Unveiling structural and dynamical features of chromatin using NMR spectroscopy

Abstract

Eukaryotic deoxyribonucleic acid (DNA) is wrapped around histone octamers (HOs) to form nucleosome core particles (NCPs), which in turn interact with linker DNA and linker histones to assemble chromatin fibers with more complex, high-order structures. The molecular properties of chromatin are dynamically regulated by several factors, such as post-translational modifications and effector proteins, to maintain genome stability. In the past two decades, high-resolution techniques have led to many breakthroughs in understanding the molecular mechanisms that govern chromatin regulation. Nuclear magnetic resonance (NMR) has emerged as one of the major techniques in this field, providing new insights into the nucleosomes and nucleosome-protein complexes in different states ranging from soluble form to condensed states. Solution-state NMR has proven valuable in elucidating the conformational dynamics and molecular interactions for histone N-terminal tails, histone core regions and DNA with the combination of specific isotopic labeling. Solid-state NMR, which is not constrained by the high molecular weights of complexes like nucleosomes, has been applied to capture the structural and dynamical characteristics of both flexible tails and rigid histone core regions in nucleosomes and their complexes with effector proteins. Furthermore, the combination of the two techniques allows tracking molecular properties of nucleosomes during phase separation processes, which potentially play essential roles in chromatin regulation. This review summarizes recent advances in NMR studies of chromatin structure and dynamics. It highlighted that NMR revealed unique molecular characteristics for nucleosomes that are often invisible experimentally by other techniques like cryogenic electron microscopy (cryo-EM) and X-ray diffraction (XRD). I envision that, with future efforts such as the development of NMR methods and optimization of sample production protocols, solution-state NMR and solid-state NMR will provide invaluable information to expand our understanding of chromatin activity and its regulatory processes.