Transcriptional Traffic Control
Nucleosomes act as a roadblock to transcription, but there are a number of mechanisms by which RNA polymerase II can successfully bypass histone complexes. For example, chemical modifications to the ‘tails’ of histone subunits can enhance transcription, as can changes in DNA-protein interactions within a nucleosome. However, little is known about how these various factors collectively impact transcription.
A series of single-molecule experiments by Bintu et al. offer new insights into this process, yielding a multi-step model to explain how the polymerase complex negotiates its way past the nucleosome. The authors used an optical tweezers setup to monitor the pausing behavior of the RNA polymerase II elongation complex (EC) as it travels along DNA containing a single nucleosome positioning sequence (NPS), and identified three different NPS regions that they termed ‘entry’, ‘center’ and ‘exit’. Histone manipulation revealed that the absence of tail domains or introduction of conditions simulating acetylation of histone lysine residues specifically reduced pausing in the entry region, whereas point mutations to the H3 and H4 histones that loosen their association with DNA decreasedpausing at the NPS center. These effects were subsequently replicated in experiments that tested how different modifications modulate the ‘tightness’ of DNA wrapping around the nucleosome complex.
Previous work suggests that transcription is dependent on ongoing fluctuations in nucleosome structure, and that the EC will backtrack along the nascent RNA strand when forward progress is thwarted. The authors also observed this, and obtained evidence that the local DNA sequence can modulate this backtracking based on the extent to which newly-transcribed RNA forms stable secondary structure. The interplay between these various factors can thus collectively have a profound effect on the transcriptional dynamics within a given stretch of chromatin.1
Bintu, L. et al. Cell151, 738–749 (2012).