Structural plasticity of single chromatin fibers revealed by torsional manipulation

Bancaud, Aurélien; Silva, Natalia Conde e; Barbi, Maria; Wagner, Gaudeline; Allemand, Jean-François; Mozziconacci, Julien; Lavelle, Christophe; Croquette, Vincent; Victor, Jean–Marc; Prunell, Ariel; Viovy, Jean‐Louis

doi:10.1038/nsmb1087

Cited by 160 publications

(226 citation statements)

References 44 publications

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“…They play essential roles in regulating the cellular level of supercoiling and the accessibility of DNA. In particular, the inherent dynamic behavior of nucleosome reorganization observed at the single-molecule level (Bancaud et al 2006) suggests that nucleosome dynamics respond to changes in supercoiling and, more specifically, to DNA torsion, which regulates binding of numerous proteins and controls cellular processes, including transcription and replication.…”

Section: Dna Twist (Torsion)-dependent Protein Activitymentioning

confidence: 99%

The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

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Section: Dna Twist (Torsion)-dependent Protein Activitymentioning

confidence: 99%

The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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“…Recent magnetic tweezers studies evaluated the response of a single chromatin fiber to applied torsion (Bancaud et al, 2006 and2007). The authors showed that nucleosomal arrays can absorb a significant amount of positive stress, without major changes to fiber length.…”

Section: Nucleosome Dynamics In Response To Torsional Stressmentioning

confidence: 99%

How are nucleosomes disrupted during transcription elongation?

Zlatanova

Victor

2009

HFSP Journal

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“…A complementary approach is to study individual chromatin fibers by using micromanipulation (Cui and Bustamante, 2000;Ladoux et al, 2000;Bennink et al, 2001;Brower-Toland et al, 2002;Leuba et al, 2003;Claudet et al, 2005;Gemmen et al, 2005;Bancaud et al, 2006). A major objective of such experiments has been the study of mechanically triggered changes in protein-DNA contacts, with an emphasis on force-driven opening of nucleosomes.…”

Section: Introductionmentioning

confidence: 99%

Micromanipulation Studies of Chromatin Fibers in Xenopus Egg Extracts Reveal ATP-dependent Chromatin Assembly Dynamics

Yan

Maresca

Skoko

et al. 2007

MBoC

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We have studied assembly of chromatin using Xenopus egg extracts and single DNA molecules held at constant tension by using magnetic tweezers. In the absence of ATP, interphase extracts were able to assemble chromatin against DNA tensions of up to 3.5 piconewtons (pN). We observed force-induced disassembly and opening-closing fluctuations, indicating our experiments were in mechanochemical equilibrium. Roughly 50-nm (150-base pair) lengthening events dominated force-driven disassembly, suggesting that the assembled fibers are chiefly composed of nucleosomes. The ATP-depleted reaction was able to do mechanical work of 27 kcal/mol per 50 nm step, which provides an estimate of the free energy difference between core histone octamers on and off DNA. Addition of ATP led to highly dynamic behavior with time courses exhibiting processive runs of assembly and disassembly not observed in the ATP-depleted case. With ATP present, application of forces of 2 pN led to nearly complete fiber disassembly. Our study suggests that ATP hydrolysis plays a major role in nucleosome rearrangement and removal and that chromatin in vivo may be subject to highly dynamic assembly and disassembly processes that are modulated by DNA tension. INTRODUCTIONTranscription, replication, and other in vivo DNA processing in eukaryotes take place in the context of chromatin. The processive nature of these activities, and the necessity to disrupt histone-DNA contacts to accomplish them, suggests that chromatin must be dynamic in its structure, with actively transcribing genes perhaps in a continual state of structural rearrangement. The simplest example of chromatin rearrangement that would allow base pair access is displacement or dissociation of part or all of the histone octamer (Felsenfeld, 1996).Chromosome visualization in vivo gives insight into chromatin dynamics at large length scales (Belmont, 2003;Levi et al., 2005) but is as yet unable to reveal events at the scale of individual nucleosome displacements. A complementary approach is to study individual chromatin fibers by using micromanipulation (Cui and Bustamante, 2000;Ladoux et al., 2000;Bennink et al., 2001;Brower-Toland et al., 2002;Leuba et al., 2003;Claudet et al., 2005;Gemmen et al., 2005;Bancaud et al., 2006). A major objective of such experiments has been the study of mechanically triggered changes in protein-DNA contacts, with an emphasis on force-driven opening of nucleosomes.However, biophysical micromanipulation experiments offer possibilities beyond simply disassembling chromatin by force; experiments in "active" solutions containing chromatin-organizing or chromatin-processing enzymes permit direct observation of chromatin dynamics, and they can reveal details of structure and mechanism concerning compaction of DNA into chromatin, chromatin remodeling, gene expression in chromatin, mitotic chromosome condensation, and how such processes are affected by DNA tension. DNA tension is physiologically relevant because pulling of chromatin is likely to occur in vivo, given the larg...

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Structural plasticity of single chromatin fibers revealed by torsional manipulation

Cited by 160 publications

References 44 publications

The dynamic interplay between DNA topoisomerases and DNA topology

The dynamic interplay between DNA topoisomerases and DNA topology

How are nucleosomes disrupted during transcription elongation?

Micromanipulation Studies of Chromatin Fibers in Xenopus Egg Extracts Reveal ATP-dependent Chromatin Assembly Dynamics

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