High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier.

Zhijie Chen,Antony Lee,Elena F Koslover,Carlos Bustamante,Aidan I Brown,César Díaz-Celis,Aixin Song,Ronen Gabizon,Craig D Kaplan,Tingting Yao

doi:10.7554/elife.48281

Abstract

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.

Highlights

Backtracking, and nucleosome hopping between wrapped states
As a mechanical and energetic barrier, the nucleosome gates the accessibility of genomic DNA, constituting a fundamental regulatory mechanism for all DNA-templated processes including replication, transcription, repair, recombination, and chromatin remodeling
Epigenetic modifications and histone variants are known to modulate all of these processes

Summary

Introduction

While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression. High-resolution optical tweezers, single molecule unzipping, nucleosome barrier, Pol II transcription, histone variant H2A.Z, ubiquitinated H2B, ‘Molecular ruler’, nucleosome topography maps, transcription regulation. 1. A single-molecule unzipping assay mimics DNA unwinding by Pol II and maps the topography of human canonical, H2A.Z and uH2B nucleosome barriers at high resolution. 4. A unified mechanical model links position-dependent dwell times of Pol II on the nucleosome with energetics of the barrier

Methods

Results

Conclusion