Functional footprinting of regulatory DNA

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


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Binding Sites
  • Carrier Proteins / genetics*
  • DNA Breaks, Double-Stranded
  • DNA Footprinting / methods*
  • DNA Repair
  • Enhancer Elements, Genetic
  • Erythrocytes / physiology
  • Erythropoiesis
  • Genome, Human
  • Genomics / methods*
  • Humans
  • Mutation
  • Nuclear Proteins / genetics*
  • Regulatory Sequences, Nucleic Acid*
  • Repressor Proteins
  • Transcription Factors / metabolism


  • BCL11A protein, human
  • Carrier Proteins
  • Nuclear Proteins
  • Repressor Proteins
  • Transcription Factors