Literature DB >> 11724736

Nucleosome formation potential of exons, introns, and Alu repeats.

V G Levitsky1, O A Podkolodnaya, N A Kolchanov, N L Podkolodny.   

Abstract

A program for constructing nucleosome formation potential profile was applied for investigation of exons, introns, and repetitive sequences. The program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/. We have demonstrated that introns and repetitive sequences exhibit higher nucleosome formation potentials than exons. This fact may be explained by functional saturation of exons with genetic code, hindering the localization of efficient nucleosome positioning sites.

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Year:  2001        PMID： 11724736     DOI： 10.1093/bioinformatics/17.11.1062

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  10 in total

1.  A new Drosophila spliceosomal intron position is common in plants.

Authors:  Rosa Tarrio; Francisco Rodríguez-Trelles; Francisco J Ayala
Journal:  Proc Natl Acad Sci U S A       Date:  2003-05-15       Impact factor: 11.205

2.  RECON: a program for prediction of nucleosome formation potential.

Authors:  Victor G Levitsky
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  "Genome design" model: evidence from conserved intronic sequence in human-mouse comparison.

Authors:  Alexander E Vinogradov
Journal:  Genome Res       Date:  2006-02-03       Impact factor: 9.043

4.  Genome size and metabolic intensity in tetrapods: a tale of two lines.

Authors:  Alexander E Vinogradov; Olga V Anatskaya
Journal:  Proc Biol Sci       Date:  2006-01-07       Impact factor: 5.349

5.  NPRD: Nucleosome Positioning Region Database.

Authors:  Victor G Levitsky; Aleksey V Katokhin; Olga A Podkolodnaya; Dagmara P Furman; Nikolay A Kolchanov
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

6.  Noncoding DNA, isochores and gene expression: nucleosome formation potential.

Authors:  Alexander E Vinogradov
Journal:  Nucleic Acids Res       Date:  2005-01-26       Impact factor: 16.971

7.  Intronic retroelements: Not just "speed bumps" for RNA polymerase II.

Authors:  Kristel Kaer; Mart Speek
Journal:  Mob Genet Elements       Date:  2012-05-01

Review 8.  The mammalian transcriptome and the function of non-coding DNA sequences.

Authors:  Svetlana A Shabalina; Nikolay A Spiridonov
Journal:  Genome Biol       Date:  2004-03-25       Impact factor: 13.583

9.  Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.

Authors:  Victor G Levitsky; Elena V Ignatieva; Elena A Ananko; Igor I Turnaev; Tatyana I Merkulova; Nikolay A Kolchanov; T C Hodgman
Journal:  BMC Bioinformatics       Date:  2007-12-19       Impact factor: 3.169

10.  Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples.

Authors:  Chun-Nan Dong; Ya-Dong Yang; Shu-Jin Li; Ya-Ran Yang; Xiao-Jing Zhang; Xiang-Dong Fang; Jiang-Wei Yan; Bin Cong
Journal:  Sci Rep       Date:  2016-05-18       Impact factor: 4.379
  10 in total

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