title: High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.
abstract: We present a method that harnesses massively parallel DNA synthesis and sequencing for the high-throughput functional analysis of regulatory sequences at single-nucleotide resolution. As a proof of concept, we quantitatively assayed the effects of all possible single-nucleotide mutations for three bacteriophage promoters and three mammalian core promoters in a single experiment per promoter. The method may also serve as a rapid screening tool for regulatory element engineering in synthetic biology.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA. rpatward@u.washington.edu
authors.forename: Rupali P
authors.initials: RP
authors.lastname: Patwardhan
authors.forename: Choli
authors.initials: C
authors.lastname: Lee
authors.forename: Oren
authors.initials: O
authors.lastname: Litvin
authors.forename: David L
authors.initials: DL
authors.lastname: Young
authors.forename: Dana
authors.initials: D
authors.lastname: Pe'er
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed / Q000379:methods*; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA