Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada
doi: https://doi.org/10.1101/177436
Toru Niina
1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Giovanni B. Brandani
1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cheng Tan
1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shoji Takada
1Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: takada@biophys.kyoto-u.ac.jp
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

While nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements.

Author summary Nucleosomes are fundamental units of chromatin folding consisting of double-stranded DNA wrapped ∼1.7 times around a histone octamer. By densely populating the eukaryotic genome, nucleosomes enable efficient genome compaction inside the cellular nucleus. However, the portion of DNA occupied by a nucleosome can hardly be accessed by other DNA-binding proteins, obstructing fundamental cellular processes such as DNA replication and transcription. DNA compaction and access by other proteins can simultaneously be achieved via the dynamical repositioning of nucleosomes, which can slide along the DNA sequence. In this study, we developed and used coarse-grained molecular dynamics simulations to reveal the molecular details of nucleosome sliding. We find that the sliding mode is highly dependent on the underlying DNA sequence. Specifically, a sequence with a strong nucleosome positioning signal slides via large jumps by five and ten base pairs, preserving the optimal DNA bending profile. On the other hand, uniform sequences without the positioning signal slide via a screw-like motion of DNA, one base pair at the time. These results show that sequence has a large effect not only on the formation of nucleosomes, but also on the kinetics of repositioning.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted August 17, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada
bioRxiv 177436; doi: https://doi.org/10.1101/177436
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada
bioRxiv 177436; doi: https://doi.org/10.1101/177436

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Biophysics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4369)
  • Biochemistry (9550)
  • Bioengineering (7071)
  • Bioinformatics (24776)
  • Biophysics (12567)
  • Cancer Biology (9925)
  • Cell Biology (14299)
  • Clinical Trials (138)
  • Developmental Biology (7931)
  • Ecology (12078)
  • Epidemiology (2067)
  • Evolutionary Biology (15958)
  • Genetics (10904)
  • Genomics (14708)
  • Immunology (9848)
  • Microbiology (23585)
  • Molecular Biology (9456)
  • Neuroscience (50703)
  • Paleontology (369)
  • Pathology (1535)
  • Pharmacology and Toxicology (2674)
  • Physiology (4001)
  • Plant Biology (8643)
  • Scientific Communication and Education (1505)
  • Synthetic Biology (2388)
  • Systems Biology (6415)
  • Zoology (1345)