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Review
. 2016 Mar;13(3):213-21.
doi: 10.1038/nmeth.3768.

Genomic footprinting

Jeff Vierstra  1   2 , John A Stamatoyannopoulos  1   2   3
Affiliations
Review

Genomic footprinting

Jeff Vierstra et al. Nat Methods. 2016 Mar.

Abstract

The advent of DNA footprinting with DNase I more than 35 years ago enabled the systematic analysis of protein-DNA interactions, and the technique has been instrumental in the decoding of cis-regulatory elements and the identification and characterization of transcription factors and other DNA-binding proteins. The ability to analyze millions of individual genomic cleavage events via massively parallel sequencing has enabled in vivo DNase I footprinting on a genomic scale, offering the potential for global analysis of transcription factor occupancy in a single experiment. Genomic footprinting has opened unique vistas on the organization, function and evolution of regulatory DNA; however, the technology is still nascent. Here we discuss both prospects and challenges of genomic footprinting, as well as considerations for its application to complex genomes.

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References

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