Pausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a “stepping” mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a “scrunching” mechanism, has not. Researchers from Rutgers University report a method that directly defines the RNAP-active-center position relative to DNA with single-nucleotide resolution (XACT-seq; “crosslink-between-active-center-and-template sequencing”). The researchers apply this method to detect and quantify pausing in initial transcription at 411 (∼4,000,000) promoter sequences in vivo in Escherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4 to 5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. These findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard coded by sequence elements similar to those for transcription-elongation pausing.
XACT-Seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing
Winkelman JT, Pukhrambam C, Vvedenskaya IO, et al. (2020) XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing. Mol Cell [published online ahead of print]. [abstract]