Single-Molecule Navigation of the Nucleosomal Transcription Landscape

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. We used ultrahigh-resolution optical tweezers to follow the trajectories of single Pol II molecules crossing a single nucleosome, obtaining the transcriptional maps of canonical, H2A.Z and monoubiquitinated H2B (ubH2B) nucleosomes at near basepair accuracy. Pol II nucleosome crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. Both H2A.Z and ubH2B greatly lengthen Pol II nucleosome crossing time, rationalizing their selective enrichment in +1 nucleosomes for regulating eukaryotic gene transcription.