Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (29)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Levitsky, V. G.
Right arrow Articles by Podkolodny, N. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Levitsky, V. G.
Right arrow Articles by Podkolodny, N. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 17 no. 11 2001
Pages 998-1010
© 2001 Oxford University Press

Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis

Victor G. Levitsky *, Olga A. Podkolodnaya , Nikolay A. Kolchanov and Nikolay L. Podkolodny

Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 630090, Lavrentiev Ave. 10, Novosibirsk, Russia

Received on December 10, 2000 ; revised on April 14, 2001 and June 28, 2001 ; accepted on July 27, 2001

Motivation: A rapid growth in the number of genes with known sequences calls for developing automated tools for their classification and analysis. It became clear that nucleosome packaging of eukaryotic DNA is very important for gene functioning. Automated computer tools for characterization of nucleosome packaging density could be useful for studying of gene regulation and genome annotation.

Results: A program for constructing nucleosome formation potential profiles of eukaryotic DNA sequences was developed. Nucleosome packaging density was analyzed for different functional types of human promoters. It was found that in promoters of tissue-specific genes, the nucleosome formation potential was essentially higher than in genes expressed in many tissues, or housekeeping genes. Hence, capability of nucleosome positioning in the promoter region may serve as a factor regulating gene expression.

Availability: The program for nucleosome sites recognition is included into the GeneExpress system; section ‘DNA Nucleosomal Organization’, http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/.

Contact: levitsky{at}bionet.nsc.ru

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
G. A. Babbitt and Y. Kim
Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast
Mol. Biol. Evol., August 1, 2008; 25(8): 1714 - 1727.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
P. P. Luedi, F. S. Dietrich, J. R. Weidman, J. M. Bosko, R. L. Jirtle, and A. J. Hartemink
Computational and experimental identification of novel human imprinted genes
Genome Res., December 1, 2007; 17(12): 1723 - 1730.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
H. E. Peckham, R. E. Thurman, Y. Fu, J. A. Stamatoyannopoulos, W. S. Noble, K. Struhl, and Z. Weng
Nucleosome positioning signals in genomic DNA
Genome Res., August 1, 2007; 17(8): 1170 - 1177.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Luykx, I. V. Bajic, and S. Khuri
NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W560 - W565.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. E. Vinogradov
Noncoding DNA, isochores and gene expression: nucleosome formation potential
Nucleic Acids Res., January 26, 2005; 33(2): 559 - 563.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. G. Levitsky, A. V. Katokhin, O. A. Podkolodnaya, D. P. Furman, and N. A. Kolchanov
NPRD: Nucleosome Positioning Region Database
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D67 - D70.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
V. G. Levitsky
RECON: a program for prediction of nucleosome formation potential
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W346 - W349.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.