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Updated: Jun 28, 2026

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
ROMA: an in vitro approach to defining target genes for transcription regulators
Shawn R Maclellan1, Warawan Eiamphungporn, John D Helmann
1Department of Microbiology, Cornell University, 327 Wing Hall, Ithaca, NY 14853-8101, USA.
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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