Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Abstract

Eukaryotic chromatin structure and dynamics play key roles in genomic regulation. In the current study, the secondary structure and intramolecular dynamics of human histone H4 (hH4) in the nucleosome core particle (NCP) and in a nucleosome array are determined by solid‐state NMR (SSNMR). Secondary structure elements are successfully localized in the hH4 in the NCP precipitated with Mg2+. In particular, dynamics on nanosecond to microsecond and microsecond to millisecond timescales are elucidated, revealing diverse internal motions in the hH4 protein. Relatively higher flexibility is observed for residues participating in the regulation of chromatin mobility and DNA accessibility. Furthermore, our study reveals that hH4 in the nucleosome array adopts the same structure and show similar internal dynamics as that in the NCP assembly while exhibiting relatively restricted motions in several regions consisting of residues in the N‐terminus, Loop 1, and the α3 helix region.

Nucleosome structure and dynamics are coming of age

“…NMR is uniquely capable of mapping protein interactions at the level of single residues even in disordered regions, or transient complexes 91,27,66 , which makes it complementary to other methods delivering static structures. Current progress of NMR for the study of larger complexes and transient interactions 92 , and of solid-state NMR 93,94 , are all relevant to the study of nucleosome dynamics and interactions with nucleosome-binding factors.…”

Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes

“…6e and Supplementary fig. 15a, b ), we obtained information about the internal dynamics of the H4 protein backbone at the μs-ms timescale 47 , 49 . In comparison with the H4K20me0 nucleosome array, the globular domain of the H4K20me1 array showed more uniform peak intensities across the protein and reduced relative intensities for several residues primarily residing in the LN and L1 regions and in the adjacent stretch of the α1 and α2 regions (Fig.…”

Solid-state NMR studies of chromatin structure and dynamics

“…The experimental line shapes are extracted from a 3D DIPSHIFT with R121 4 symmetry dipolar recoupling pulses. Reprinted from (Shi, Prasanna et al 2018 (Shi, Prasanna et al 2018 (Vasudevan, Chua et al 2010). (C) SNH mapped onto the H4 structure (PDB: 3LZ0 (Davey, Sargent et al 2002)).…”

“…(C) Regions in redbox highlighted on the hH4 structure PDB: 3LZ0 (Vasudevan, Chua et al 2010). Adapted from (Shi, Prasanna et al 2018 ............................................................................................................................................ 94 Figure 25. Reconstitution of 'Widom' NCP with 13 C,15 N-labeled H3 analyzed on 6% native PAGE.…”

“…hH3 residues are colored blue and the rest of the NCP is colored grey. Adapted from (Shi, Prasanna et al 2018 (Shi, Prasanna et al 2018). Copyright Wiley-VCH.…”