Single-base resolution nucleosome mapping on dna sequences

I. Gabdank; D. Barash; E. N. Trifonov

doi:10.1080/07391102.2010.10507347

Single-base resolution nucleosome mapping on dna sequences

I. Gabdank, D. Barash, E. N. Trifonov

Department of Computer Science

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

33 Scopus citations

Abstract

Nucleosome DNA bendability pattern extracted from large nucleosome DNA database of C. elegans is used for construction of full length (116 dinucleotide positions) nucleosome DNA bendability matrix. The matrix can be used for sequence-directed mapping of the nucleosomes on the sequences. Several alternative positions for a given nucleosome are typically predicted, separated by multiples of nucleosome DNA period. The corresponding computer program is successfully tested on best known experimental examples of accurately positioned nucleosomes. The uncertainty of the computational mapping is ±1 base. The procedure is placed on publicly accessible server and can be applied to any DNA sequence of interest.

Original language	English
Pages (from-to)	107-121
Number of pages	15
Journal	Journal of Biomolecular Structure and Dynamics
Volume	28
Issue number	1
DOIs	https://doi.org/10.1080/07391102.2010.10507347
State	Published - 1 Jan 2010

Keywords

Chromatin code
DNA bendability
Nucleosome DNA
Nucleosome positioning
Nucleosome structure

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1080/07391102.2010.10507347

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title = "Single-base resolution nucleosome mapping on dna sequences",

abstract = "Nucleosome DNA bendability pattern extracted from large nucleosome DNA database of C. elegans is used for construction of full length (116 dinucleotide positions) nucleosome DNA bendability matrix. The matrix can be used for sequence-directed mapping of the nucleosomes on the sequences. Several alternative positions for a given nucleosome are typically predicted, separated by multiples of nucleosome DNA period. The corresponding computer program is successfully tested on best known experimental examples of accurately positioned nucleosomes. The uncertainty of the computational mapping is ±1 base. The procedure is placed on publicly accessible server and can be applied to any DNA sequence of interest.",

keywords = "Chromatin code, DNA bendability, Nucleosome DNA, Nucleosome positioning, Nucleosome structure",

author = "I. Gabdank and D. Barash and Trifonov, {E. N.}",

note = "Funding Information: The work has been supported by Israel Science Foundation (grant 222/09), by Czech Ministry of Education (grant MSM0021622415), and by Pratt fellowship and the Lynn and William Frankel Center for Computer Sciences at Ben Gurion University.",

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Single-base resolution nucleosome mapping on dna sequences

Abstract

Keywords

ASJC Scopus subject areas

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