Revealing transient structures of nucleosomes as DNA unwinds

Yujie Chen; Joshua M Tokuda; Traci Topping; Julie L Sutton; Steve P Meisburger; Suzette A Pabit; Lisa M Gloss; Lois Pollack

doi:10.1093/nar/gku562

Back

Revealing transient structures of nucleosomes as DNA unwinds

Journal article

Open access

Peer reviewed

Revealing transient structures of nucleosomes as DNA unwinds

Yujie Chen, Joshua M Tokuda, Traci Topping, Julie L Sutton, Steve P Meisburger, Suzette A Pabit, Lisa M Gloss and Lois Pollack

Nucleic acids research, Vol.42(13), pp.8767-8776

07/2014

DOI: https://doi.org/10.1093/nar/gku562

Handle:

https://hdl.handle.net/2376/113081

PMCID: PMC4117781

PMID: 24990379

Files and links (1)

url

https://doi.org/10.1093/nar/gku562View

Published (Version of record) Open

Abstract

Scattering, Small Angle

DNA - chemistry

Nucleic Acid Conformation

Nucleosomes - chemistry

X-Ray Diffraction

Sodium Chloride - chemistry

The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) consists of 147 bp of DNA wrapped around a symmetric octamer of histone proteins. The dynamics of DNA packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including DNA positioning sequence, histone variants and modifications. Although the structure of the intact NCP has been studied by crystallography at atomic resolution, little is known about the structures of the partially unwrapped, transient intermediates relevant to nucleosome dynamics in processes such as transcription, DNA replication and repair. We apply a new experimental approach combining contrast variation with time-resolved small angle X-ray scattering (TR-SAXS) to determine transient structures of protein and DNA constituents of NCPs during salt-induced disassembly. We measure the structures of unwrapping DNA and monitor protein dissociation from Xenopus laevis histones reconstituted with two model NCP positioning constructs: the Widom 601 sequence and the sea urchin 5S ribosomal gene. Both constructs reveal asymmetric release of DNA from disrupted histone cores, but display different patterns of protein dissociation. These kinetic intermediates may be biologically important substrates for gene regulation.

Metrics

12 Record Views

See more details

Details

Title: Revealing transient structures of nucleosomes as DNA unwinds
Creators: Yujie Chen - School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
Joshua M Tokuda - School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
Traci Topping - School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
Julie L Sutton - School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
Steve P Meisburger - School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
Suzette A Pabit - School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
Lisa M Gloss - School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
Lois Pollack - School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA lp26@cornell.edu
Publication Details: Nucleic acids research, Vol.42(13), pp.8767-8776
Academic Unit: Graduate School
Publisher: England
Grant note: P41 GM103485 / NIGMS NIH HHS R01-GM085062 / NIGMS NIH HHS R01-GM088645 / NIGMS NIH HHS T32 GM008267 / NIGMS NIH HHS T32GM008267 / NIGMS NIH HHS GM073787 / NIGMS NIH HHS
Identifiers: 99900547707101842
Language: English
Resource Type: Journal article