Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR

Emmerik, Clara L van; Ingen, Hugo van

doi:10.1016/j.pnmrs.2019.01.002

Cited by 36 publications

(21 citation statements)

References 197 publications

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“…A major goal of the present work is to develop an NMR approach to study structural and motional properties of both the DNA and the protein components in high-molecular-weight nucleic acid-protein complexes. The NCP is one such example and to date NMR studies of this important complex have focused on the histone proteins exclusively, using largely 15 N-based experiments to quantify the dynamics of the disordered protein tails (51, 52) and methyl-TROSY approaches to study the more rigid and structured elements of the histones and interactions between histones and other proteins that play important roles in regulating NCP function (53)(54)(55)(56)(57)(58). Fig.…”

Section: Resultsmentioning

confidence: 99%

A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

Abramov

Vėlyvis

Rennella

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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The development of methyl-transverse relaxation-optimized spectroscopy (methyl-TROSY)–based NMR methods, in concert with robust strategies for incorporation of methyl-group probes of structure and dynamics into the protein of interest, has facilitated quantitative studies of high-molecular-weight protein complexes. Here we develop a one-pot in vitro reaction for producing NMR quantities of methyl-labeled DNA at the C5 and N6 positions of cytosine (5mC) and adenine (6mA) nucleobases, respectively, enabling the study of high-molecular-weight DNA molecules using TROSY approaches originally developed for protein applications. Our biosynthetic strategy exploits the large number of naturally available methyltransferases to specifically methylate DNA at a desired number of sites that serve as probes of structure and dynamics. We illustrate the methodology with studies of the 153-base pair Widom DNA molecule that is simultaneously methyl-labeled at five sites, showing that high-quality13C-1H spectra can be recorded on 100 μM samples in a few minutes. NMR spin relaxation studies of labeled methyl groups in both DNA and the H2B histone protein component of the 200-kDa nucleosome core particle (NCP) establish that methyl groups at 5mC and 6mA positions are, in general, more rigid than Ile, Leu, and Val methyl probes in protein side chains. Studies focusing on histone H2B of NCPs wrapped with either wild-type DNA or DNA methylated at all 26 CpG sites highlight the utility of NMR in investigating the structural dynamics of the NCP and how its histone core is affected through DNA methylation, an important regulator of transcription.

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Section: Resultsmentioning

confidence: 99%

A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

Abramov

Vėlyvis

Rennella

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…In these cases, however, one needs to bear in mind that Hi-C maps, and sequencing techniques in general, often give an average picture of the genome. Ab initio models, on the other hand, take properties that have been observed or even hypothesized about chromatin as a starting point, and aim to reproduce them through the application of constraints and potentials (Tompitak, 2017;Lequieu et al, 2019). The mathematical nature of these models can sometimes lead to a simplification of biological factors at play.…”

Section: Multiscale Modelsmentioning

confidence: 99%

Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment

Bendandi

Dante

Zia

et al. 2020

Front. Mol. Biosci.

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Understanding the mechanisms that trigger chromatin compaction, its patterns, and the factors they depend on, is a fundamental and still open question in Biology. Chromatin compacts and reinforces DNA and is a stable but dynamic structure, to make DNA accessible to proteins. In recent years, computational advances have provided larger amounts of data and have made large-scale simulations more viable. Experimental techniques for the extraction and reconstitution of chromatin fibers have improved, reinvigorating theoretical and experimental interest in the topic and stimulating debate on points previously considered as certainties regarding chromatin. A great assortment of approaches has emerged, from all-atom single-nucleosome or oligonucleosome simulations to various degrees of coarse graining, to polymer models, to fractal-like structures and purely topological models. Different fiber-start patterns have been studied in theory and experiment, as well as different linker DNA lengths. DNA is a highly charged macromolecule, making ionic and electrostatic interactions extremely important for chromatin topology and dynamics. Indeed, the repercussions of varying ionic concentration have been extensively examined at the computational level, using all-atom, coarse-grained, and continuum techniques. The presence of high-curvature AT-rich segments in DNA can cause conformational variations, attesting to the fact that the role of DNA is both structural and electrostatic. There have been some tentative attempts to describe the force fields governing chromatin conformational changes and the energy landscapes of these transitions, but the intricacy of the system has hampered reaching a consensus. The study of chromatin conformations is an intrinsically multiscale topic, influenced by a wide range of biological and physical interactions, spanning from the atomic to the chromosome level. Therefore, powerful modeling techniques and carefully planned experiments are required for an overview of the most relevant phenomena and interactions. The topic provides fertile ground for interdisciplinary studies featuring a synergy between theoretical and experimental scientists from different fields and the cross-validation of respective results, with a multi-scale perspective. Here, we summarize some of the most representative approaches, and focus on the importance of electrostatics and solvation, often overlooked aspects of chromatin modeling.

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“…Size is also a limiting factor in their case [116,117]. The highly complex interactome (see previous Section) around the chromatin involves dynamic and flexible parts, exacerbating the difficulty of unraveling the machinery [112,118]. These difficulties often lead to experimental structures of complexes with N-terminal histone peptides of only 10-15 amino acids [81,95].…”

Section: Conformational Diversity and Water-mediated Weak Interactionsmentioning

confidence: 99%

Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome

Zsidó

Hetényi

2020

IJMS

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Development of valid structure–activity relationships (SARs) is a key to the elucidation of pathomechanisms of epigenetic diseases and the development of efficient, new drugs. The present review is based on selected methodologies and applications supplying molecular structure, binding affinity and biological activity data for the development of new SARs. An emphasis is placed on emerging trends and permanent challenges of new discoveries of SARs in the context of proteins as epigenetic drug targets. The review gives a brief overview and classification of the molecular background of epigenetic changes, and surveys both experimental and theoretical approaches in the field. Besides the results of sophisticated, cutting edge techniques such as cryo-electron microscopy, protein crystallography, and isothermal titration calorimetry, examples of frequently used assays and fast screening techniques are also selected. The review features how different experimental methods and theoretical approaches complement each other and result in valid SARs of the epigenome.

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Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR

Cited by 36 publications

References 197 publications

A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment

Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome

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