title: Human repetitive sequence densities are mostly negatively correlated with R/Y-based nucleosome-positioning motifs and positively correlated with W/S-based motifs.
abstract: We examined statistical correlations between the frequencies of seven proposed nucleosome positioning motifs and the densities of repetitive sequences in the human genome. For both parametric and non-parametric measures of statistical correlations there is a tendency for repetitive sequence density to be negatively correlated with the density of R/Y-based nucleosome positioning motifs, while being positively correlated with that of W/S-based motifs. These results largely hold even when motifs are examined only within repeat-filtered sequences. The RRRRRYYYYY motif and its 5-base shift YYYYYRRRRR, in particular, is over-represented in the human genome; and its negative correlation is consistently present at different regions and at different length scales. For some other nucleosome positioning motifs, the relationship with repeats can be regional or length scale dependent. Considering the importance of nucleosome formation in epigenetic regulations, these results may provide new insight to the evolution of repetitive sequences.
authors.affiliation: The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, 350 Community Drive, NY 11030, USA. Electronic address: wtli2012@gmail.com.
authors.forename: Wentian
authors.initials: W
authors.lastname: Li
authors.affiliation: Facultad de Ciencias, Universidad Nacional Autónoma de México, México 04510 DF, Mexico; Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México 04510 DF, Mexico.
authors.forename: Daniela
authors.initials: D
authors.lastname: Sosa
authors.affiliation: Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apdo Postal 70228, México 04510 DF, Mexico.
authors.forename: Marco V
authors.initials: MV
authors.lastname: Jose
mesh_terms: D002890:Chromosomes, Human, Pair 20; D015894:Genome, Human; D006801:Humans; D009707:Nucleosomes / Q000235:genetics*; D059372:Nucleotide Motifs; D012091:Repetitive Sequences, Nucleic Acid; D058067:Wavelet Analysis
chemical_list: D009707:Nucleosomes