Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility

Thuy Ngo, Qiucen Zhang, Ruobo Zhou, Jaya G. Yodh, Taekjip Ha

Research output: Contribution to journalArticle

101 Citations (Scopus)

Abstract

Dynamics of the nucleosome and exposure of nucleosomal DNA play key roles in many nuclear processes, but local dynamics of the nucleosome and its modulation by DNA sequence are poorly understood. Using single-molecule assays, we observed that the nucleosome can unwrap asymmetrically and directionally under force. The relative DNA flexibility of the inner quarters of nucleosomal DNA controls the unwrapping direction such that the nucleosome unwraps from the stiffer side. If the DNA flexibility is similar on two sides, it stochastically unwraps from either side. The two ends of the nucleosome are orchestrated such that the opening of one end helps to stabilize the other end, providing a mechanism to amplify even small differences in flexibility to a large asymmetry in nucleosome stability. Our discovery of DNA flexibility as a critical factor for nucleosome dynamics and mechanical stability suggests a novel mechanism of gene regulation by DNA sequence and modifications.

Original languageEnglish (US)
Pages (from-to)1135-1144
Number of pages10
JournalCell
Volume160
Issue number6
DOIs
StatePublished - Mar 15 2015
Externally publishedYes

Fingerprint

Nucleosomes
DNA
DNA sequences
Mechanical stability
Gene expression
Assays
Modulation
Molecules
Genes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. / Ngo, Thuy; Zhang, Qiucen; Zhou, Ruobo; Yodh, Jaya G.; Ha, Taekjip.

In: Cell, Vol. 160, No. 6, 15.03.2015, p. 1135-1144.

Research output: Contribution to journalArticle

Ngo, Thuy ; Zhang, Qiucen ; Zhou, Ruobo ; Yodh, Jaya G. ; Ha, Taekjip. / Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility. In: Cell. 2015 ; Vol. 160, No. 6. pp. 1135-1144.
@article{194f5df3735043598fd3ba9b8d196a08,
title = "Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility",
abstract = "Dynamics of the nucleosome and exposure of nucleosomal DNA play key roles in many nuclear processes, but local dynamics of the nucleosome and its modulation by DNA sequence are poorly understood. Using single-molecule assays, we observed that the nucleosome can unwrap asymmetrically and directionally under force. The relative DNA flexibility of the inner quarters of nucleosomal DNA controls the unwrapping direction such that the nucleosome unwraps from the stiffer side. If the DNA flexibility is similar on two sides, it stochastically unwraps from either side. The two ends of the nucleosome are orchestrated such that the opening of one end helps to stabilize the other end, providing a mechanism to amplify even small differences in flexibility to a large asymmetry in nucleosome stability. Our discovery of DNA flexibility as a critical factor for nucleosome dynamics and mechanical stability suggests a novel mechanism of gene regulation by DNA sequence and modifications.",
author = "Thuy Ngo and Qiucen Zhang and Ruobo Zhou and Yodh, {Jaya G.} and Taekjip Ha",
year = "2015",
month = "3",
day = "15",
doi = "10.1016/j.cell.2015.02.001",
language = "English (US)",
volume = "160",
pages = "1135--1144",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "6",

}

TY - JOUR

T1 - Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility

AU - Ngo, Thuy

AU - Zhang, Qiucen

AU - Zhou, Ruobo

AU - Yodh, Jaya G.

AU - Ha, Taekjip

PY - 2015/3/15

Y1 - 2015/3/15

N2 - Dynamics of the nucleosome and exposure of nucleosomal DNA play key roles in many nuclear processes, but local dynamics of the nucleosome and its modulation by DNA sequence are poorly understood. Using single-molecule assays, we observed that the nucleosome can unwrap asymmetrically and directionally under force. The relative DNA flexibility of the inner quarters of nucleosomal DNA controls the unwrapping direction such that the nucleosome unwraps from the stiffer side. If the DNA flexibility is similar on two sides, it stochastically unwraps from either side. The two ends of the nucleosome are orchestrated such that the opening of one end helps to stabilize the other end, providing a mechanism to amplify even small differences in flexibility to a large asymmetry in nucleosome stability. Our discovery of DNA flexibility as a critical factor for nucleosome dynamics and mechanical stability suggests a novel mechanism of gene regulation by DNA sequence and modifications.

AB - Dynamics of the nucleosome and exposure of nucleosomal DNA play key roles in many nuclear processes, but local dynamics of the nucleosome and its modulation by DNA sequence are poorly understood. Using single-molecule assays, we observed that the nucleosome can unwrap asymmetrically and directionally under force. The relative DNA flexibility of the inner quarters of nucleosomal DNA controls the unwrapping direction such that the nucleosome unwraps from the stiffer side. If the DNA flexibility is similar on two sides, it stochastically unwraps from either side. The two ends of the nucleosome are orchestrated such that the opening of one end helps to stabilize the other end, providing a mechanism to amplify even small differences in flexibility to a large asymmetry in nucleosome stability. Our discovery of DNA flexibility as a critical factor for nucleosome dynamics and mechanical stability suggests a novel mechanism of gene regulation by DNA sequence and modifications.

UR - http://www.scopus.com/inward/record.url?scp=84924589156&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84924589156&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2015.02.001

DO - 10.1016/j.cell.2015.02.001

M3 - Article

VL - 160

SP - 1135

EP - 1144

JO - Cell

JF - Cell

SN - 0092-8674

IS - 6

ER -