Bonocora, Richard P. Smith, Carol Lapierre, Pascal Wade, Joseph T. Genome-Scale Mapping of <i>Escherichia coli</i> σ<sup>54</sup> Reveals Widespread, Conserved Intragenic Binding <div><p>Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ<sup>70</sup> family and the σ<sup>54</sup> family. Members of the σ<sup>54</sup> family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of <i>Escherichia coli</i> σ<sup>54</sup>, the archetypal member of the σ<sup>54</sup> family. Thus, we vastly expand the list of known σ<sup>54</sup> binding sites to 135. Moreover, we estimate that there are more than 250 σ<sup>54</sup> sites in total. Strikingly, the majority of σ<sup>54</sup> binding sites are located inside genes. The location and orientation of intragenic σ<sup>54</sup> binding sites is non-random, and many intragenic σ<sup>54</sup> binding sites are conserved. We conclude that many intragenic σ<sup>54</sup> binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ<sup>54</sup> promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs.</p></div> binding;RNA polymerase holoenzyme;bind promoter DNA;σ factor;Escherichia coli σ54;bind promoter DNA sequences;site;utr;intragenic;Conserved Intragenic Binding 2015-10-01
    https://plos.figshare.com/articles/dataset/Genome_Scale_Mapping_of_Escherichia_coli_54_Reveals_Widespread_Conserved_Intragenic_Binding/1561534
10.1371/journal.pgen.1005552