NPRD: Nucleosome Positioning Region Database

Nucleosome Positioning Region Database (NPRD), which is compiling the available experimental data on locations and characteristics of nucleosome formation sites (NFSs), is the first curated NFS-oriented database. The object of the database is a single NFS described in an individual entry. When annotating results of NFS experimental mapping, we pay special attention to several important functional characteristics, such as the relationship between type of gene activity and nucleosome positioning, the influence of non-histone proteins on nucleosome formation, type of the variant of nucleosome positioning (translational or rotational), indication of tissue types and states of cell activity, description of experimental methods used and accuracy of nucleosome position determination, and the results of applying theoretical and computer methods to the analysis of contextual and conformational DNA properties. At present, the NPRD database contains 438 entries and integrates the data described in 124 original papers. The database URL: http://srs6.bionet.nsc.ru/srs6/. Then click the button ‘Databank’ and open the link NUCLEOSOME.

[1]  Claes Wahlestedt,et al.  NotI flanking sequences: a tool for gene discovery and verification of the human genome. , 2002, Nucleic acids research.

[2]  Victor G. Levitsky,et al.  RECON: a program for prediction of nucleosome formation potential , 2004, Nucleic Acids Res..

[3]  I. Talianidis,et al.  Dynamics of enhancer-promoter communication during differentiation-induced gene activation. , 2002, Molecular cell.

[4]  R. Kingston,et al.  What does 'chromatin remodeling' mean? , 2000, Trends in biochemical sciences.

[5]  E. Trifonov,et al.  Nucleosomal DNA sequence database. , 1993, Nucleic acids research.

[6]  Victor G. Levitsky,et al.  Nucleosome formation potential of exons, introns, and Alu repeats , 2001, Bioinform..

[7]  J. Widom.  Structure, dynamics, and function of chromatin in vitro. , 1998, Annual review of biophysics and biomolecular structure.

[8]  E. Trifonov.  [Genetic level of DNA sequences is determined by superposition of many codes]. , 1997, Молекулярная биология.

[9]  Alexander E. Kel,et al.  Transcription Regulatory Regions Database (TRRD): its status in 1999 , 1999, Nucleic Acids Res..

[10]  R. Kornberg,et al.  Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome , 1999, Cell.

[11]  Andrey N. Naumochkin,et al.  Transcription Regulatory Regions Database (TRRD): its status in 2002 , 2002, Nucleic Acids Res..

[12]  Victor G. Levitsky,et al.  Nucleosomal DNA property database , 1999, Bioinform..

[13]  Victor G. Levitsky,et al.  Nucleosomal DNA Organization: An Integrated Information System , 2004 .

[14]  Podkolodnyĭ Nl,et al.  [Locus-controlling regions: description in the LCR-TRRD data base]. , 2001 .

[15]  Victor G. Levitsky,et al.  Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis , 2001, Bioinform..

[16]  P. Becker.  Nucleosome sliding: facts and fiction , 2002, The EMBO journal.