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

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 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

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

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

IGA score for genes covered by BLACK and YELLOW chromatin.

<p><i>X</i> axis shows the number of IGAs within OLs assigned to genes; gene counts are shown on the <i>Y</i> axis.</p

Late Replication Domains Are Evolutionary Conserved in the <i>Drosophila</i> Genome

<div><p><i>Drosophila</i> chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 <i>Drosophila</i> species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the <i>Drosophila</i> genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the <i>D. melanogaster</i> genome consistently display two-fold lower gene density across different <i>Drosophila</i> species.</p></div