Structural and dynamic properties of linker histone H1 binding to DNA

TL;DR

This study investigates how linker histone H1 binds and reorganizes DNA using microfluidic X-ray diffraction, revealing a two-step binding process involving initial unspecific attachment followed by structural rearrangement.

Contribution

It introduces a microfluidic X-ray diffraction method to analyze the real-time structural dynamics of H1/DNA interactions at microscale resolution.

Findings

H1/DNA interaction occurs in two steps: initial binding and subsequent rearrangement.

Rearrangement involves increased lattice spacing and decreased correlation length.

DNA bending is likely involved in the structural changes.

Abstract

Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists from a chromatin organization deciphering point of view, and for physicists from the study of polyelectrolyte interactions point of view. Hence, H1/DNA binding processes, structural and dynamical information about these self-assemblies is of broad importance. Targeting a quantitative understanding of H1 induced DNA compaction mechanisms our strategy is based on using small angle X-ray microdiffraction in combination with microfluidics. The usage of microfluidic hydrodynamic focusing devices facilitate a microscale control of these self-assembly processes. In addition, the method enables time-resolved access to structure formation in situ, in particular to transient intermediate states. The observed time dependent structure evolution shows that the interaction of H1 with DNA can be described as a two step process: an initial unspecific binding of H1 to DNA is followed by a rearrangement of molecules within the formed assemblies. The second step is most likely induced by interactions between the charged side chains of the protein and DNA. This leads to an increase in lattice spacing within the DNA/protein assembly and induces a decrease in the correlation length of the mesophases, probably due to a local bending of the DNA.