Polymer Reptation and Nucleosome Repositioning

Schiessel, Helmut; Widom, Jonathan; Bruinsma, Robijn; Gelbart, William M.

doi:10.1103/physrevlett.86.4414

Cited by 120 publications

(157 citation statements)

References 15 publications

(18 reference statements)

Supporting

Mentioning

147

Contrasting

Order By: Relevance

“…The on-off dynamics by themselves, which generate essentially a first-order line-filling reaction that ''jams'' after covering Ϸ75% of the DNA, cannot describe experiment, where a slow final filling occurs. By adding sliding of nucleosomes along DNA (24,25) to our theory, we obtain exactly the slow final relaxation observed experimentally, while maintaining the initial first-order-like reaction. Data for the extract-based reactions indicate that nucleosome sliding occurs at a rate 5 bp 2 /s (Ϸ5 ϫ 10 Ϫ15 cm 2 /s).…”

Section: Discussionmentioning

confidence: 70%

“…However, if nucleosomes are able to diffuse laterally, a slow reorganization and further assembly can be expected to occur. Despite experiments suggesting that nucleosome sliding occurs (23) and extensive theoretical modeling (24,25), quantitative measures of nucleo-some sliding diffusion rates have not been forthcoming. Intriguingly, a recent study indicates that the ATP-independent histone chaperone NAP-1, which is present in Xenopus extracts, stimulates nucleosome sliding (26).…”

Section: Nucleosome Dynamics In Xenopus Egg Extractsmentioning

confidence: 99%

“…Schiessel et al (24) have proposed a mechanism and have made quantitative predictions for thermally activated nucleosome sliding diffusion at zero force [D(0); see supporting information (SI) Appendix]. Thermally excited unwrapping and readsorption events known to occur in nucleosomes (7,8) can cause small intranucleosomal DNA loop-bulges of length ⌬L Ϸ 10 bp, which can transfer DNA length through a nucleosome (24,25).…”

Section: Theorymentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts

Padinhateeri

Yan

Marko

2007

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

View full text Add to dashboard Cite

Chromatin function in vivo is intimately connected with changes in its structure: a prime example is occlusion or exposure of regulatory sequences via repositioning of nucleosomes. Cell extracts used in concert with single-DNA micromanipulation can control and monitor these dynamics under in vivo-like conditions. We analyze a theory of the assembly-disassembly dynamics of chromatin fiber in such experiments, including effects of lateral nucleosome diffusion (''sliding'') and sequence positioning. Experimental data determine the force-dependent on-and off-rates as well as the nucleosome sliding diffusion rate. The resulting theory simply explains the very different nucleosome displacement kinetics observed in constant-force and constant-pulling velocity experiments. We also show that few-piconewton tensions comparable to those generated by polymerases and helicases drastically affect nucleosome positions in a sequence-dependent manner and that there is a long-lived structural ''memory'' of force-driven nucleosome rearrangement events.chromatin assembly ͉ chromatin disassembly I n the nucleus, chromatin undergoes continual structural rearrangement. Chromatin fibers have been observed to undergo large-scale diffusion-like motions (1, 2) and rapid local motions (3), possibly caused by the action of processive enzymes such as nucleic acid polymerases and helicases. At smaller scales, fluorescence recovery after photobleaching studies in vivo have shown histones to be mobile to some degree (4). Both large-scale conformational and nucleosomal rearrangements are biologically important, e.g., through their influence on gene regulation (5, 6).These in vivo results are complemented by biochemical experiments indicating that DNA can be transiently released from nucleosomes (7,8) and recent DNA-pulling experiments that show nucleosome disruption by forces ranging from a few to tens of piconewtons (9-12). Single-nucleosome or single-chromatinfiber experiments carried out in protein-free buffers provide useful quantifications of histone-DNA interaction strengths and force-driven opening rates. However, affinities and rates obtained from studies of isolated fibers may be very different relative from those occurring in vivo because of the very high levels of chromatin-acting enzymes found in the cell. This issue can be addressed by combining cell extracts with single-molecule methods for reading out folding and unfolding of protein-DNA complexes in real time, which permits observation of singlechromatin fiber dynamics under conditions close to those found in vivo (10,(13)(14)(15)(16).Here, we present a theory of chromatin fiber dynamics in Xenopus egg extracts, based on assembly, displacement, and lateral diffusion (''sliding'') of nucleosome units. Recent experimental data for sequence dependence of nucleosome affinities (17), combined with measurements of single-chromatin fiber assembly and disassembly in Xenopus egg extracts, constrain the theory sufficiently to determine force-dependent nucleosome on-and off-rates, the seque...

show abstract

Section: Discussionmentioning

confidence: 70%

Section: Nucleosome Dynamics In Xenopus Egg Extractsmentioning

confidence: 99%

Section: Theorymentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts

Padinhateeri

Yan

Marko

2007

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

View full text Add to dashboard Cite

show abstract

“…It has also been proposed that thermal energy alone is responsible for the initial dissociation of DNA from the ends of the nucleosome. (95) Another version of this looping model suggests that the remodeling factor pushes the DNA toward the histone octamer.…”

Section: How Might Chromatin Remodeling Occur?mentioning

confidence: 99%

Chromatin remodeling by ATP‐dependent molecular machines

2003

View full text Add to dashboard Cite

SummaryThe eukaryotic genome is packaged into a periodic nucleoprotein structure termed chromatin. The repeating unit of chromatin, the nucleosome, consists of DNA that is wound nearly two times around an octamer of histone proteins. To facilitate DNA-directed processes in chromatin, it is often necessary to rearrange or to mobilize the nucleosomes. This remodeling of the nucleosomes is achieved by the action of chromatin-remodeling complexes, which are a family of ATP-dependent molecular machines. Chromatin-remodeling factors share a related ATPase subunit and participate in transcriptional regulation, DNA repair, homologous recombination and chromatin assembly. In this review, we provide an overview of chromatin-remodeling enzymes and discuss two possible mechanisms by which these factors might act to reorganize nucleosome structure.

show abstract

Opening and Closing DNA: Theories on the Nucleosome

Kulić

Schiessel

2007

DNA Interactions With Polymers and Surfactants

View full text Add to dashboard Cite

INTRODUCTIONDNA-the carrier of the genetic information-is at the base of many central life processes [1]: replication, transcription, and repair of genetic material depend on the unique properties of DNA, especially the base pairing. One has, however, to appreciate the fact that the molecular machinery of eucaryotes (plants and animals) does not deal with naked DNA but with chromatin, a DNA-protein complex in which DNA is wrapped and folded in a hierarchical fashion [2]. On the lowest level DNA is wrapped nearly twice around an octamer of histone proteins. A short stretch of the "linker DNA" connects to the next such protein spool. The resulting string of so-called nucleosomes folds into higher order structures, the details of which are still under debate (see Figure 7.1).The structure of the nucleosome core particle (NCP), the particle that is left when the linker DNA is digested away, is known in exquisite detail from X-ray crystallography at 2.8 A resolution [3] and more recently at 1.9 A[4]. The octamer is composed of two molecules each of the four core histone proteins H2A, H2B, H3, and H4. At physiological conditions the stable oligomeric aggregates of the core histones are the H3-H4 tetramer (an aggregate of two H3 and two H4 proteins) and the H2A-H2B dimer; the octamer is then only stable if it is associated with DNA [5]. The two dimers and the tetramer are put together in such a way that the resulting octamer forms a cylinder with about a 65 A diameter and about a 60 A height. With grooves, ridges, and binding sites the octamer defines the wrapping path of the DNA, a left-handed helical ramp of 1 and 3/4 turns, a 147 base-pairs (bp) length, and a roughly 28 A pitch. This aggregate has a twofold axis of symmetry (the dyad axis) that is perpendicular to the superhelix axis. A schematic view of the NCP is given in Figure 7.2. DNA Interactions with Polymers and Surfactants Edited by Rita Dias and Bj€ orn Lindman

show abstract

Polymer Reptation and Nucleosome Repositioning

Cited by 120 publications

References 15 publications

Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts

Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts

Chromatin remodeling by ATP‐dependent molecular machines

Opening and Closing DNA: Theories on the Nucleosome

Contact Info

Product

Resources

About