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/.
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/.
Authors: Alexey S Kutsenko; Rinat Z Gizatullin; Ali N Al-Amin; Fuli Wang; Sergei M Kvasha; Raf M Podowski; Yuri G Matushkin; Anita Gyanchandani; Olga V Muravenko; Viktor G Levitsky; Nikolay A Kolchanov; Alexei I Protopopov; Vladimir I Kashuba; Lev L Kisselev; Wyeth Wasserman; Claes Wahlestedt; Eugene R Zabarovsky Journal: Nucleic Acids Res Date: 2002-07-15 Impact factor: 16.971
Authors: Philippe P Luedi; Fred S Dietrich; Jennifer R Weidman; Jason M Bosko; Randy L Jirtle; Alexander J Hartemink Journal: Genome Res Date: 2007-11-30 Impact factor: 9.043
Authors: Thijn van der Heijden; Joke J F A van Vugt; Colin Logie; John van Noort Journal: Proc Natl Acad Sci U S A Date: 2012-08-20 Impact factor: 11.205