Gene density profile reveals the marking of late replicated domains in the Drosophila melanogaster genome
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Regulation of replication timing has been a focus of many studies. It has been shown that numerous chromosomal regions switch their replication timing on cell differentiation in Drosophila and mice. However, it is not clear which features of these regions are essential for such regulation. In this study, we examined the organization of late underreplicated regions (URs) of the Drosophila melanogaster genome. When compared with their flanks, these regions showed decreased gene density. A detailed view revealed that these regions originate from unusual combination of short genes and long intergenic spacers. Furthermore, gene expression study showed that this pattern is mostly contributed by short testis-specific genes abundant in the URs. Based on these observations, we developed a genome scanning algorithm and identified 110 regions possessing similar gene density and transcriptional profiles. According to the published data, replication of these regions has been significantly shifted towards late S-phase in two Drosophila cell lines and in polytene chromosomes. Our results suggest that genomic organization of the underreplicated areas of Drosophila polytene chromosomes may be associated with the regulation of their replication timing.
KeywordsIntergenic Region Gene Density Polytene Chromosome Salivary Gland Polytene Chromosome SuUR Gene
We thank Dr. Gareth Lycett and Dr. Igor Makunin for the discussion of the results and critical reading of the manuscript. The microarray slides were received through DGRC. This work was supported by Russian Foundation for Basic Research (Grant No. 08-04-01105a to S.N.B. and V.V.S.), Program of Presidium of Russian Academy of Sciences “Molecular and Cellular Biology” (Grant No. 22.4), and Interdisciplinary Integration Project of Siberian Branch of Russian Academy of Sciences (Grant No. 37) and Science Schools (Grant No. 5104.2008.4.). The manuscript was edited for proper English language by SPi Technologies, Inc (www.prof-editing.com).
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