Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles

Alexander W Mauney; Joshua M Tokuda; Lisa M Gloss; Oscar Gonzalez; Lois Pollack

doi:10.1016/j.bpj.2018.07.009

Back

Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles

Journal article

Open access

Peer reviewed

Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles

Alexander W Mauney, Joshua M Tokuda, Lisa M Gloss, Oscar Gonzalez and Lois Pollack

Biophysical journal, Vol.115(5), pp.773-781

09/04/2018

DOI: https://doi.org/10.1016/j.bpj.2018.07.009

Handle:

https://hdl.handle.net/2376/111070

PMCID: PMC6127449

PMID: 30072033

Files and links (1)

url

https://doi.org/10.1016/j.bpj.2018.07.009View

Published (Version of record) Open

Abstract

Nucleic Acids and Genome Biophysics

DNA is tightly wrapped around histone proteins in nucleosome core particles (NCPs) yet must become accessible for processing in the cell. This accessibility, a key component of transcription regulation, is influenced by the properties of both the histone proteins and the DNA itself. Small angle x-ray scattering with contrast variation is used to examine how sequence variations affect DNA unwrapping from NCPs at different salt concentrations. Salt destabilizes NCPs, populating multiple unwrapped states as many possible unwrapping pathways are explored by the complexes. We apply coarse-grained Monte Carlo methods to generate realistic sequence-dependent unwrapped structures for the nucleosomal DNA with thermal variations. An ensemble optimization method is employed to determine the composition of the overall ensemble as electrostatic interactions are weakened. Interesting DNA-sequence-dependent differences are revealed in the unwrapping paths and equilibrium constants. These differences are correlated with specific features within the nucleic acid sequences.

Metrics

6 Record Views

See more details

Details

Title: Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles
Creators: Alexander W Mauney - School of Applied and Engineering Physics, Cornell University, Ithaca, New York
Joshua M Tokuda - School of Applied and Engineering Physics, Cornell University, Ithaca, New York
Lisa M Gloss - School of Molecular Biosciences, Washington State University, Pullman, Washington
Oscar Gonzalez - Department of Mathematics, University of Texas, Austin, Texas
Lois Pollack - School of Applied and Engineering Physics, Cornell University, Ithaca, New York
Publication Details: Biophysical journal, Vol.115(5), pp.773-781
Academic Unit: Graduate School
Publisher: The Biophysical Society
Identifiers: 99900547153701842
Language: English
Resource Type: Journal article