Dinucleotide distribution of +1 nucleosome. Group 1 (top panels) of apoptotic [14] + 1 nucleosomes has higher AT/GC ratio than set of normal CD4⁺ cells [8].

<p>Set of CD4⁺ has phased AA, TT dinucleotides and AA-TT peak at the center of nucleosome. Group 2 is at the bottom panel. +1 nucleosome of CD4+ cells has counter phased GG and CC dinucleotide.</p

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone-7

<p><b>Copyright information:</b></p><p>Taken from "Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone"</p><p>http://www.biomedcentral.com/1472-6807/7/76</p><p>BMC Structural Biology 2007;7():76-76.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2216022.</p><p></p> vector from the anisotropic fluctuation to the crystal coordinates for the trimer as shown in the front and top view in the first slowest mode

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone-2

<p><b>Copyright information:</b></p><p>Taken from "Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone"</p><p>http://www.biomedcentral.com/1472-6807/7/76</p><p>BMC Structural Biology 2007;7():76-76.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2216022.</p><p></p>al modes. The amplitude of fluctuation is graded from black to red (i.e., from the rigid to the flexible domains, respectively). For an easy understanding, the closest view of the color coded monomeric histone tetramer of the left side nucleosome in dimer in the first global mode is shown (middle) in the subdiagram and the secondary structures of the four histones (H3, H4, H2A.Z and H2B) are labeled individually

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone-4

<p><b>Copyright information:</b></p><p>Taken from "Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone"</p><p>http://www.biomedcentral.com/1472-6807/7/76</p><p>BMC Structural Biology 2007;7():76-76.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2216022.</p><p></p>litude of fluctuation is graded the same as Figure 4

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone-8

<p><b>Copyright information:</b></p><p>Taken from "Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone"</p><p>http://www.biomedcentral.com/1472-6807/7/76</p><p>BMC Structural Biology 2007;7():76-76.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2216022.</p><p></p> vector from the anisotropic fluctuation to the crystal coordinates for the tetramer as shown in the front and right side view in the first slowest mode

Apoptotic Lymphocytes of <i>H. sapiens</i> Lose Nucleosomes in GC-Rich Promoters

<div><p>We analyzed two sets of human CD4⁺ nucleosomal DNA directly sequenced by Illumina (Solexa) high throughput sequencing method. The first set has ∼40 M sequences and was produced from the normal CD4+ T lymphocytes by micrococcal nuclease. The second set has ∼44 M sequences and was obtained from peripheral blood lymphocytes by apoptotic nucleases. The different nucleosome sets showed similar dinucleotide positioning AA/TT, GG/CC, and RR/YY (R is purine, Y - pyrimidine) patterns with periods of 10–10.4 bp. Peaks of GG/CC and AA/TT patterns were shifted by 5 bp from each other. Two types of promoters in <i>H. sapiens</i>: AT and GC-rich were identified. AT-rich promoters in apoptotic cell had +1 nucleosome shifts 50–60 bp downstream from those in normal lymphocytes. GC-rich promoters in apoptotic cells lost 80% of nucleosomes around transcription start sites as well as in total DNA. Nucleosome positioning was predicted by combination of {AA, TT}, {GG, CC}, {WW, SS} and {RR, YY} patterns. In our study we found that the combinations of {AA, TT} and {GG, CC} provide the best results and successfully mapped 33% of nucleosomes 147 bp long with precision ±15 bp (only 31/147 or 21% is expected).</p></div

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone-10

<p><b>Copyright information:</b></p><p>Taken from "Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone"</p><p>http://www.biomedcentral.com/1472-6807/7/76</p><p>BMC Structural Biology 2007;7():76-76.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2216022.</p><p></p>ond nucleosomes in dimer (I), (II) and (III) crystal structures; the amplitude of interactions follow the same color coding as Figure 2

Portion of predicted nucleosomes by two {AA, TT} and {GG, CC} patterns of human nucleosome and HMM [21].

<p>Portion of predicted nucleosomes by two {AA, TT} and {GG, CC} patterns of human nucleosome and HMM <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003760#pcbi.1003760-Xi1" target="_blank">[21]</a>.</p

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone-9

<p><b>Copyright information:</b></p><p>Taken from "Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone"</p><p>http://www.biomedcentral.com/1472-6807/7/76</p><p>BMC Structural Biology 2007;7():76-76.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2216022.</p><p></p>rst nucleosomes in dimer (I), (II) and (III) crystal structures. The uncorrelated regions (colored black) separate the correlated (where the amplitude increases from blue to red) and anti-correlated regions (colored cyan)

Dinucleotide distributions of (A) AA-TT and (B) GG-CC dinucleotides, (C) WW (adenine or thymine), and (D) SS (guanine or cytosine) around nucleosome dyad symmetry, whole sets.

<p>Apoptotic lymphocytes, data is from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003760#pcbi.1003760-Bettecken1" target="_blank">[14]</a>; CD4⁺ cells, data is from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003760#pcbi.1003760-Schones1" target="_blank">[8]</a>.</p