Literature DB >> 18948201

ROMA: an in vitro approach to defining target genes for transcription regulators.

Shawn R Maclellan1, Warawan Eiamphungporn, John D Helmann.   

Abstract

We describe an in vitro transcription-based method called ROMA (run-off transcription-microarray analysis) for the genome-wide analysis of transcription regulated by sigma factors and other transcriptional regulators. ROMA uses purified RNA polymerase with and without a regulatory protein to monitor products of transcription from a genomic DNA template. Transcribed RNA is converted to cDNA and hybridized to gene arrays allowing for the identification of genes that are specifically activated by the regulator. We discuss the use of ROMA to define sigma factor regulons in Bacillus subtilis and its broad application to defining regulons for other transcriptional regulators in various species.

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Year:  2008        PMID： 18948201      PMCID： PMC2632846          DOI： 10.1016/j.ymeth.2008.10.009

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


  35 in total

1.  Rapid purification of His(6)-tagged Bacillus subtilis core RNA polymerase.

Authors:  L C Anthony; I Artsimovitch; V Svetlov; R Landick; R R Burgess
Journal:  Protein Expr Purif       Date:  2000-08       Impact factor: 1.650

Review 2.  Bacterial RNA polymerases: the wholo story.

Authors:  Katsuhiko S Murakami; Seth A Darst
Journal:  Curr Opin Struct Biol       Date:  2003-02       Impact factor: 6.809

Review 3.  The extracytoplasmic function (ECF) sigma factors.

Authors:  John D Helmann
Journal:  Adv Microb Physiol       Date:  2002       Impact factor: 3.517

4.  Antibiotics that inhibit cell wall biosynthesis induce expression of the Bacillus subtilis sigma(W) and sigma(M) regulons.

Authors:  Min Cao; Tao Wang; Rick Ye; John D Helmann
Journal:  Mol Microbiol       Date:  2002-09       Impact factor: 3.501

5.  Activation of archaeal transcription by recruitment of the TATA-binding protein.

Authors:  Mohamed Ouhammouch; Robert E Dewhurst; Winfried Hausner; Michael Thomm; E Peter Geiduschek
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-11       Impact factor: 11.205

6.  New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome.

Authors:  Kerry Hollands; Stephen J W Busby; Georgina S Lloyd
Journal:  FEMS Microbiol Lett       Date:  2007-06-30       Impact factor: 2.742

7.  The Bacillus subtilis sigma(M) regulon and its contribution to cell envelope stress responses.

Authors:  Warawan Eiamphungporn; John D Helmann
Journal:  Mol Microbiol       Date:  2008-01-02       Impact factor: 3.501

8.  A previously unidentified sigma factor and two accessory proteins regulate oxalate decarboxylase expression in Bacillus subtilis.

Authors:  Shawn R MacLellan; Tina Wecke; John D Helmann
Journal:  Mol Microbiol       Date:  2008-06-28       Impact factor: 3.501

9.  Alkaline shock induces the Bacillus subtilis sigma(W) regulon.

Authors:  T Wiegert; G Homuth; S Versteeg; W Schumann
Journal:  Mol Microbiol       Date:  2001-07       Impact factor: 3.501

10.  Defining the Bacillus subtilis sigma(W) regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches.

Authors:  Min Cao; Phil A Kobel; Maud M Morshedi; Ming Fang Winston Wu; Chris Paddon; John D Helmann
Journal:  J Mol Biol       Date:  2002-02-22       Impact factor: 5.469
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  2 in total

1.  Genome-wide identification of targets for the archaeal heat shock regulator phr by cell-free transcription of genomic DNA.

Authors:  Annette M Keese; Gerrit J Schut; Mohamed Ouhammouch; Michael W W Adams; Michael Thomm
Journal:  J Bacteriol       Date:  2009-12-18       Impact factor: 3.490

2.  Evidence classification of high-throughput protocols and confidence integration in RegulonDB.

Authors:  Verena Weiss; Alejandra Medina-Rivera; Araceli M Huerta; Alberto Santos-Zavaleta; Heladia Salgado; Enrique Morett; Julio Collado-Vides
Journal:  Database (Oxford)       Date:  2013-01-17       Impact factor: 3.451
  2 in total

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