Nucleosome‐remodelling machines and other molecular motors observed at the single‐molecule level

Lavelle, Christophe; Praly, Elise; Bensimon, David; Cam, Eric Le; Croquette, Vincent

doi:10.1111/j.1742-4658.2011.08280.x

Cited by 12 publications

(9 citation statements)

References 105 publications

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“…While sophisticated in vitro experiments have provided a wealth of information on the mechanisms and features of chromatin‐remodelling complexes [1,7,46], much less is known about their activity in the cell. Recently, we analyzed the dynamics and interaction behavior of Snf2H, Snf2L, inactive Snf2L+13 as well as Acf1 in living cells using a fluorescence fluctuation microscopy approach that combined fluorescence bleaching and correlation spectroscopy experiments [22,26].…”

Section: Iswi Chromatin Remodellers In Living Cellsmentioning

confidence: 99%

Chromatin remodelling in mammalian cells by ISWI‐type complexes – where, when and why?

Erdel¹,

Rippe²

2011

The FEBS Journal

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Mammalian imitation switch-type chromatin remodelling complexesChromatin structure is a key determinant of gene regulation. The wrapping of the DNA around the histone octamer protein core in the nucleosome impedes the access of other protein factors to the DNA sequence information. To mediate access, a diverse chromatinremodelling machinery exists in the eukaryotic cell nucleus to translocate, remove or assemble nucleosomes as needed. It is centered around numerous different types of ATP-driven molecular machines that can move the nucleosomal DNA with respect to the histone octamer core via an ATP-driven mechanism, as described by Owen-Hughes & Flaus in this issue [1]. One of the best-conserved ATPase families involved in chromatin remodelling is the imitation switch (ISWI) family [2] (Fig. 1). It consists of the two ATPases sucrose nonfermenting 2 homologue (Snf2H) and

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Section: Iswi Chromatin Remodellers In Living Cellsmentioning

confidence: 99%

Chromatin remodelling in mammalian cells by ISWI‐type complexes – where, when and why?

Erdel¹,

Rippe²

2011

The FEBS Journal

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“…The second field where optical and magnetic tweezers have given very interesting results is precisely the study on the interaction of DNA with enzymes. These studies include the action of topoisomerases [25,26], of RNAP during transcription initiation [27,28], or of remodelling enzymes [29]. For a more exhaustive review on tweezers set-up and applications, see Lavelle et al [30].…”

Section: Magnetic Tweezers: Wrapping Dnamentioning

confidence: 99%

On the topology of chromatin fibres

et al. 2012

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The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method for computing topological properties (twist, writhe and linking number) of the DNA embedded in those fibres. The relevance of the method is reviewed through the analysis of magnetic tweezers single molecule experiments that revealed unexpected properties of the chromatin fibre. Possible biological implications of these results are discussed.Keywords: chromatin; topology; DNA DNA SUPERCOILING AND TRANSCRIPTIONAccording to the 'central dogma' of molecular biology, the DNA double helix codes for the sequence of all proteins in the cell. However, in eukaryotic cells, the coding sequences can vary from 90 per cent (in yeast) to less than 1.5 per cent of the DNA sequence (in higher eukaryotes, such as humans). A role of non-coding DNA in the assembling of the hierarchical architecture of the genome has been, therefore, proposed. This architecture must, at a time, compact DNA in the nucleus and let it be accessible when requested by the cell functioning. Besides the geometrical puzzling that these questions imply, the architecture of DNA and its dynamical modifications have to deal with the mechanical response of DNA that behaves as a rather rigid screw. In particular, gene transcription imposes strong mechanical constraints. The crucial step of protein synthesis, the transcription elongation, is performed by a dedicated enzyme, the RNA-polymerase (RNAP). RNAP opens locally the double helix, reads it and makes a copy of the coding DNA template onto a RNA stretch. The transcription activation requires the formation of a large protein complex, consisting of up to 60 different proteins. Owing to the large dimension of the transcription complex, it is very unlikely that the RNAP rotates around DNA during the elongation process [1]: the DNA has, therefore, to rotate inside the RNAP. This process leads to topological and mechanical constraints upstream and downstream of the transcription site. Indeed, as the elongation complex progresses along the genomic sequence, the DNA double helix in front of it becomes overwound ( positively supercoiled), whereas the DNA behind it becomes underwound (negatively supercoiled). This is the so-called twin-supercoiled-domain (TSD) model, first introduced by Liu & Wang [2] and extensively acknowledged since (for a review, see Lavelle [3]). In this paper, we will deal with the problem of building the appropriate theoretical frame where mechanical and topological constraints acting on DNA can be accounted for, in the perspective of studying the implications of these constraints for different biological proce...

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“…The structure, stability and dynamics of nucleosomes have furthermore been shown to be extensively regulated by post-translational modifications (16), chaperones (17), and ATP-dependent remodelers (18). Furthermore, nucleosome composition and dynamics can be altered by forces and torques generated by molecular motors that process the genome (19,20). Such external influences, as well as changes in the ambient conditions, can cause nucleosomes to reorganize into different (sub)structures (21).…”

Section: Introductionmentioning

confidence: 99%

DNA sequence is a major determinant of tetrasome dynamics

Ordu

Lusser

Dekker

2019

Preprint

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Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4) 2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left-and right-handed conformations, which may prevent torque build-up in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a highaffinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono-and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono-and divalent salt concentrations counteracted this behaviour. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome, but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites. STATEMENT OF SIGNIFICANCECanonical (H3-H4) 2 tetrasomes possess high conformational flexibility, as evidenced by their spontaneous flipping between states of left-and right-handed DNA wrapping. Here, we show that these conformational dynamics of tetrasomes cannot be described by a fixed set of rates over all conditions. Instead, an accurate description of their behavior must take into account details of their loading, in particular the underlying DNA sequence. In vivo, differences in tetrasome flexibility could be regulated by modifications of the histone core or the tetrasomal DNA, and as such constitute an intriguing, potentially adjustable mechanism for chromatin to accommodate the torsional stress generated by processes such as transcription and replication.Recent research has provided significant new insights into the structure and especially the dynamics of nucleosomes (10). For example, studies using single-molecule techniques have revealed the intrinsically dynamic nature of nucleosomes in the form of 'breathing', i.e. the transient un-and rewrapping of the

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Nucleosome‐remodelling machines and other molecular motors observed at the single‐molecule level

Cited by 12 publications

References 105 publications

Chromatin remodelling in mammalian cells by ISWI‐type complexes – where, when and why?

Chromatin remodelling in mammalian cells by ISWI‐type complexes – where, when and why?

On the topology of chromatin fibres

DNA sequence is a major determinant of tetrasome dynamics

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