Accession numbers of chromosome proteins.

<p>*modENCODE data used (<a href="http://www.modencode.org/Genomes.shtml" target="_blank">http://www.modencode.org/Genomes.shtml</a>).</p><p>**GEO data used (<a href="http://www.ncbi.nlm.nih.gov/gds/" target="_blank">http://www.ncbi.nlm.nih.gov/gds/</a>).</p

Localization of proteins and DNA elements in 9F13 – 10B3 region of nonpolytene chromosomes (according to data of modENCODE).

<p>The positions of proteins were located as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#s4" target="_blank">Material and Methods</a>. <b>A</b> - physical map of DNA; positions of <i>v</i> and <i>sev</i> genes are taken from FlyBase, arrows 1–4 indicate position of probes for FISH on physical map. <b>B</b> - <i>P</i>-elements density in the region calculated as number of insertions per 1 kb in 10 kb interval (data on insertions are taken from FlyBase) <b>C</b> - interband specific and active chromatin specific proteins in S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48]</a>, <b>D</b> - DNase I hypersensitivity sites (DHS) in S2, BG3 and Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48] </a><b>E</b> - ORC2-binding sites in S2, BG3 and Kc cultural and salivary gland cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Eaton1" target="_blank">[59] </a><b>F</b> - histone H1 dips localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Braunschweig1" target="_blank">[45] </a><b>G</b> - histone H3.3 localization in S2 cells (modENCODE, Henikoff group) <b>H</b> - 30 chromatin states in BG3 and S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48]</a>, and 5 chromatin types in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47] </a><b>I</b> - nucleosome turnover dynamics in S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Deal1" target="_blank">[60]</a>, <b>J</b> - D1 localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47]</a>, <b>K</b> - SUUR localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47]</a>, <b>L</b> - Lamin localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47] </a><b>M</b> - early (up) and late (down) replication in S2, Kc and BG3 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Schwaiger1" target="_blank">[61] </a><b>N</b> - gene density (number of genes per 10 kb of DNA) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Belyakin2" target="_blank">[54]</a>.</p

DNA compaction ratio of the bands in the 9F13 -10B3 region.

a<p>– estimated on electron microscope sections of 50 polytene chromosomes.</p><p>Notes: IB-interband; B-band.</p><p>Data of release FB2011_03 were used.</p

Comparison of extents of band/interbands in polytene chromosomes according to Flybase r5.25 (A, B) and to the data of this study (C).

<p>Physical DNA map is situated between 10792800 and 11220400 positions of the map of Flybase.</p

Relation of genetic map, and band/interband pattern in the region 9F13 – 10B3.

<p><b>A</b> - predicted bands <b>B</b> - FlyBase genes <b>C</b> – 30 chromatin states in BG3 and S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48] </a><b>D</b> - DNase I hypersensitivity sites (DHS) in S2, BG3 and Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48] </a><b>E</b> - ORC-binding sites in S2, BG3 and Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Eaton1" target="_blank">[59] </a><b>F</b> – Nucleosome Density (modENCODE, Henikoff group) <b>G</b> - active chromatin specific <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48]</a> and - interbands specific proteins. Predicted interbands (dotted vertical lines are according to peaks in distribution of corresponding elements, solid lines reflect the edges of distributions of different characteristics).</p

Colocalization of DNA probes limiting the band 10B1–2, and Chriz/CHRO protein.

<p>Banding pattern in the region 10A–B (DAPI) (<b>A</b>), immunostaining of Chriz/CHRO and FISH of the DNA probe (<b>A</b>), immunostaining of Chriz/CHRO, FISH of the DNA probe and DAPI (<b>C</b>). Bar represents 5 µm.</p

Localization in polytene chromosomes of DNA fragments, which according to modEncode data are located in the predicted interbands flanking the 10A1–2 and 10B1–2 bands of the nonpolytene chromosomes.

<p>Banding pattern in the region under phase contrast microscope (<b>A, D</b>), pairwise FISH mapping of DNA fragments, limiting the bands 10A1–2 (probes CG15208 and Vago) (<b>B, C</b>) and 10B1–2 (CG32668 and l(1)10Bb) (<b>E, F</b>).</p

Comparison of several Electron Microscope sections of the region 9F11-12 – 10B (A, B) with revised Bridges map

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Bridges1" target="_blank">[<b>56</b>] </a><b>(C).</b> Vertical lines connect homologous bands. Scale represents 1 µm.</p

Coordinates and sizes of bands and interbands on physical map of the 9F13 – 10B3 region.

<p>Notes: IB-interband; B-band.</p><p>Data of release FB2011_03 were used.</p

Coordinates and descriptions of probes, selected for FISH mapping on polytene chromosomes in the region 9F13 – 10B3 (coordinates correspond to the version dm3 (r5.24), FlyBase).

<p>Coordinates and descriptions of probes, selected for FISH mapping on polytene chromosomes in the region 9F13 – 10B3 (coordinates correspond to the version dm3 (r5.24), FlyBase).</p