Effect of single-strand DNA breaks on transcription of nucleosomes

Previous studies revealed the inhibitory eff ect of single-stranded breaks in a non-template DNA strand (NT-SSB) on RNA polymerase transcription through the nucleosome. The observed effect was explained within the model of chromatin transcription mechanism with the formation of intranucleosomal DNA loops (i-loops) – intermediates in which the enzyme is locked in the DNA loop on the histone octamer. According to the model, NT-SBs reduce the tension in the DNA structure caused by transcription and hinders the opening of the i-loop with the enzyme and further elongation. In this work, the boundaries of such i-loops are determined. Nucleosomes with NT-SSBs were transcribed. It was determined that the formation of contacts between DNA and histones behind RNAP occurs at a distance of more than 17 base pairs from the active center of the enzyme.