We propose an interdisciplinary data-driven experimental study, SiD, that will enable improved understanding of transcriptional regulation in bacteria. In SiD, we will develop a high-throughput microfluidics-based in vitro transcription method, coupled to in vivo screening efforts with DNA and RNA sequencing. The experimental efforts will allow us to determine the cis-acting DNA sequences for 21 sigma-factors, belonging to three bacterial species, Escherichia coli, Pseudomonas putida and Bacillus subtilis, at the single-nucleotide resolution. With the large-scale data, we will perform in silico data analysis, using statistics and machine learning, to develop algorithms that can infer sigma-factor-specific cis-binding motifs within bacterial promoters. The proposed methodology can be applied to any host of interest, and thus opens up the possibility to expand our knowledge on transcriptional regulation to a wide range of microorganisms. The generated big data will be stored on Norwegian nationwide Sigma2 platform, and the metadata will be made accessible to all interested parties based on the four principles of Findability, Accessibility, Interoperability and Reusability. A project-specific website will also be established following Open Science practices, making scientific research, data and dissemination output of SiD easily and openly accessible. To meet these ambitious goals, SiD requires an interdisciplinary approach, and therefore it integrates the fields of synthetic and computational biology (NTNU,Norway) with research partners from the fields of biophysics (NTNU, Norway), genomics (UNIBI, Germany), biochemistry (UU, Sweden) and synthetic biology (CSIC, Spain).
Project leader: Rahmi Lale
Institution: NORGES TEKNISK-NATURVITENSKAPELIGE UNIVERSITET NTNU