title: REMap: Operon map of M. tuberculosis based on RNA sequence data.
abstract: A map of the transcriptional organization of genes of an organism is a basic tool that is necessary to understand and facilitate a more accurate genetic manipulation of the organism. Operon maps are largely generated by computational prediction programs that rely on gene conservation and genome architecture and may not be physiologically relevant. With the widespread use of RNA sequencing (RNAseq), the prediction of operons based on actual transcriptome sequencing rather than computational genomics alone is much needed. Here, we report a validated operon map of Mycobacterium tuberculosis, developed using RNAseq data from both the exponential and stationary phases of growth. At least 58.4% of M. tuberculosis genes are organized into 749 operons. Our prediction algorithm, REMap (RNA Expression Mapping of operons), considers the many cases of transcription coverage of intergenic regions, and avoids dependencies on functional annotation and arbitrary assumptions about gene structure. As a result, we demonstrate that REMap is able to more accurately predict operons, especially those that contain long intergenic regions or functionally unrelated genes, than previous operon prediction programs. The REMap algorithm is publicly available as a user-friendly tool that can be readily modified to predict operons in other bacteria.
authors.affiliation: Center for Tuberculosis Research, School of Medicine, Johns Hopkins University, 1550 Orleans St, Baltimore, MD 21287, USA.
authors.forename: Shaaretha
authors.initials: S
authors.lastname: Pelly
authors.affiliation: Center for Tuberculosis Research, School of Medicine, Johns Hopkins University, 1550 Orleans St, Baltimore, MD 21287, USA.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Winglee
authors.affiliation: Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Fang Fang
authors.initials: FF
authors.lastname: Xia
authors.affiliation: Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Rick L
authors.initials: RL
authors.lastname: Stevens
authors.affiliation: Center for Tuberculosis Research, School of Medicine, Johns Hopkins University, 1550 Orleans St, Baltimore, MD 21287, USA.|Howard Hughes Medical Institute, Center for Tuberculosis Research, Johns Hopkins University School of Medicine, 1550 Orleans St, Baltimore, MD 21231.
authors.forename: William R
authors.initials: WR
authors.lastname: Bishai
authors.affiliation: Center for Tuberculosis Research, School of Medicine, Johns Hopkins University, 1550 Orleans St, Baltimore, MD 21287, USA.
authors.forename: Gyanu
authors.initials: G
authors.lastname: Lamichhane
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030541:Databases, Genetic; D003663:Decision Trees; D015964:Gene Expression Regulation, Bacterial; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D009876:Operon; D012329:RNA, Bacterial / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D012329:RNA, Bacterial
keywords: Mycobacterium tuberculosis; Operon; RNAseq