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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In D. melanogaster polytene chromosomes, intercalary heterochromatin (IH) appears as large dense bands scattered in euchromatin and comprises clusters of repressed genes. IH displays distinctly low gene density, indicative of their particular regulation. Genes embedded in IH replicate late in the S phase and become underreplicated. We asked whether localization and organization of these late-replicating domains is conserved in a distinct cell type. Using published comprehensive genome-wide chromatin annotation datasets (modENCODE and others), we compared IH organization in salivary gland cells and in a Kc cell line. We first established the borders of 60 IH regions on a molecular map, these regions containing underreplicated material and encompassing ∼12% of Drosophila genome. We showed that in Kc cells repressed chromatin constituted 97% of the sequences that corresponded to IH bands. This chromatin is depleted for ORC-2 binding and largely replicates late. Differences in replication timing between the cell types analyzed are local and affect only sub-regions but never whole IH bands. As a rule such differentially replicating sub-regions display open chromatin organization, which apparently results from cell-type specific gene expression of underlying genes. We conclude that repressed chromatin organization of IH is generally conserved in polytene and non-polytene cells. Yet, IH domains do not function as transcription- and replication-regulatory units, because differences in transcription and replication between cell types are not domain-wide, rather they are restricted to small “islands” embedded in these domains. IH regions can thus be defined as a special class of domains with low gene density, which have narrow temporal expression patterns, and so displaying relatively conserved organization.

Telomeres are generally considered heterochromatic. On the basis of DNA composition, the telomeric region of Drosophila melanogaster contains two distinct subdomains: a subtelomeric region of repetitive DNA, termed TAS, and a terminal array of retrotransposons, which perform the elongation function instead of telomerase. We have identified several P-element insertions into this retrotransposon array and compared expression levels of transgenes with similar integrations into TAS and euchromatic regions. In contrast to insertions in TAS, which are silenced, reporter genes in the terminal HeT-A, TAHRE, or TART retroelements did not exhibit repressed expression in comparison with the same transgene construct in euchromatin. These data, in combination with cytological studies, provide evidence that the subtelomeric TAS region exhibits features resembling heterochromatin, while the terminal retrotransposon array exhibits euchromatic characteristics. D NA sequences at the ends of eukaryotic chromosomes are the products of a telomere elongation process. In most eukaryotes, these sequences are simple repeating units that are synthesized by telomerase, but in Drosophila melanogaster they are tandem head-to-tail arrays of three non-long terminal repeat retrotransposons, HeT-A, TAHRE, and TART ( Despite these differences, a common feature of eukaryotic chromosomes is a region of complex repeats located adjacent to the terminal sequences. These complex repeats are referred to as subtelomeric regions, or telomere-associated sequences (TAS), and differ in sequence, structure, and length among species and among telomeres within an individual (Pryde et al. 1997). The repetitive nature and the high density of transposable elements in these subtelomeric regions (Mefford and Trask 2002) are reminiscent of heterochromatin. In D. melanogaster, TAS consist of several kilobases of complex repeats, which exhibit similarities between the different chromosome ends. Sequences of the 2L and X TAS regions have been described in detail (Karpen and Spradling 1992;Walter et al. 1995), and in situ hybridizations to polytene chromosomes showed that 2L TAS share homology with 3L TAS, while X TAS share homology with 2R and 3R TAS. The 2L TAS appear to be 15 kb in length and composed of relatively simple