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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.

SUBMITTER: Patwardhan RP 

PROVIDER: S-EPMC2849652 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis.

Patwardhan Rupali P RP   Lee Choli C   Litvin Oren O   Young David L DL   Pe'er Dana D   Shendure Jay J  

Nature biotechnology 20091201 12

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 biolo  ...[more]