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

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

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

Apoptotic Lymphocytes of <i>H. sapiens - Figure 1 </i> Lose Nucleosomes in GC-Rich Promoters

<p>(<b>A</b>) <b>Distribution of nucleosomes around transcription start sites; blue line corresponds to apoptotic lymphocytes <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003760#pcbi.1003760-Bettecken1" target="_blank">[14]</a>; black line corresponds to normal CD4⁺ cells <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003760#pcbi.1003760-Schones1" target="_blank">[8]</a>.</b> (<b>B</b>) Distribution of nucleosomes around transcription start sites; 32,038 promoters were divided into two groups by nucleosome occupancy in apoptotic lymphocytes <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003760#pcbi.1003760-Bettecken1" target="_blank">[14]</a>, K-means clustering method: blue line corresponds to the first group of 16670 promoters with normal occurrence (one nucleosome per 250 bp) of nucleosomes; black line corresponds to the second group of 15368 promoters with low occurrence (one nucleosome per 1000 bp) of nucleosomes around TSS. (<b>C</b>) Distribution of nucleosomes around transcription start sites. Blue and red lines correspond to promoters of the first group with normal occupancy of nucleosomes, apoptotic lymphocytes and CD4⁺ cells respectively. These promoters have the similar average occupancy of nucleosomes, position of +1 nucleosome from set of apoptotic lymphocytes <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003760#pcbi.1003760-Bettecken1" target="_blank">[14]</a> is shifted 50–60 bp downstream. Black and orange lines correspond to promoters with low occupancy of nucleosomes during apoptosis, apoptotic lymphocytes and normal CD4+ cells respectively. These promoters lost 80% of nucleosomes around TSS during apoptosis.</p

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

Nucleosome occurrence per promoter (±1000 bp around TSS).

<p>Nucleosome occurrence per promoter (±1000 bp around TSS).</p

Curvature distributions of big AT-rich mesophilic genomes in the neighborhood of the end of translation

<p><b>Copyright information:</b></p><p>Taken from "Involvement of DNA curvature in intergenic regions of prokaryotes"</p><p>Nucleic Acids Research 2006;34(8):2316-2327.</p><p>Published online 5 May 2006</p><p>PMCID:PMC1458280.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> and are representative of the group of mesophilic genomes with A+T composition over 50% in their non-coding regions and with genome size over 1.4 million bp. For each genome the sets of regions ±400 bases in length around the end of translation were compiled. Also, only genes longer than 125 nt and flanked by downstream intergenic regions longer than 125 nt were processed. The program CURVATURE with a window size of 125 nt was used to predict curvature distributions. () The -axis represents the DNA curvature measured in curvature units (0.08/0.16 cu) and the -axis represents the position around the end of translation. The red line represents a profile obtained by averaging the distributions of all fragments from the same genome. The SEs were estimated by the bootstrap method using 1000 runs. For better visibility, error bars corresponding to several distances around the 3′ end, are shown separately from the curvature maps. The dashed lines represent curvature distributions obtained by averaging the distribution of analogous shuffled fragments as explained in Methods. () The -axis represents the curvature excess in standard deviation units (−4/13 SD). Curvature excess was obtained by estimation apparent deviation between genomic and random curvature values. () The 3D trajectories of DNA in terminator regions of chosen convergent genes are shown. Arrows indicate the positions of the stop codons. The coding strands are colored in green and the complementary strand in blue. In the region of the hairpin terminator predicted by Mfold program, the two strands of DNA were colored in red

Curvature distributions in the neighborhood of the end of translation in convergent genes

<p><b>Copyright information:</b></p><p>Taken from "Involvement of DNA curvature in intergenic regions of prokaryotes"</p><p>Nucleic Acids Research 2006;34(8):2316-2327.</p><p>Published online 5 May 2006</p><p>PMCID:PMC1458280.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> From 15 selected genomes, which had relatively high curvature excess (DIE), only convergent genes were extracted. The program CURVATURE with a window size of 125 nt was used to predict curvature distributions. Only genes with intergenic region longer than 50 nt were processed. (781 genes), (543 genes), (578 genes), (488 genes), (632 genes), (327 genes), (290 genes), (301 genes), (755 genes), (534 genes), (277 genes), (626 genes), (778 genes), chromosome I (781 genes) and chromosome I (477 genes). DNA curvature calculations for the real and reshuffled convergent genes of every genome were performed as described in the legend to

Curvature distributions of hyperthermophilic archaea and bacteria in the neighborhood of the end of translation

<p><b>Copyright information:</b></p><p>Taken from "Involvement of DNA curvature in intergenic regions of prokaryotes"</p><p>Nucleic Acids Research 2006;34(8):2316-2327.</p><p>Published online 5 May 2006</p><p>PMCID:PMC1458280.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> and were representative of the group of hyperthermophilic genomes. DNA curvature calculations for the real and the reshuffled genomes were performed as described in the legend to . () The -axis represents the DNA curvature measured in curvature units (0.07/0.13 cu) and the -axis represents the position around the end of translation. () The -axis represents the curvature excess in SD units (−4/13 SD). Curvature excess was obtained by estimation apparent deviation between genomic and random curvature values. () The 3D trajectories of DNA in terminator region of chosen genes are shown. Arrows indicate the positions of the stop codons. The coding strands are colored in green and the complementary strand in blue. In the region of the hairpin terminator predicted by Mfold program, the two strands of DNA were colored in red