Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5′ ends of housekeeping genes. As a rule, interbands display preferential “head-to-head” orientation of genes. They are enriched for “broad” class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5′-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called “grey” bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.

IntroductionTelomeres are specialized DNA-protein complexes that cap the termini of linear chromosomes. They compensate for incomplete DNA replication and contribute to the stability of chromosomes and karyotype (Muller, 1932;Pardue and Debaryshe, 1999;Biessmann and Mason, 2003). Telomeres also participate in nuclear architecture maintenance, and are known to associate with nuclear lamina (Hochstrasser et al., 1986;Marshall et al., 1996;Hari et al., 2001) or with nuclear matrix (de Lange, 1992;Luderus et al., 1996). However, the factors that underlie these phenomena, as well as the mechanisms of telomere functioning, remain poorly understood in Drosophila melanogaster.In eukaryotes, such as budding yeast, fission yeast and humans, telomeres are considered to be essentially heterochromatic (Perrod and Gasser, 2003). Heterochromatin is characterized by a high degree of DNA compaction, late replication in S phase, and by association with specific silencing proteins (Richards and Elgin, 2002). Intercalary (IH) and pericentric heterochromatin regions in many Diptera species are characterized by DNA underreplication and nonhomologous (ectopic) pairing of chromosomal regions in polytene chromosomes (Zhimulev, 1998). The question whether D. melanogaster telomeres are heterochromatic in

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The structural and functional analyses of heterochromatin are essential to understanding how heterochromatic genes are regulated and how centromeric chromatin is formed. Because the repetitive nature of heterochromatin hampers its genome analysis, new approaches need to be developed. Here, we describe how, in double mutants for Su(var)3-9 and SuUR genes encoding two structural proteins of heterochromatin, new banded heterochromatic segments appear in all polytene chromosomes due to the strong suppression of under-replication in pericentric regions. FISH on salivary gland polytene chromosomes from these double mutant larvae allows high resolution of heterochromatin mapping. In addition, immunostaining experiments with a set of antibodies against euchromatic and heterochromatic proteins reveal their unusual combinations in the newly appeared segments: binding patterns for HP1 and HP2 are coincident, but both are distinct from H3diMetK9 and H4triMetK20. In several regions, partial overlapping staining is observed for the proteins characteristic of active chromatin RNA Pol II, H3triMetK4, Z4, and JIL1, the boundary protein BEAF, and the heterochromatin-enriched proteins HP1, HP2, and SU(VAR)3-7. The exact cytological position of the centromere of chromosome 3 was visualized on salivary gland polytene chromosomes by using the centromeric dodeca satellite and the centromeric protein CID. This region is enriched in H3diMetK9 and H4triMetK20 but is devoid of other proteins analyzed.Drosophila melanogaster ͉ genome analysis

SummaryInteraction between the Drosophila heterochromatin proteins SUUR and HP1