Chromosoma

, Volume 119, Issue 6, pp 589–600 | Cite as

Gene density profile reveals the marking of late replicated domains in the Drosophila melanogaster genome

  • Stepan N. Belyakin
  • Vladimir N. Babenko
  • Daniil A. Maksimov
  • Viktor V. Shloma
  • Evgeny Z. Kvon
  • Elena S. Belyaeva
  • Igor F. Zhimulev
Research Article

Abstract

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.

Supplementary material

412_2010_280_MOESM1_ESM.eps (856 kb)
High resolution image file (EPS 1,089 kb)
412_2010_280_MOESM2_ESM.xls (24 kb)
Online Resource 2The list of oligos used in the standard curve assay to estimate polytenization in the predicted regions in salivary glands. Cytological names of the regions and target genes are presented (XLS 24 kb)
412_2010_280_MOESM3_ESM.txt (623 kb)
Online Resource 3UCSC track for the whole genome polytenization profile in polytene chromosomes adapted from Belyakin et al. (2005). The track represents normalized data obtained from the large scale microarray analysis of under-replication in Drosophila melanogaster genome published in Belyakin et al., 2005. Each point represents a ratio of DNA representation in salivary glands in 4xSuUR strain where the under-replication is enhanced due to additional copies of the SuUR functional allele and in SuUR mutant strain where the under-replication is suppressed (TXT 622 kb)
412_2010_280_MOESM4_ESM.txt (2 kb)
Online Resource 4Positions of 51 UR regions formatted for UCSC genome browser. The track demarcates 51 sample UR regions (excluded is 39D histone cluster) resulted from the large-scale microarray analysis of underreplication in Drosophila melanogaster genome published in (Belyakin et al., 2005) (TXT 1 kb)
412_2010_280_MOESM5_ESM.txt (10 kb)
Online Resource 5The list of genes from 51 sample URs adapted from Belyakin et al. (2005); (TXT 9 kb)
412_2010_280_MOESM6_ESM.txt (9 kb)
Online Resource 6The list of genes from 101 flanks as described in the text (TXT 8 kb)
412_2010_280_MOESM7_ESM.txt (14 kb)
Online Resource 7The list of testis-specific genes determined in this study using the data from Chintapalli et al. (2007); (TXT 14 kb)
412_2010_280_MOESM8_ESM.txt (7 kb)
Online Resource 8The list of ovary-specific genes determined in this study using the data from Chintapalli et al. (2007); (TXT 7 kb)
412_2010_280_MOESM9_ESM.eps (1.1 mb)
High resolution image file (EPS 855 kb)
412_2010_280_MOESM10_ESM.txt (161 kb)
Online Resource 10Gene density through the Drosophila genome. The UCSC track depicts the number of gene starts within the non-overlapping windows of 100 kb in length and 10 kb shift with the subsequent averaging over the 5 neighbor values based on the Flybase 5.12 genome annotation (dm3); (TXT 160 kb)
412_2010_280_MOESM11_ESM.txt (3 kb)
Online Resource 11Positions of 110 predicted regions formatted for UCSC genome browser. The track demarcates 110 predicted regions resulted from the genome scan performed in this study (TXT 2 kb)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Stepan N. Belyakin
    • 1
  • Vladimir N. Babenko
    • 2
  • Daniil A. Maksimov
    • 1
  • Viktor V. Shloma
    • 1
  • Evgeny Z. Kvon
    • 2
    • 3
  • Elena S. Belyaeva
    • 1
  • Igor F. Zhimulev
    • 1
  1. 1.Department of Molecular and Cellular BiologyInstitute of Chemical Biology and Fundamental Medicine SD RASNovosibirskRussia
  2. 2.Institute of Cytology and Genetics SD RASNovosibirskRussia
  3. 3.Research Institute of Molecular PathologyViennaAustria

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