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Nat Methods. 2015 Oct;12(10):927-30. doi: 10.1038/nmeth.3554. Epub 2015 Aug 31.

Functional footprinting of regulatory DNA.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
2
Sangamo BioSciences, Pt. Richmond, California, USA.
3
Department of Medicine, Division of Hematology, University of Washington, Seattle, Washington, USA.
4
Boston Children's Hospital, Division of Hematology/Oncology, Boston, Massachusetts, USA.
5
Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA.
6
Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington, USA.

Abstract

Regulatory regions harbor multiple transcription factor (TF) recognition sites; however, the contribution of individual sites to regulatory function remains challenging to define. We describe an approach that exploits the error-prone nature of genome editing-induced double-strand break repair to map functional elements within regulatory DNA at nucleotide resolution. We demonstrate the approach on a human erythroid enhancer, revealing single TF recognition sites that gate the majority of downstream regulatory function.

PMID:
26322838
PMCID:
PMC5381659
DOI:
10.1038/nmeth.3554
[Indexed for MEDLINE]
Free PMC Article

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