Transcript hairpin structures are not required for RNA polymerase pausing in the gene encoding the E. coli RNase P RNA, M1 RNA

Abstract

Strong pauses at nucleotides + I 18 and + I21 relative to the transcriptional star1 occur during in vitro transcription of the E. co/i npB gene encoding the catalytic MI RNA subunit of Ribonucleasc P. These pauses arc immediately downstream of 2 phylogcne~ically conserved stem-loop structures in the RNA. In the prescnl work, single-base changes which disrupted Watson-Crick base-pairing in the hairpins wcrc introduced into r@. Transcription studies in vhro with these modified tcmplaics revealed that none of the nucleotide changes predicted to increase or decrease the stability of the first hairpin significamly affected the ptWX hair-lives. A mutation which disruplcd the second hairpin increased the pause half-IiFc a-fold. The data suggest that 111c upstream stem and loop structures in the transcript arc not involved in the pausing event.RNA structure; Transcription

Detecting sequence dependent transcriptional pauses from RNA and protein number time series

“…By removing the region of the DNA that codes for loop, the duration is reduced to 4.6 s, and becomes exponentially distributed [7]. Unlike his pauses, other sequence dependent long pause sites do not require the formation of RNA secondary structures [8]. …”