Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH

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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Figure 1: DNase-FLASH for the parallel detection of TF binding and nucleosome positioning in vivo.
Figure 2: DNase I fragment length parallels TF occupancy.
Figure 3: Transcription factors position nucleosomes and organize chromatin structure in regulatory regions.
Figure 4: Boundary TFs demarcate the regulatory DNA–nucleosome interface.
Figure 5: Nucleosome organization, TSS selection and promoter activity.

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Acknowledgements

J.V. is supported by a US National Science Foundation Graduate Research Fellowship under grant DGE-071824. This work was supported by US National Institutes of Health NHGRI grants U54HG004592 and U54HG007010 to J.A.S.

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J.V. and J.A.S. designed the experiments. J.V. performed the DNase I experiments and analyzed the data. H.W. produced the MNase data. R.S. and S.J. assisted in data analysis. J.V., S.J. and J.A.S. wrote the paper.

Corresponding author

Correspondence to John A Stamatoyannopoulos.

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The authors declare no competing financial interests.

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Supplementary Figures 1–11 and Supplementary Table 1 (PDF 8647 kb)

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Vierstra, J., Wang, H., John, S. et al. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. Nat Methods 11, 66–72 (2014). https://doi.org/10.1038/nmeth.2713

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