Chromatin fibers stabilize nucleosomes under torsional stress

Kaczmarczyk, Artur; Meng, He; Ordu, Orkide; Noort, John van; Dekker, Nynke H.

doi:10.1038/s41467-019-13891-y

Cited by 59 publications

(71 citation statements)

References 75 publications

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“…Single molecule pulling experiments on chromatin fibers, [5][6][7][8][9][10][11] and arrays of nucleosomes and a single nucleosome 5,[12][13][14][15][16] have given quantitative insights into their nanomechanics. Of particular relevance here are the pulling experiments on single nucleosomes using the Widom 601 sequence, 12 which established that the fully wrapped DNA unravels in two major stages upon application of mechanical force, f (Figure 1).…”

mentioning

confidence: 99%

Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

Reddy¹,

Thirumalai

2020

Preprint

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Nucleosomes, the building blocks of chromosomes, are also transcription regulators. Single molecule pulling experiments have shown that nucleosomes unwrap in two major stages, releasing nearly equal length of DNA in each stage. The first stage, attributed to the rupture of the outer turn is reversible, occurs at low forces (≈ (3 - 5) pNs) whereas in the second stage the inner turn ruptures irreversibly at high forces (between ≈ (9 - 15) or higher) pNs. We show that Brownian dynamics simulations using the Self-Organized Polymer model of the nucleosome capture the experimental findings, thus permitting us to discern the molecular details of the structural changes not only in DNA but also in the Histone Protein Core (HPC). Upon unwrapping of the outer turn, which is independent of the pulling direction, there is a transition from 1.6 turns to 1.0 turn DNA wound around the HPC. In contrast, the rupture of the inner turn, leading to less than 0.5 turn DNA around the HPC, depends on the pulling direction, and is controlled by energetic and kinetic barriers. The latter arises because the mechanical force has to produce sufficient torque to rotate (in an almost directed manner) the HPC by 180°. In contrast, during the rewrapping process, HPC rotation is stochastic, with the quenched force fQ playing no role. Interestingly, if fQ = 0 the HPC rotation is not required for rewrapping because the DNA ends are unconstrained. The assembly of the outer wrap upon force quench, as assessed by the decrease in the end-to-end distance (Ree) of the DNA, nearly coincides with the increase in Ree as force is increased, confirming the reversible nature of the 1.6 turns to 1.0 turn transition. The asymmetry in HPC rotation during unwrapping and rewrapping accounts for the observed hysteresis in the stretch-release cycles in single molecule pulling experiments. Experiments that could validate the prediction that HPC rotation, which gives rise to the kinetic barrier in the unwrapping process, are proposed.

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mentioning

confidence: 99%

Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

Reddy¹,

Thirumalai

2020

Preprint

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“… 38 These nucleosomes package DNA into a beads-on-a-string structure, thus compacting DNA by shortening the total polymer length, changing the level of supercoiling, 131 and altering flexibility of the DNA fiber. 132 Nucleosome-like structures have also been identified in archaea, albeit with different properties as compared to eukaryotes, such as oligomerization. 133 In bacteria, DNA-binding proteins known as nucleoid-associated proteins (NAPs) similarly condense the chromosome.…”

Section: An Overview Of Chromosome Building Blocksmentioning

confidence: 99%

Genome-in-a-Box: Building a Chromosome from the Bottom Up

Birnie

Dekker

2020

ACS Nano

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Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA–protein interactions. Here, we introduce “genome-in-a-box” (GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.

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“…For example, the presence of (+) supercoiling in a chromatin molecule is known to favor nucleosome disassembly, thereby potentially altering the local chromatin structure [ 30 ]. It is unknown, however, whether this temporal structural alteration has in vivo consequences for genome stability and gene expression, or whether the biophysical properties of chromatin fibers constitute a topological buffer to accommodate torsional strain, as has been suggested based on single-molecule studies [ 31 ]. Furthermore, translocating transcription machineries are often tethered through gene gating.…”

Section: Threats Imposed By Dna Topological Strain To Stalled Replmentioning

confidence: 99%

Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication

Ahmed

Dröge

2020

IJMS

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Key DNA transactions, such as genome replication and transcription, rely on the speedy translocation of specialized protein complexes along a double-stranded, right-handed helical template. Physical tethering of these molecular machines during translocation, in conjunction with their internal architectural features, generates DNA topological strain in the form of template supercoiling. It is known that the build-up of transient excessive supercoiling poses severe threats to genome function and stability and that highly specialized enzymes—the topoisomerases (TOP)—have evolved to mitigate these threats. Furthermore, due to their intracellular abundance and fast supercoil relaxation rates, it is generally assumed that these enzymes are sufficient in coping with genome-wide bursts of excessive supercoiling. However, the recent discoveries of chromatin architectural factors that play important accessory functions have cast reasonable doubts on this concept. Here, we reviewed the background of these new findings and described emerging models of how these accessory factors contribute to supercoil homeostasis. We focused on DNA replication and the generation of positive (+) supercoiling in front of replisomes, where two accessory factors—GapR and HMGA2—from pro- and eukaryotic cells, respectively, appear to play important roles as sinks for excessive (+) supercoiling by employing a combination of supercoil constrainment and activation of topoisomerases. Looking forward, we expect that additional factors will be identified in the future as part of an expanding cellular repertoire to cope with bursts of topological strain. Furthermore, identifying antagonists that target these accessory factors and work synergistically with clinically relevant topoisomerase inhibitors could become an interesting novel strategy, leading to improved treatment outcomes.

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Chromatin fibers stabilize nucleosomes under torsional stress

Cited by 59 publications

References 75 publications

Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome

Genome-in-a-Box: Building a Chromosome from the Bottom Up

Chromatin Architectural Factors as Safeguards against Excessive Supercoiling during DNA Replication

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