26 Citations (Scopus)

Abstract

Mechanisms that can alter nucleosome structure to enhance DNA accessibility are of great interest because of their potential involvement in genomic processes. One such mechanism is H2A/H2B release from nucleosomes; it occurs in vivo and is involved in the in vitro activities of several transcription- associated complexes. Using fluorescence approaches based on Förster resonance energy transfer, we previously detected sequence-dependent structure/stability variations between 5S and two types of promoter nucleosomes (from yeast GAL10 or mouse mammary tumor virus promoters). Those variations included differing responses when nucleosomes were diluted to concentrations (sub-nM) known to produce H2A/H2B loss. Here, we show that treatment of these same three types of nucleosomes with the histone chaperone yNAP-1, which causes H2A/H2B release from nucleosomes in vitro, produces the same differential Förster resonance energy transfer responses, again demonstrating sequence-dependent variations associated with conditions that produce H2A/H2B loss. Single-molecule population data indicate that DNA dynamics on the particles produced by diluting nucleosomes to sub-nM concentrations follow two-state behavior. Rate information (determined by fluorescence correlation spectroscopy) suggests that these dynamics are enhanced in MMTV-B or GAL10 compared to 5S particles. Taken together, the results indicate that H2A/H2B loss has differing effects on 5S compared to these two promoter nucleosomes and the differences reflect sequence-dependent structure/stability variations in the depleted particles.

Original languageEnglish (US)
Pages (from-to)147-158
Number of pages12
JournalBiophysical Journal
Volume94
Issue number1
DOIs
StatePublished - Jan 1 2008

Fingerprint

Nucleosomes
Energy Transfer
Histone Chaperones
Mouse mammary tumor virus
DNA
Fluorescence Spectrometry
Carcinogens
Yeasts
Fluorescence

ASJC Scopus subject areas

  • Biophysics

Cite this

Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes. / Kelbauskas, L.; Chan, N.; Bash, R.; DeBartolo, P.; Sun, J.; Woodbury, Neal; Lohr, D.

In: Biophysical Journal, Vol. 94, No. 1, 01.01.2008, p. 147-158.

Research output: Contribution to journalArticle

Kelbauskas, L, Chan, N, Bash, R, DeBartolo, P, Sun, J, Woodbury, N & Lohr, D 2008, 'Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes', Biophysical Journal, vol. 94, no. 1, pp. 147-158. https://doi.org/10.1529/biophysj.107.111906
Kelbauskas, L. ; Chan, N. ; Bash, R. ; DeBartolo, P. ; Sun, J. ; Woodbury, Neal ; Lohr, D. / Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes. In: Biophysical Journal. 2008 ; Vol. 94, No. 1. pp. 147-158.
@article{a9a7046a0a0f4d278805f70dd714816b,
title = "Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes",
abstract = "Mechanisms that can alter nucleosome structure to enhance DNA accessibility are of great interest because of their potential involvement in genomic processes. One such mechanism is H2A/H2B release from nucleosomes; it occurs in vivo and is involved in the in vitro activities of several transcription- associated complexes. Using fluorescence approaches based on F{\"o}rster resonance energy transfer, we previously detected sequence-dependent structure/stability variations between 5S and two types of promoter nucleosomes (from yeast GAL10 or mouse mammary tumor virus promoters). Those variations included differing responses when nucleosomes were diluted to concentrations (sub-nM) known to produce H2A/H2B loss. Here, we show that treatment of these same three types of nucleosomes with the histone chaperone yNAP-1, which causes H2A/H2B release from nucleosomes in vitro, produces the same differential F{\"o}rster resonance energy transfer responses, again demonstrating sequence-dependent variations associated with conditions that produce H2A/H2B loss. Single-molecule population data indicate that DNA dynamics on the particles produced by diluting nucleosomes to sub-nM concentrations follow two-state behavior. Rate information (determined by fluorescence correlation spectroscopy) suggests that these dynamics are enhanced in MMTV-B or GAL10 compared to 5S particles. Taken together, the results indicate that H2A/H2B loss has differing effects on 5S compared to these two promoter nucleosomes and the differences reflect sequence-dependent structure/stability variations in the depleted particles.",
author = "L. Kelbauskas and N. Chan and R. Bash and P. DeBartolo and J. Sun and Neal Woodbury and D. Lohr",
year = "2008",
month = "1",
day = "1",
doi = "10.1529/biophysj.107.111906",
language = "English (US)",
volume = "94",
pages = "147--158",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "1",

}

TY - JOUR

T1 - Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes

AU - Kelbauskas, L.

AU - Chan, N.

AU - Bash, R.

AU - DeBartolo, P.

AU - Sun, J.

AU - Woodbury, Neal

AU - Lohr, D.

PY - 2008/1/1

Y1 - 2008/1/1

N2 - Mechanisms that can alter nucleosome structure to enhance DNA accessibility are of great interest because of their potential involvement in genomic processes. One such mechanism is H2A/H2B release from nucleosomes; it occurs in vivo and is involved in the in vitro activities of several transcription- associated complexes. Using fluorescence approaches based on Förster resonance energy transfer, we previously detected sequence-dependent structure/stability variations between 5S and two types of promoter nucleosomes (from yeast GAL10 or mouse mammary tumor virus promoters). Those variations included differing responses when nucleosomes were diluted to concentrations (sub-nM) known to produce H2A/H2B loss. Here, we show that treatment of these same three types of nucleosomes with the histone chaperone yNAP-1, which causes H2A/H2B release from nucleosomes in vitro, produces the same differential Förster resonance energy transfer responses, again demonstrating sequence-dependent variations associated with conditions that produce H2A/H2B loss. Single-molecule population data indicate that DNA dynamics on the particles produced by diluting nucleosomes to sub-nM concentrations follow two-state behavior. Rate information (determined by fluorescence correlation spectroscopy) suggests that these dynamics are enhanced in MMTV-B or GAL10 compared to 5S particles. Taken together, the results indicate that H2A/H2B loss has differing effects on 5S compared to these two promoter nucleosomes and the differences reflect sequence-dependent structure/stability variations in the depleted particles.

AB - Mechanisms that can alter nucleosome structure to enhance DNA accessibility are of great interest because of their potential involvement in genomic processes. One such mechanism is H2A/H2B release from nucleosomes; it occurs in vivo and is involved in the in vitro activities of several transcription- associated complexes. Using fluorescence approaches based on Förster resonance energy transfer, we previously detected sequence-dependent structure/stability variations between 5S and two types of promoter nucleosomes (from yeast GAL10 or mouse mammary tumor virus promoters). Those variations included differing responses when nucleosomes were diluted to concentrations (sub-nM) known to produce H2A/H2B loss. Here, we show that treatment of these same three types of nucleosomes with the histone chaperone yNAP-1, which causes H2A/H2B release from nucleosomes in vitro, produces the same differential Förster resonance energy transfer responses, again demonstrating sequence-dependent variations associated with conditions that produce H2A/H2B loss. Single-molecule population data indicate that DNA dynamics on the particles produced by diluting nucleosomes to sub-nM concentrations follow two-state behavior. Rate information (determined by fluorescence correlation spectroscopy) suggests that these dynamics are enhanced in MMTV-B or GAL10 compared to 5S particles. Taken together, the results indicate that H2A/H2B loss has differing effects on 5S compared to these two promoter nucleosomes and the differences reflect sequence-dependent structure/stability variations in the depleted particles.

UR - http://www.scopus.com/inward/record.url?scp=37749035092&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=37749035092&partnerID=8YFLogxK

U2 - 10.1529/biophysj.107.111906

DO - 10.1529/biophysj.107.111906

M3 - Article

C2 - 17933873

AN - SCOPUS:37749035092

VL - 94

SP - 147

EP - 158

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 1

ER -