Functional footprinting of regulatory DNA

Nature Methods
Jeff VierstraJohn A Stamatoyannopoulos

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.

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Methods Mentioned

BETA
PCR
footprinting
fluorescence-activated cell sorting
transfection
genotyping
in vitro transcription
transfections
amplicon sequencing

Software Mentioned

R
robustbase

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