118 promoters were screened for enough activeity to test for stalled RNAP complexes. 34 active promoters were found and assayed for complexes by KMnO4 footprinting in vivo (Hartoum, 2008)
Three screening procedures were used to identiify promoters likely to have stalled RNAP complexes. Since only 7/118 promoters did have complexes the screening logic may not have yielded much enrichment, leading the authors to describe this promoter set as essentially random.
The first approach used RNA expression and phenotype arrays to identify 50 candidate genes with differences between wildtype and RpoDL402F strains. 11 of these were active assayable promoters, including lacZp, tnaAp and cspA2.
The second approach was to search ~700 known promoters compiled at EcoCyc (http://www.biocyc.org) and promEC (http://margalit.huji.ac.il/promec/index.html) for palusible variants of the lambda pause sequence ANNNTSSS starting between positions +1 and +10 relative to the tsp. 34 such candidates were found and 7 had active and assayable promoters, none of which had proximal stalled RNAPs.
The third approach was to screen the RNA expression array data at ASAP (https://asap.ahabs.wisc.edu/asap/experiment_data.php) for genes that were highly expressed during growth in rich medium. 35 candidates were screened to find 15 asssayable promoters including rspAp1, rplKp, and rpsUp2. A final candidate cpsDp was chosen to assay another csp gene ( Hartoum, 2008).
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