Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA

Tadasu Nozaki; Nozomu Yachie; Ryu Ogawa; Rintaro Saito; Masaru Tomita

doi:10.1016/j.gene.2011.02.004

Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA

Tadasu Nozaki, Nozomu Yachie, Ryu Ogawa, Rintaro Saito, Masaru Tomita

Faculty of Environment and Information Studies

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Abstract

Eukaryotic chromosomal DNA coils around histones to form nucleosomes. Although histone affinity for DNA depends on DNA sequence patterns, how nucleosome positioning is determined by them remains unknown. Here, we show relationships between nucleosome positioning and two structural characteristics of DNA conferred by DNA sequence. Analysis of bendability and hydroxyl radical cleavage intensity of nucleosomal DNA sequences indicated that nucleosomal DNA is bendable and fragile and that nucleosome positional stability was correlated with characteristics of DNA. This result explains how histone positioning is partially determined by nucleosomal DNA structure, illuminating the optimization of chromosomal DNA packaging that controls cellular dynamics.

Original language	English
Pages (from-to)	10-14
Number of pages	5
Journal	Gene
Volume	476
Issue number	1-2
DOIs	https://doi.org/10.1016/j.gene.2011.02.004
Publication status	Published - 2011 May 1

Keywords

Bendability
Cleavage intensity
DNA structure
Epigenetics
Histone
Nucleosome

ASJC Scopus subject areas

Genetics

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10.1016/j.gene.2011.02.004

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title = "Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA",

abstract = "Eukaryotic chromosomal DNA coils around histones to form nucleosomes. Although histone affinity for DNA depends on DNA sequence patterns, how nucleosome positioning is determined by them remains unknown. Here, we show relationships between nucleosome positioning and two structural characteristics of DNA conferred by DNA sequence. Analysis of bendability and hydroxyl radical cleavage intensity of nucleosomal DNA sequences indicated that nucleosomal DNA is bendable and fragile and that nucleosome positional stability was correlated with characteristics of DNA. This result explains how histone positioning is partially determined by nucleosomal DNA structure, illuminating the optimization of chromosomal DNA packaging that controls cellular dynamics.",

keywords = "Bendability, Cleavage intensity, DNA structure, Epigenetics, Histone, Nucleosome",

author = "Tadasu Nozaki and Nozomu Yachie and Ryu Ogawa and Rintaro Saito and Masaru Tomita",

note = "Funding Information: This research was supported by research funds from the Yamagata Prefectural Government and the City of Tsuruoka, Japan , and by a grant-in-aid from the Japan Society for the Promotion of Science (JSPS) to N.Y. (grant no. 1924 ). During this research, N.Y. was supported by a JSPS Postdoctoral Fellowship (PD) and a JSPS Postdoctoral Fellowship for Research Abroad . The source code of ORChID was kindly provided by Dr. Steve Parker. ",

year = "2011",

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doi = "10.1016/j.gene.2011.02.004",

language = "English",

volume = "476",

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journal = "Gene",

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T1 - Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA

AU - Nozaki, Tadasu

AU - Yachie, Nozomu

AU - Ogawa, Ryu

AU - Saito, Rintaro

AU - Tomita, Masaru

N1 - Funding Information: This research was supported by research funds from the Yamagata Prefectural Government and the City of Tsuruoka, Japan , and by a grant-in-aid from the Japan Society for the Promotion of Science (JSPS) to N.Y. (grant no. 1924 ). During this research, N.Y. was supported by a JSPS Postdoctoral Fellowship (PD) and a JSPS Postdoctoral Fellowship for Research Abroad . The source code of ORChID was kindly provided by Dr. Steve Parker.

PY - 2011/5/1

Y1 - 2011/5/1

N2 - Eukaryotic chromosomal DNA coils around histones to form nucleosomes. Although histone affinity for DNA depends on DNA sequence patterns, how nucleosome positioning is determined by them remains unknown. Here, we show relationships between nucleosome positioning and two structural characteristics of DNA conferred by DNA sequence. Analysis of bendability and hydroxyl radical cleavage intensity of nucleosomal DNA sequences indicated that nucleosomal DNA is bendable and fragile and that nucleosome positional stability was correlated with characteristics of DNA. This result explains how histone positioning is partially determined by nucleosomal DNA structure, illuminating the optimization of chromosomal DNA packaging that controls cellular dynamics.

AB - Eukaryotic chromosomal DNA coils around histones to form nucleosomes. Although histone affinity for DNA depends on DNA sequence patterns, how nucleosome positioning is determined by them remains unknown. Here, we show relationships between nucleosome positioning and two structural characteristics of DNA conferred by DNA sequence. Analysis of bendability and hydroxyl radical cleavage intensity of nucleosomal DNA sequences indicated that nucleosomal DNA is bendable and fragile and that nucleosome positional stability was correlated with characteristics of DNA. This result explains how histone positioning is partially determined by nucleosomal DNA structure, illuminating the optimization of chromosomal DNA packaging that controls cellular dynamics.

KW - Bendability

KW - Cleavage intensity

KW - DNA structure

KW - Epigenetics

KW - Histone

KW - Nucleosome

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JO - Gene

JF - Gene

IS - 1-2

ER -

Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA

Abstract

Keywords

ASJC Scopus subject areas

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