Nucleosome Repositioning Via Loop Formation

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2003 Apr 30

PMID 12719249

Citations 29

Authors

I M Kulic

H Schiessel

Affiliations

Soon will be listed here.

Abstract

Active (catalyzed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eukaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by earlier works. The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model-being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed, and compared to existing experimental findings.

Citing Articles

Sequence Dependence in Nucleosome Dynamics.

Khatua P, Tang P, Ghosh Moulick A, Patel R, Manandhar A, Loverde S J Phys Chem B. 2024; 128(13):3090-3101.

PMID: 38530903 PMC: 11181342. DOI: 10.1021/acs.jpcb.3c07363.

The role of transcript regions and amino acid choice in nucleosome positioning.

Yadav M, Zuiddam M, Schiessel H NAR Genom Bioinform. 2023; 5(3):lqad080.

PMID: 37705829 PMC: 10495542. DOI: 10.1093/nargab/lqad080.

Multiplexing mechanical and translational cues on genes.

Zuiddam M, Shakiba B, Schiessel H Biophys J. 2022; 121(22):4311-4324.

PMID: 36230003 PMC: 9703045. DOI: 10.1016/j.bpj.2022.10.011.

Visualizing Conformational Ensembles of the Nucleosome by NMR.

Musselman C, Kutateladze T ACS Chem Biol. 2022; 17(3):495-502.

PMID: 35196453 PMC: 9089449. DOI: 10.1021/acschembio.1c00954.

Ensembles of Breathing Nucleosomes: A Computational Study.

van Deelen K, Schiessel H, De Bruin L Biophys J. 2019; 118(9):2297-2308.

PMID: 31882248 PMC: 7202939. DOI: 10.1016/j.bpj.2019.11.3395.

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