High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.
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.
Patwardhan
Rupali P
RP
Department of Genome Sciences, University of Washington, Seattle, Washington, USA. rpatward@u.washington.edu
Lee
Choli
C
Litvin
Oren
O
Young
David L
DL
Pe'er
Dana
D
Shendure
Jay
J
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*
D004247:DNA