome architecture, via analysis of larger DNA fragments, in a single assay. DNase-FLASH enables coupling of individual TF footprints to nucleosome occupancy, identifying TFs that precisely demarcate the regulatory DNA-nucleosome interface.

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PMID:
24185839
DOI:
10.1038/nmeth.2713
[Indexed for MEDLINE]
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