Fig. 2.

Genome-wide coupling between transcription and DNA topology. a Dynamic (−) DNA supercoiling around transcription start sites (TSSs) for genes with low, medium, or high expression levels. The vertical axis shows the ∆CL, which is the difference between CL values derived from transcription inhibited and uninhibited cells, and reflects DNA supercoiling induced by transcription. b A model for DNA supercoiling regulation by Topo I and Topo II. In this model, Topo I is diffusely recruited to the DNA supercoiling regions (diffuse mode), while Topo II is recruited in a focused manner to the most dynamic (−) supercoiling region (focal mode). For a moderately expressed gene, dynamic supercoiling is mainly managed by Topo I, which is recruited to a broad range upstream of the TSSs. For a highly transcribed gene, dynamic supercoiling is resolved efficiently by Topo II, which is recruited focally to the TSSs. Adapted from Kouzine et al. (2013) with permission