Chromosomal protein HMG1 removes the transcriptional block caused by the cruciform in supercoiled DNA

Abstract

The binding of chromosomal protein HMG1 to a palindromic sequence that can form the cruciform structure in supercoiled DNA and the subsequent effect on the transcription of the sequence were examined with pBR322 and its derivative plasmids. The plasmid DNA under negative supercoiling showed a selective sensitivity to nuclease S1. HMG1 protected against the nuclease S1 digestion. The results of the filter binding assay indicated that the primary binding target of HMG1 is the single-stranded region within the cruciform in supercoiled DNA. In the transcription from pBR322 DNA in the absence of HMG1, intermediate transcripts of RNA-I, which are encoded from a DNA region containing the palindromic sequence that can form a cruciform, were accumulated with the increase in negative superhelical density whereas the full-length RNA-I was synthesized without an accumulation of intermediate transcripts in the presence of HMG1. The intermediates that accumulated in the absence of HMG1 were elongated to the final product by adding HMG1. These results suggest that the cruciform structure formed under negative supercoiling blocks transcription and that HMG1 can remove the block by altering the DNA conformation to allow the stalled RNA polymerase at the block to resume transcription.