Ireland, William Thornton, Beeler, Suzannah, Flores-Bautista, Emanuel, Belliveau, Nathan, Sweredoski, Michael, Moradian, Annie, Kinney, Justin Block, Phillips, Robert (January 2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. BioRxiv. (Unpublished)
Abstract
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli , for approximately 65% of the promoters we remain completely ignorant of their regulation. Until we have cracked this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method (Reg-Seq) linking a massively-parallel reporter assay and mass spectrometry to produce a base pair resolution dissection of more than 100 promoters in E. coli in 12 different growth conditions. First, we show that our method recapitulates regulatory information from known sequences. Then, we examine the regulatory architectures for more than 80 promoters in the E. coli genome which previously had no known regulation. In many cases, we also identify which transcription factors mediate their regulation. The method introduced here clears a path for fully characterizing the regulatory genome of model organisms, with the potential of moving on to an array of other microbes of ecological and medical relevance.
| Item Type: | Paper |
|---|---|
| Subjects: | organism description > bacteria bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes |
| CSHL Authors: | |
| Communities: | CSHL labs > Kinney lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 18 January 2020 |
| Date Deposited: | 21 May 2021 20:43 |
| Last Modified: | 21 May 2021 20:43 |
| URI: | https://repository.cshl.edu/id/eprint/40127 |
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