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

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

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

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

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

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

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

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

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