, 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. ZhimulevEmail author
Research Article


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.


Intergenic Region Gene Density Polytene Chromosome Salivary Gland Polytene Chromosome SuUR Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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 (

Supplementary material

412_2010_280_Fig7_ESM.gif (21 kb)
Online Resource 1

The scoring function coefficients optimization using ROC curves. Relative operating characteristic (ROC) curves of gene density (a), testis-ovary expression skew (b), and intergenic regions length (c) that were used for optimization of coefficients in the resulting scoring function. Abscissa: coefficients of the scoring function. Left ordinate: number of experimentaly discovered URs (1) that were not predicted at each coefficient value (red curve). Right ordinate: number of de novo predicted regions at each coefficient value. Asterisks designate the coefficients resulting in lowest false prediction rate at the maximal prediction force (GIF 24 kb)

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 2 The 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 3 UCSC 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 4 Positions 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 5 The 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 6 The list of genes from 101 flanks as described in the text (TXT 8 kb)
412_2010_280_MOESM7_ESM.txt (14 kb)
Online Resource 7 The 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 8 The list of ovary-specific genes determined in this study using the data from Chintapalli et al. (2007); (TXT 7 kb)
412_2010_280_Fig8_ESM.gif (25 kb)
Online Resource 9

Averaged expression of genes from URs, their flanks and whole genome through the Drosophila development (a) and in 11 adult organs (b) (Chintapalli et al., 2007). Ordinates are the averaged log2 transformed expression data (GIF 21 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 10 Gene 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 11 Positions 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)


  1. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195CrossRefPubMedGoogle Scholar
  2. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP (2002) Gene expression during the life cycle of Drosophila melanogaster. Science 297:2270–2275CrossRefPubMedGoogle Scholar
  3. Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N et al (1999) An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. Genetics 153:179–219PubMedGoogle Scholar
  4. Belyaeva ES, Zhimulev IF, Volkova EI, Alekseyenko AA, Moshkin YM, Koryakov DE (1998) Su(UR)ES: a gene suppressing DNA underreplication in intercalary and pericentric heterochromatin of Drosophila melanogaster polytene chromosomes. Proc Natl Acad Sci U S A 95:7532–7537CrossRefPubMedGoogle Scholar
  5. Belyakin SN, Christophides GK, Alekseyenko AA, Kriventseva EV, Belyaeva ES, Nanayev RA, Makunin IV, Kafatos FC, Zhimulev IF (2005) Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proc Natl Acad Sci U S A 102:8269–8274CrossRefPubMedGoogle Scholar
  6. Berezney R, Dubey DD, Huberman JA (2000) Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 108:471–484CrossRefPubMedGoogle Scholar
  7. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI (2002) Large clusters of co-expressed genes in the Drosophila genome. Nature 420:666–669CrossRefPubMedGoogle Scholar
  8. Chintapalli VR, Wang J, Dow JA (2007) Using Fly Atlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39:715–720CrossRefPubMedGoogle Scholar
  9. Cimbora DM, Schubeler D, Reik A, Hamilton J, Francastel C, Epner EM, Groudine M (2000) Long-distance control of origin choice and replication timing in the human beta-globin locus are independent of the locus control region. Mol Cell Biol 20:5581–5591CrossRefPubMedGoogle Scholar
  10. Hiratani I, Gilbert DM (2009) Replication timing as an epigenetic mark. Epigenetics 4:93–97CrossRefPubMedGoogle Scholar
  11. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schubeler D, Gilbert DM (2008) Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6:e245CrossRefPubMedGoogle Scholar
  12. Huvet M, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Arneodo A, Thermes C (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res 17:1278–1285CrossRefPubMedGoogle Scholar
  13. Kalisch WE, Hagele K (1976) Correspondence of banding patterns to 3 h-thymidine labeling patterns in polytene chromosomes. Chromosoma 57:19–23CrossRefPubMedGoogle Scholar
  14. Ma H, Samarabandu J, Devdhar RS, Acharya R, Cheng PC, Meng C, Berezney R (1998) Spatial and temporal dynamics of DNA replication sites in mammalian cells. J Cell Biol 143:1415–1425CrossRefPubMedGoogle Scholar
  15. MacAlpine DM, Rodriguez HK, Bell SP (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18:3094–3105CrossRefPubMedGoogle Scholar
  16. Moshkin YM, Alekseyenko AA, Semeshin VF, Spierer A, Spierer P, Makarevich GF, Belyaeva ES, Zhimulev IF (2001) The bithorax complex of Drosophila melanogaster: Underreplication and morphology in polytene chromosomes. Proc Natl Acad Sci U S A 98:570–574CrossRefPubMedGoogle Scholar
  17. Pindyurin AV, Moorman C, de Wit E, Belyakin SN, Belyaeva ES, Christophides GK, Kafatos FC, van Steensel B, Zhimulev IF (2007) SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila. J Cell Sci 120:2344–2351CrossRefPubMedGoogle Scholar
  18. Schuebeler D, Scalzo D, Kooperberg C, van Steensel B, Delrow J, Groudine M (2002) Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet 32:438–442CrossRefGoogle Scholar
  19. Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schubeler D (2009) Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. Genes Dev 23:589–601CrossRefPubMedGoogle Scholar
  20. Shevelyov YY, Lavrov SA, Mikhaylova LM, Nurminsky ID, Kulathinal RJ, Egorova KS, Rozovsky YM, Nurminsky DI (2009) The B-type lamin is required for somatic repression of testis-specific gene clusters. Proc Natl Acad Sci U S A 106:3282–3287CrossRefPubMedGoogle Scholar
  21. Simon I, Tenzen T, Mostoslavsky R, Fibach E, Lande L, Milot E, Gribnau J, Grosveld F, Fraser P, Cedar H (2001) Developmental regulation of DNA replication timing at the human beta globin locus. EMBO J 20:6150–6157CrossRefPubMedGoogle Scholar
  22. Spellman PT, Rubin GM (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1:5CrossRefPubMedGoogle Scholar
  23. Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP (2004) Replication timing of the human genome. Hum Mol Genet 13:191–202CrossRefPubMedGoogle Scholar
  24. Zhimulev IF (1998) Polytene chromosomes, heterochromatin, and position effect variegation. Adv Genet 37:1–566CrossRefPubMedGoogle Scholar
  25. Zhimulev IF, Belyaeva ES (2003) Intercalary heterochromatin and genetic silencing. Bioessays 25:1040–1051CrossRefPubMedGoogle Scholar
  26. Zhimulev IF, Belyaeva ES, Makunin IV, Pirrotta V, Volkova EI, Alekseyenko AA, Andreyeva EN, Makarevich GF, Boldyreva LV, Nanayev RA et al (2003) Influence of the SuUR gene on intercalary heterochromatin in Drosophila melanogaster polytene chromosomes. Chromosoma 111:377–398CrossRefPubMedGoogle Scholar

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
    Email author
  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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