Fig. 2

DNA negative supercoiling and R-loop formation during transcription. When RNA polymerase (green) reads a G + C-rich DNA template, stalls and backtracks, it leaves a domain of hyper-negatively supercoiled behind. The associated stalling of transcription may allow the RNA transcript (red) to base pair with its DNA template strand (blue), leaving the non-transcribed strand as a single-stranded bubble. Other impediments to RNA polymerase progression include head-on collisions with other transcription units or with replisomes (the barrier is represented by the red vertical dotted line). Loss of the DNA relaxing activity of topoisomerase I promotes R-loop formation because it encourages the accumulation of hyper-negative-superhelicity in DNA that is being transcribed (or replicated). Failure to process and remove RNA loops can lead to DNA damage, including double-stranded breaks and hyper-recombination. RNase H eliminates R-loops by removing the RNA component of the RNA:DNA hybrid in the R-loop. The Rho transcription terminating helicase can suppress R-loop formation by preventing RNA polymerase backtracking