Regulatory Network
We are performing a comprehensive empirically-derived reconstruction of the regulatory interaction network of M. tuberculosis. To systematically map transcription factor binding sites, we are performing ChIP-Seq using FLAG-tagged transcription factors episomally expressed under the control of the mycobacterial tetracycline-inducible promoter. This method allows us to target all ~200 regulators in the M. tuberculosis genome in a consistent and comparable manner independent of regulatory function or the conditions under which each regulatory is expressed. Regulators are induced with ATc during mid-log-phase growth, ChIP is performed using a protocol optimized for mycobacteria and related actinomycetes, preparations are sequenced using Illumina, and reads analyzed using a custom pipeline.
This work, performed as part of the TB Systems Biology Consortium, is a collaboration between the Sherman Lab at SBRI and the Galagan Lab at Boston University and the Broad Institute.
In particular, inducible clones were developed by Kyle Minch, and ChIP preparations performed by Kyle Minch, William Brabant, and Tige Rustad at SBRI using a protocol developed by Saha Raman and Sang Tae Park. Library preparation and sequencing is performed by Chris Mawhinney at the BU Illumina Sequencing Core Facility. Analysis and data integration is performed by Matt Peterson, Anna Lyubetskya, Antonio Gomes, Thomas Abeel, Elham Azizi, Brian Weiner, and others in the Galagan Lab. This site was developed by Peter Sisk and Christian Stolte in the Galagan Lab.
We are preparing a manuscript describing these and other contract data in detail. But we are happy to provide our raw mapping data for unrestricted use by the scientific community. Data will be updated on a regular basis. Please feel free to contact any member of the consortium with questions