Cryo-electron microscopy of chromatin biology

Wilson, Marcus D.; Costa, Alessandro

doi:10.1107/s2059798317004430

Cited by 21 publications

(22 citation statements)

References 62 publications

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“…Local resolution is highest (~3.5 Å) for the histone octamer core, while DNA density on the outer perimeter tends to decrease (~4-4.5 Å), as observed previously for other NCP structures (Supplementary Figure 1) 25–27 . Nevertheless, we could confidently model the DNA phosphate backbone for the entire assembly.…”

Section: Resultssupporting

confidence: 81%

“…These efforts led to describing the NCP architecture at an atomic level 7–9 , explained how DNA sequence can influence wrapping of the double helix 32 , and how common docking sites on the histone octamer are recognised by different interactors 33–37 . Over the last four years, cryo-EM has started to provide a dynamic view of the NCP 25,38–41 . Recent data indicated that NCPs are more flexible in solution, with the histone octamer visiting more compacted or extended states, compared with a nucleosome trapped in a crystal lattice 42 .…”

Section: Discussionmentioning

confidence: 99%

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Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer

Wilson

Renault

Maskell

et al. 2019

Preprint

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24Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-25 transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal 26 structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the 27 histone octamer at the site of integration. To clarify the mechanism of DNA looping by 28 integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome 29 engaged with a nucleosome core particle. The structural data along with complementary 30 single-molecule Förster resonance energy transfer measurements reveal twisting and sliding 31 of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA 32 by approximately two base pairs along the histone octamer accommodates the necessary 33 DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. 34Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for 35 nucleosomal DNA repositioning, bearing unexpected similarities with chromatin remodelers. 36 37 38 42 function, a multimer of IN assembles on viral DNA (vDNA) ends forming a highly stable 43 nucleoprotein complex, known as the intasome 2-4 . In its first catalytic step, IN resects 3' ends 44 of the vDNA downstream of the invariant CA dinucleotides (3'-processing reaction). It then 45 utilises the freshly released 3'-hydroxyl groups as nucleophiles to attack a pair of 46 phosphodiester bonds on opposing strands of chromosomal DNA, cleaving host DNA and 47 simultaneously joining it to 3' vDNA ends (strand transfer reaction) 5,6 .48 Many important questions pertaining to the nature of the host-virus transactions on 49 chromatin remain unanswered. In particular, it is unclear what role chromatin structure plays 50 in the integration process. Strikingly, although only a fraction of the nucleosomal DNA 51 surface is exposed within the nucleosome core particle (NCP) 7-9 , nucleosomal DNA packing 52 does not impede and rather stimulates integration 10-15 . Because retroviral INs have long 53 been known to prefer bent or distorted DNA targets, DNA bending as it wraps around the 54 histone octamer was thought to facilitate integration into NCPs 12,13 . However, recent 55 structural data revealed that retroviral intasomes require target DNA to adopt a considerably 56 sharper deformation than the smooth bend observed on NCPs 15-19 .57 Intasome structures from several retroviral genera have been determined by X-ray 58 crystallography and cryo-EM 4,17-20 . Despite considerable variability, all intasomes were 59 found to contain the structurally conserved intasomal core assembly minimally comprising 60 four IN subunits synapsing a pair of vDNA ends. Depending on the retroviral species, the 61 core assembly can be decorated by a number of additional IN subunits. The nucleoprotein 62 complex from the prototype foamy virus (PFV) contains only a tetramer of IN, making this 63 well-characterised intasome an ideal model to study the basic mech...

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Section: Resultssupporting

confidence: 81%

Section: Discussionmentioning

confidence: 99%

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer

Wilson

Renault

Maskell

et al. 2019

Preprint

Self Cite

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“…Integrative approaches allow a variety of investigations on the dynamics of nucleosome and their associated protein factors—in particular, NMR, smFRET, SAXS, and AUC, as well as other biochemical/biophysical and computational biology techniques. [ 12,13,17,27,57,60,63,83 ]…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

“…[ 8 ] More recently, cryo‐electron microscopy (cryo‐EM) has become extremely powerful, and has had notable success in the structural characterization of nucleosomes and several nucleosome‐bound complexes, as has been reviewed in the past. [ 9–12 ] Significant contributions to our understanding of these complex machineries and their dynamics have also come from the complementary biophysical techniques such as nuclear magnetic resonance (NMR) spectroscopy, [ 13–16 ] Förster resonance energy transfer (FRET), [ 17–19 ] small‐angle X‐ray scattering (SAXS), [ 15,20–23 ] small‐angle neutron scattering, [ 23 ] native electro‐spray ionization mass spectrometry, [ 21 ] size‐exclusion chromatography—multi‐angle light scattering (SEC‐MALS), [ 24,25 ] analytical ultra centrifugation (AUC), [ 16,24,26 ] and hydroxyl radical footprinting, [ 21,27 ] along with Molecular Dynamics (MD) simulation, modeling, and docking studies. [ 15–17,23,27 ] The different chromatin factors and viral proteins use specific features on the nucleosome such as the nucleosomal acidic patch, specific super‐helical locations, PTM marks, and the histone tails to interact with and modulate the nucleosome.…”

Section: Introductionmentioning

confidence: 99%

Structural Basis of Nucleosome Recognition and Modulation

Sundaram

Vasudevan

2020

BioEssays

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Chromatin structure and dynamics regulate key cellular processes such as DNA replication, transcription, repair, remodeling, and gene expression, wherein different protein factors interact with the nucleosomes. In these events, DNA and RNA polymerases, chromatin remodeling enzymes and transcription factors interact with nucleosomes, either in a DNA‐sequence‐specific manner and/or by recognizing different structural features on the nucleosome. The molecular details of the recognition of a nucleosome by different viral proteins, remodeling enzymes, histone post‐translational modifiers, and RNA polymerase II, have been explored in the recent past. The present review puts forth critical insights into the basic mechanisms of nucleosome recognition by the various protein factors and the role of distinct surface epitopes on a nucleosome. These determinants of the underlying specificity include features such as the acidic patch, arginine anchor, histone post‐translational modifications, core DNA, DNA lesions, and linker DNA.

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“…Hi-C (8,9), Micro-C (10) and other chromosome conformation capture methods (11,12) provide distance constraints as a measure of the large scale organization of chromatin structure. Super resolution microscopy (13,14) provides optical visualization of 3D structure at nanometer scale resolution, while electron microscopy (15), NMR (16), * To whom correspondence should be addressed. Tel: +1 318 257 5209; Fax: +1 318 257 4000; Email: bishop@latech.edu and X-ray crystallography (17) provideångström scale resolution of individual nucleosomes and nucleosome arrays.…”

Section: Introductionmentioning

confidence: 99%

Genome dashboards: Framework and Examples

Sun

Bishop

2019

Preprint

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Genomics is a sequence-based informatics science and a 3D structure-based material science. Here we describe a framework for developing genome dashboards specifically designed to unify informatics with studies of chromatin structure and dynamics. The framework is based on the mathematical representation of geometrically exact rod models and the generalization of DNA base pair step parameters. A Model-View-Controller software design approach is proposed to implement genome dashboards as finite state machines either as desktop or web based applications. Two examples are demonstrated using our minimal genome dashboard called G-Dash-min. The data unification achieved with a genome dashboard supports the bi-directional exchange of data between informatics and structure. Thus any experimentally or theoretically determined sequence based informatics track can inform DNA, nucleosome or chromatin modeling (e.g. nucleosome positions) and structure features can be analyzed as informatics tracks in a genome browser (e.g. DNA base pair step parameters: Roll, Tilt, Twist). Here the framework is applied to chromatin, but genome dashboards are more broadly applicable. Genome dashboards are a novel means of investigating structure-function relationships for regions of the genome ranging from base pairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

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Cryo-electron microscopy of chromatin biology

Cited by 21 publications

References 62 publications

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer

Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer

Structural Basis of Nucleosome Recognition and Modulation

Genome dashboards: Framework and Examples

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