Transcription 4:4, 162–166; July/August 2013; © 2013 Landes Bioscience

New approaches using biotinylated-psoralen as a probe for investigat-ing DNA structure have revealed new insights into the relationship between DNA supercoiling, transcription and chromatin compaction. We explore a hypothesis that divergent RNA tran-scription generates negative supercoiling at promoters facilitating initiation com-plex formation and subsequent promoter clearance. Packaging DNA into chromatin creates a repressive environment. This is thought to reduce transcriptional noise and provide additional levels of gene regulation. Many processes have been described that alter chromatin architecture and facilitate or repress transcription. These include tran-scription factor binding, recruitment of RNA polymerases, ATP-dependent chro-matin remodeling and changes in histone modifications. The level of DNA super-coiling is also known to be important for transcription but remains poorly under-stood, as few techniques are available for directly investigating it. This is about to change: new approaches have recently been used for analyzing DNA topology in cells1-3 and show transcription dependent changes in DNA supercoiling that impact on higher levels of chromatin structure. Furthermore, new data indicates that DNA supercoiling and divergent RNA transcription are linked providing new ideas for understanding the role of DNA topology in regulating gene transcription. The structure of DNA within mamma-lian cells is not known, although it is often thought to be in a B-form configuration. However, this will depend on the base Divergent RNA transcription A role in promoter unwinding