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The Mycobacterium tuberculosis regulatory network and hypoxia

(2013) NATURE. 499(7457). p.178-183
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.
Keywords
PHOP, REACTIVATION, BIOSYNTHESIS, INSIGHTS, PROTEIN, FREE MYCOLIC ACIDS, CONTROLLING GENE-EXPRESSION, DEVR DOSR REGULON, VIRULENCE, CHOLESTEROL-METABOLISM

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Citation

Please use this url to cite or link to this publication:

MLA
Galagan, James E, Kyle Minch, Matthew Peterson, et al. “The Mycobacterium Tuberculosis Regulatory Network and Hypoxia.” NATURE 499.7457 (2013): 178–183. Print.
APA
Galagan, J. E., Minch, K., Peterson, M., Lyubetskaya, A., Azizi, E., Sweet, L., Gomes, A., et al. (2013). The Mycobacterium tuberculosis regulatory network and hypoxia. NATURE, 499(7457), 178–183.
Chicago author-date
Galagan, James E, Kyle Minch, Matthew Peterson, Anna Lyubetskaya, Elham Azizi, Linsday Sweet, Antonio Gomes, et al. 2013. “The Mycobacterium Tuberculosis Regulatory Network and Hypoxia.” Nature 499 (7457): 178–183.
Chicago author-date (all authors)
Galagan, James E, Kyle Minch, Matthew Peterson, Anna Lyubetskaya, Elham Azizi, Linsday Sweet, Antonio Gomes, Tige Rustad, Gregory Dolganov, Irina Glotova, Thomas Abeel, Chris Mahwinney, Adam D Kennedy, René Allard, William Brabant, Andrew Krueger, Suma Jaini, Brent Honda, Wen-Han Yu, Mark J Hickey, Jeremy Zucker, Christopher Garay, Brian Weiner, Peter Sisk, Christian Stolte, Jessica K Winkler, Yves Van de Peer, Paul Iazzetti, Diogo Camacho, Jonathan Dreyfuss, Yang Liu, Anca Dorhoi, Hans-Joachim Mollenkopf, Paul Drogaris, Julie Lamontagne, Yiyong Zhou, Julie Piquenot, Sang Tae Park, Sahadevan Raman, Stefan HE Kaufmann, Robert P Mohney, Daniel Chelsky, D Branch Moody, David R Sherman, and Gary K Schoolnik. 2013. “The Mycobacterium Tuberculosis Regulatory Network and Hypoxia.” Nature 499 (7457): 178–183.
Vancouver
1.
Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, et al. The Mycobacterium tuberculosis regulatory network and hypoxia. NATURE. 2013;499(7457):178–83.
IEEE
[1]
J. E. Galagan et al., “The Mycobacterium tuberculosis regulatory network and hypoxia,” NATURE, vol. 499, no. 7457, pp. 178–183, 2013.
@article{4121562,
  abstract     = {We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.},
  author       = {Galagan, James E and Minch, Kyle and Peterson, Matthew and Lyubetskaya, Anna and Azizi, Elham and Sweet, Linsday and Gomes, Antonio and Rustad, Tige and Dolganov, Gregory and Glotova, Irina and Abeel, Thomas and Mahwinney, Chris and Kennedy, Adam D and Allard, René and Brabant, William and Krueger, Andrew and Jaini, Suma and Honda, Brent and Yu, Wen-Han and Hickey, Mark J and Zucker, Jeremy and Garay, Christopher and Weiner, Brian and Sisk, Peter and Stolte, Christian and Winkler, Jessica K and Van de Peer, Yves and Iazzetti, Paul and Camacho, Diogo and Dreyfuss, Jonathan and Liu, Yang and Dorhoi, Anca and Mollenkopf, Hans-Joachim and Drogaris, Paul and Lamontagne, Julie and Zhou, Yiyong and Piquenot, Julie and Park, Sang Tae and Raman, Sahadevan and Kaufmann, Stefan HE and Mohney, Robert P and Chelsky, Daniel and Moody, D Branch and Sherman, David R and Schoolnik, Gary K},
  issn         = {0028-0836},
  journal      = {NATURE},
  keywords     = {PHOP,REACTIVATION,BIOSYNTHESIS,INSIGHTS,PROTEIN,FREE MYCOLIC ACIDS,CONTROLLING GENE-EXPRESSION,DEVR DOSR REGULON,VIRULENCE,CHOLESTEROL-METABOLISM},
  language     = {eng},
  number       = {7457},
  pages        = {178--183},
  title        = {The Mycobacterium tuberculosis regulatory network and hypoxia},
  url          = {http://dx.doi.org/10.1038/nature12337},
  volume       = {499},
  year         = {2013},
}

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