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.
Highlights
In the nuclei of eukaryotic cells, approximately 2 m of DNA must be packaged and organized for efficient gene regulation and DNA replication (Figure 1A)
magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR) can offer unique advantages as often chromatin modulators are too large to study by solution NMR or they form dynamic, viscous and heterogenous phase separated states that cannot be dissected by single particle techniques such as cryo-EM
While still few in number, the recent applications of MAS NMR have demonstrated its versatile capabilities in the structural analysis of chromatin samples
Summary
In the nuclei of eukaryotic cells, approximately 2 m of DNA must be packaged and organized for efficient gene regulation and DNA replication (Figure 1A). MAS NMR can detect both slow and fast biomolecular motions by using solution-state (INEPT) experiments that depend on through-bond scalar-couplings (Morris and Freeman, 1979; Andronesi et al, 2005) or by using solid-state cross-polarization (CP) experiments (Hartmann and Hahn, 1962; Pines et al, 1973) that rely on through-space dipolar interactions (Figure 2B) These two experiment types allow for qualitative dynamics-based spectral filtering (Matlahov and van der Wel, 2018), where INEPT selects for nuclei that undergo dynamic isotropic motion, and CP builds up signal for nuclei in rigid networks that maintain strong dipolar couplings. MAS NMR can resolve distance parameters by recoupling spatially informative anisotropic interactions via pulse sequences matched to the sample spinning rate These features of MAS NMR suit chromatin, a heterogenous polymer that forms an amorphous solid in vitro and in nucleo (Strickfaden et al, 2020), and that bears nucleosomes with both rigid histone cores and dynamic histone tails (Fierz and Poirier, 2019). Readers interested in chromatin applications of other structural techniques such as solution NMR spectroscopy, X-ray crystallography and cryo-EM are referred to several recent comprehensive reviews on these topics (van Emmerik and van Ingen, 2019; Zhou et al, 2019; McGinty and Tan, 2021)
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