Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology

Abstract

The eukaryotic genome is packaged into chromatin, a polymer of DNA and histone proteins that regulates gene expression and the spatial organization of nuclear content. The repetitive character of chromatin is diversified into rich layers of complexity that encompass DNA sequence, histone variants and post-translational modifications. Subtle molecular changes in these variables can often lead to global chromatin rearrangements that dictate entire gene programs with far reaching implications for development and disease. Decades of structural biology advances have revealed the complex relationship between chromatin structure, dynamics, interactions, and gene expression. Here, we focus on the emerging contributions of magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR), a relative newcomer on the chromatin structural biology stage. Unique among structural biology techniques, MAS NMR is ideally suited to provide atomic level information regarding both the rigid and dynamic components of this complex and heterogenous biological polymer. In this review, we highlight the advantages MAS NMR can offer to chromatin structural biologists, discuss sample preparation strategies for structural analysis, summarize recent MAS NMR studies of chromatin structure and dynamics, and close by discussing how MAS NMR can be combined with state-of-the-art chemical biology tools to reconstitute and dissect complex chromatin environments.

Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding

“…15 N- and/or 13 C-isotopically labeled HP1α constructs for NMR spectroscopy were prepared using minimal media (M9) supplemented with ammonium chloride ( 15 N, 99%) and glucose (U- 13 C6, 99%). The expression, purification, and refolding protocols were adapted from the following references ( 31 , 54 ).…”

Visualizing Conformational Ensembles of the Nucleosome by NMR

“…Advances in solution NMR spectroscopy are allowing for unprecedented insight into the conformational dynamics of both the histone core and histone tails . Furthermore, solid-state NMR techniques provide additional tools to examine compacted nucleosomes and nucleosome arrays . Here we review what these studies are revealing about the conformational landscape of the nucleosome in a variety of chromatin environments and discuss how various factors modulate nucleosomal ensembles.…”

“…8 Furthermore, solid-state NMR techniques provide additional tools to examine compacted nucleosomes and nucleosome arrays. 9 Here we review what these studies are revealing about the conformational landscape of the nucleosome in a variety of chromatin environments and discuss how various factors modulate nucleosomal ensembles.…”

Recent Advances in Investigating Functional Dynamics of Chromatin

“…This intrinsic size limitation is overcome by using solid-state NMR (SSNMR) that has developed as an emerging powerful technique in studying chromatin. This revealed structure and dynamics for several nucleosomes and nucleosome–protein complexes ( Ackermann and Debelouchina, 2021 ; le Paige et al, 2021 ). NMR techniques require isotope labeling to gain sufficient sensitivity and sometimes also require fragment labeling (e.g., labeling one of the histones) to reduce signal complexity.…”

“…It was noted that the observed stable conformations represent the averaged conformations of a large assembly of N-terminal tail states that likely involve fast exchange. Recent advances in SSNMR studies of chromatin allows elucidating the structure and dynamics for both the highly flexible tails and the rigid core for samples in compact states, where the water contents of the nucleosome samples are around 50–90% ( Gao et al, 2013 ; Shi et al, 2018 ; Xiang et al, 2018 ; Ackermann and Debelouchina, 2021 ; Zandian et al, 2021 ). The determined motional amplitudes for amino acid backbone groups of histones in the NCPs suggest that motions at the nanosecond-microsecond timescale closely correlate with the structures ( Shi et al, 2018 ; Shi et al, 2020a ).…”