title: Genome-Wide Mapping of the Distribution of CarD, RNAP σA, and RNAP β on theMycobacterium smegmatisChromosome using Chromatin Immunoprecipitation Sequencing.
abstract: CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile ofMycobacterium smegmatisandMycobacterium tuberculosis(6). We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed Chromatin Immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout theM. smegmatischromosome. The distribution of RNAP subunits β and σAwere also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σAwould be predominantly enriched at promoters based on work inEscherichia coli(3), however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σAand CarD led us to propose thatin vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 (5) as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164).
authors.affiliation: Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
authors.affiliation: Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
authors.forename: Azra
authors.initials: A
authors.lastname: Krek
authors.affiliation: Immunology Program, Sloan-Kettering Institute, and Division of Infectious Diseases, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Glickman
authors.affiliation: Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
authors.forename: Nicholas D
authors.initials: ND
authors.lastname: Socci
authors.affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Christina L
authors.initials: CL
authors.lastname: Stallings
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