Physical map and molecular features of the band 59D1-2.

<p>Vertical lines delimit the borders of this IH band. Data on protein profiling and replication timing are from: (1) – Belyakin et al., 2005 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Belyakin1" target="_blank">[14]</a>; (2) – Kharchenko et al., 2011 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Kharchenko1" target="_blank">[30]</a>; (3) –Filion et al., 2010 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Filion1" target="_blank">[32]</a>; (4) – Belyakin et al., 2010 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Belyakin2" target="_blank">[15]</a>; (5) – Kharchenko et al., 2011 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Kharchenko1" target="_blank">[30]</a>; (6) – MacAlpine et al., 2010 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-MacAlpine2" target="_blank">[29]</a>; (6)* - Eaton et al., 2011 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Eaton1" target="_blank">[37]</a>; (7) – Nordman et al., 2011 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Nordman1" target="_blank">[31]</a>; [8] – Schwaiger et al., 2009 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Schwaiger1" target="_blank">[22]</a>.</p

Physical map and molecular features of the region 79E1-4.

<p>Legends are the same as on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone-0030035-g001" target="_blank">Fig. 1</a>. IH band has an early-replicating region, which corresponds to two active (RED) fragments.</p

Correlation of sizes of open chromatin (RED and YELLOW) fragments with the length of early replication areas.

<p>Correlation of sizes of open chromatin (RED and YELLOW) fragments with the length of early replication areas.</p

DNA replication in 10A-11A region of the polytene chromosome.

<p><b>A–C</b> – Immunostaining for pre-replication complex component DUP/CDF1. Pre-replication complex is not detected in IH bands 10A1-2, 10B1-2, 11A6-9. <b>A</b> – phase contrast; <b>B</b> – immunolocalization; <b>C</b>- merge; <b>D–G</b> – immunostaining for PCNA at consecutive replication steps (further description in text).</p

Nomenclature, sizes of IH regions and overlapping with LADs.

<p>*% overlap was calculated as a ratio between the length of overlapping region and the length of IH band.</p

Proportion of various chromatin types in IH regions.

<p><b>A</b> – 5 color chromatin types by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Filion1" target="_blank">[32]</a>. <b>B</b> – 9 chromatin states as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone.0030035-Kharchenko1" target="_blank">[30]</a> (states 6–9 correspond to repressed chromatin).</p

Proportion of the DNA sequences covered by the corresponding proteins (%).

<p>Proportion of the DNA sequences covered by the corresponding proteins (%).</p

Physical map and molecular features of the region 12E.

<p>Legends are the same as on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030035#pone-0030035-g001" target="_blank">Figure 1</a>. The region consists of two bands, 12E1-2 (left) and 12E8-9 (right).</p

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