Abstract
Nucleosome positioning DNA sequence patterns (NPS)—usually distributions of particular dinucleotides or other sequence elements in nucleosomal DNA—at least partially determine chromatin structure and arrangements of nucleosomes that in turn affect gene expression. Statistically, NPS are defined as oscillations of the dinucleotide periodicity of about 10 base pairs (bp) which reflects the double helix period. We compared the nucleosomal DNA patterns in mouse, human and yeast organisms and observed few distinctive patterns that can be termed as packing and regulatory referring to distinctive modes of chromatin function. For the first time the NPS patterns in nucleus accumbens cells (NAC) in mouse brain were characterized and compared to the patterns in human CD4+ and apoptotic lymphocyte cells and well studied patterns in yeast. The NPS patterns in human CD4+ cells and mouse brain cells had very high positive correlation. However, there was no correlation between them and patterns in human apoptotic lymphocyte cells and yeast, but the latter two were highly correlated with each other. By their dinucleotide arrangements the analyzed NPS patterns classified into stable canonical WW/SS (W = A or T and S = C or G dinucleotide) and less stable RR/YY (R = A or G and Y = C or T dinucleotide) patterns and anti-patterns. In the anti-patterns positioning of the dinucleotides is flipped compared to those in the regular patterns. Stable canonical WW/SS patterns and anti-patterns are ubiquitously observed in many organisms and they had high resemblance between yeast and human apoptotic cells. Less stable RR/YY patterns had higher positive correlation between mouse and normal human cells. Our analysis and evidence from scientific literature lead to idea that various distinct patterns in nucleosomal DNA can be related to the two roles of the chromatin: packing (WW/SS) and regulatory (RR/YY and “anti”).
Highlights
Nucleosomes bring order to eukaryote genome and serve three primary functions [1]: provide measures of packaging and stabilize negative super coiling of DNA in vivo; provide epigenetic layer of information guiding interactions of trans-acting proteins with the genome through their histone modification; directly regulate access to the functional elements of the genome by their positioning
We investigated patterns formed by WW/SS and RR/YY pairs of dinucleotides and individual AA/TT/TA and CC/GG dinucleotides which carry nucleosome positioning signals by their periodical arrangements
How the patterns compare in mouse brain nucleus accumbens cells (NAC), human CD4+ and apoptotic cells is shown in Section 1 Figures 1-5 in S2 Appendix
Summary
Nucleosomes bring order to eukaryote genome and serve three primary functions [1]: provide measures of packaging and stabilize negative super coiling of DNA in vivo; provide epigenetic layer of information guiding interactions of trans-acting proteins with the genome through their histone modification; directly regulate access to the functional elements of the genome by their positioning. Nucleosomes have inhibitory effects on transcription by reducing access of transcription machinery to genomic DNA. Positioning and occupancy of nucleosomes contribute to the heterogeneity and flexibility of gene expression [2] and take part in chromatin activity. Biological consequences of nucleosome positioning and occupancy vary between cell types and conditions [3]. It is thought that certain numbers of nucleosomes [5] in genomes are positioned by a preference of some DNA sequence patterns over the other
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call