Table 1.
Summary of aligned GSE54263 original sequences from [19] and total counts of RefSeq genes and sequences of first well phased nucleosome within 1000bp downstream of mm9 Refseq gene TSS.
Fig 1.
Similarities between dinucleotide patterns in nucleosomal DNA in mouse and human cells.
For each composite (WW, SS, RR, YY) and individual (AA, TT, CC, GG) dinucleotide a similarity between the patterns in human CD4+ cells as cd4, human apoptotic lymphocyte cells as apo and NAC cells of mouse brains in control as con, stress-resilient as res and stress-susceptible as sus is shown. The similarity is quantized by a Pearson correlation coefficient a magnitude of which is shown in each cell of correlation matrix. Two representations of similarity are depicted for each dinucleotide: a heatmap in which color-coded cells show a Pearson correlation coefficient between two profles and color provides a direction—red is positive, blue is negative. The similarity dendrograms are computed from the correlation matrix shown in heat map and illustrate hierarchical complete linkage clustering of the patterns.
Fig 2.
Distribution of WW/SS and RR/YY peaks in human, mouse and yeast.
The ladder diagrams represent half of nucleosome with a dyad position at the bottom and proceeding up from -1 base pair position to the -72 base pair. The positions corresponding to the major grooves are shown in red and the minor are blue (as in cartoon of Fig. 3 in [10] labeled by SHL numbers). The WW peaks are coded in green, the SS in red, the RR are coded in magenta shades and YY in orange shades. Each indicated peak inside the cell is labeled by a letter indicating which organism it belongs to (H- for human CD4+ cells, M- for NAC of control mouse, Y yeast and A for human apoptotic lymphocyte cells). The SS1/WW1 and RR1/YY1 diagrams show the peak distributions in human and mouse. The SS2/WW2 and RR2/YY2 diagrams show peak distributions in yeast and human apoptotic cells. The numbers 1 and 2 designate these separate pattern classes. The ladder diagrams illustrate a synchronization between the peak occurrences. The WW peaks in human and mouse have SS peak counterparts in yeast and apoptotic cells and vice versa. The RR1/YY1 patterns appear to be very regular. The RR2/YY2 has less regular appearance in which peaks are mostly concentrated in SHL zones ±2.5, ±3.5 and ±4.5.
Fig 3.
Comparison of peak counts across SHL zones in human and mouse.
The bars show number of counts of peak sites across SHL in human CD4+ and apoptotic lymphocyte cells compared to the counts in mouse NAC in control, susceptible and resilient to stress mice.
Table 2.
Proportions of patterns best mapping the nucleosomes in nucleosome occupancy change locations in promoters and gene body in stress-susceptible and stress-resilient mice.