Advertisement

Chromosoma

, Volume 123, Issue 3, pp 253–264 | Cite as

Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster

  • Daniil A. Maksimov
  • Dmitry E. Koryakov
  • Stepan N. BelyakinEmail author
Research Article

Abstract

Eukaryotic genomes are organized in large chromatin domains that maintain proper gene activity in the cell. These domains may be permissive or repressive to the transcription of underlying genes. Based on its protein makeup, chromatin in Drosophila cell culture has been recently categorized into five color-coded states. Suppressor of Under-Replication (SUUR) protein was found to be the major component present in all three repressive chromatin states named BLACK, BLUE, and GREEN and to be depleted from the active YELLOW and RED chromatin types. Here, we addressed the question of developmental dynamics of SUUR binding as a marker of repressed chromatin types. We established genomewide SUUR binding profiles in larval salivary gland, brain, and embryos using DNA adenine methyltransferase identification (DamID) technique, performed their pairwise comparisons and comparisons with the published data from Drosophila Kc cells. SUUR binding pattern was found to vary between the samples. Increase in SUUR binding predominantly correlated with local gene repression suggesting heterochromatin formation. Reduction in SUUR binding often coincided with activation of tissue-specific genes probably reflecting the transition to permissive chromatin state and increase in accessibility to specific transcription factors. SUUR binding plasticity accompanied by the regulation of the underlying genes was mainly observed in BLACK, BLUE, and RED chromatin types. Our results provide novel insight into the developmental dynamics of repressive chromatin and reveal a link to the chromatin-guided regulation of gene expression.

Keywords

Salivary Gland Polytene Chromosome Repressive Chromatin Larval Salivary Gland Chromatin Type 
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.

Notes

Acknowledgments

We thank Dr. Tim Westwood and Canadian Drosophila Microarray Center who performed microarray hybridizations and Dr. Bas van Steensel for Dam-containing vectors. The datasets for this paper have been deposited at NCBI under the reference series GSE33873. The work was supported by the Russian Foundation for Basic Research grants 12-04-00160, 12-04-33080, and 12-01-31128 and by the Program of Presidium of the Russian Academy of Sciences “Molecular and Cellular Biology” (grant no. 6.3).

Supplementary material

412_2013_445_Fig6_ESM.jpg (70 kb)
Supplementary Figure 1

hsp70 promoter from pUAST vector ensures a very low level of Dam-Myc expression. Western blot detection of Dam-Myc protein with the anti-Myc-tag antibodies in salivary glands of y,w strain (negative control, first lane), hsp70 > Dam-Myc strain (second lane) and in hsp70 > Dam-Myc strain induced with salivary gland-specific AB1 Gal4 driver (positive control, third lane). anti-Tubuline antibodies were used as a load control. Asterisk shows a non-specific band appearing due to over-exposure of the membrane. (JPEG 69 kb)

412_2013_445_MOESM1_ESM.eps (454 kb)
High Resolution Image (EPS 454 kb)
412_2013_445_Fig7_ESM.jpg (751 kb)
Supplementary Figure 2

Effect of data normalization. A – distribution of the raw DamID data in the four samples. B – the same after the normalization step. Scale – Log2(Dam-Myc-SUUR/Dam-Myc). C – K-means clustering of the normalized data in the four samples reveals a substantial variation of SUUR binding in different cell types. (JPEG 750 kb)

412_2013_445_MOESM2_ESM.eps (1.4 mb)
High Resolution Image (EPS 1465 kb)
412_2013_445_Fig8_ESM.jpg (497 kb)
Supplementary Figure 3

Examples of SUUR profile variability in different biological samples. The colors and legends are the same as on the Fig. 1. (JPEG 496 kb)

412_2013_445_MOESM3_ESM.eps (4.2 mb)
High Resolution Image (EPS 4302 kb)
412_2013_445_Fig9_ESM.jpg (582 kb)
Supplementary Figure 4

Correlation of SUUR binding dynamics and gene activity in six pairs of samples. The legend is the same as in Fig. 3c. (JPEG 581 kb)

412_2013_445_MOESM4_ESM.eps (2.3 mb)
High Resolution Image (EPS 2377 kb)
412_2013_445_Fig10_ESM.jpg (458 kb)
Supplementary Figure 5

Variability of SUUR binding near the borders and towards the centers of domains in different chromatin types. Portions of differentially bound genes in 1 kb bins starting from the borders of the domains of different types are presented. No differences from the distributions presented in the Fig.  5a were found indicating that observed variation of SUUR binding is not a bias stemming from the domain borders. (JPEG 457 kb)

412_2013_445_MOESM5_ESM.eps (937 kb)
High Resolution Image (EPS 936 kb)
412_2013_445_Fig11_ESM.jpg (228 kb)
Supplementary Figure 6

A test study of H3K36me3 variability between Kc cells and 0-12h embryos. A – distribution of H3K36me3 histone mark across five chromatin types. B – variability of H3K36me3 levels in five chromatin types assessed with the same analytic tools as for SUUR. GREEN chromatin tends to loose H3K36me3 in embryos while BLUE chromatin accumulates H3K36me3. Other chromatin types do not follow this pattern. This picture is strikingly different from the observed variability of SUUR (Fig.  5a). (JPEG 227 kb)

412_2013_445_MOESM6_ESM.eps (586 kb)
High Resolution Image (EPS 585 kb)
412_2013_445_MOESM7_ESM.xls (2.3 mb)
Supplementary Table 1 (XLS 2334 kb)
412_2013_445_MOESM8_ESM.xls (34 kb)
Supplementary Table 2 (XLS 34 kb)
412_2013_445_MOESM9_ESM.xls (42 kb)
Supplementary Table 3 (XLS 42 kb)
412_2013_445_MOESM10_ESM.xls (149 kb)
Supplementary Table 4 (XLS 149 kb)
412_2013_445_MOESM11_ESM.xls (117 kb)
Supplementary Table 5 (XLS 117 kb)

References

  1. Bell O, Schwaiger M, Oakeley EJ, Lienert F, Beisel C, Stadler MB, Schubeler D (2010) Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. Nat Struct Mol Biol 17(7):894–900. doi: 10.1038/nsmb.1825 PubMedCrossRefGoogle Scholar
  2. 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(13):7532–7537PubMedCentralPubMedCrossRefGoogle Scholar
  3. Belyaeva ES, Boldyreva LV, Volkova EI, Nanayev RA, Alekseyenko AA, Zhimulev IF (2003) Effect of the suppressor of underreplication (SuUR) gene on position-effect variegation silencing in Drosophila melanogaster. Genetics 165(3):1209–1220PubMedCentralPubMedGoogle Scholar
  4. 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(23):8269–8274PubMedCentralPubMedCrossRefGoogle Scholar
  5. Belyakin SN, Babenko VN, Maksimov DA, Shloma VV, Kvon EZ, Belyaeva ES, Zhimulev IF (2010) Gene density profile reveals the marking of late replicated domains in the Drosophila melanogaster genome. Chromosoma 119(6):589–600. doi: 10.1007/s00412-010-0280-y PubMedCrossRefGoogle Scholar
  6. Bischof J, Maeda RK, Hediger M, Karch F, Basler K (2007) An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc Natl Acad Sci U S A 104(9):3312–3317PubMedCentralPubMedCrossRefGoogle Scholar
  7. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19(2):185–193PubMedCrossRefGoogle Scholar
  8. Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118(2):401–415PubMedGoogle Scholar
  9. Chintapalli VR, Wang J, Dow JA (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39(6):715–720PubMedCrossRefGoogle Scholar
  10. da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57CrossRefGoogle Scholar
  11. de Wit E, Greil F, van Steensel B (2005) Genome-wide HP1 binding in Drosophila: developmental plasticity and genomic targeting signals. Genome Res 15(9):1265–1273PubMedCentralPubMedCrossRefGoogle Scholar
  12. Demakova OV, Pokholkova GV, Kolesnikova TD, Demakov SA, Andreyeva EN, Belyaeva ES, Zhimulev IF (2007) The SU(VAR)3-9/HP1 complex differentially regulates the compaction state and degree of underreplication of X chromosome pericentric heterochromatin in Drosophila melanogaster. Genetics 175(2):609–620. doi: 10.1534/genetics.106.062133 PubMedCentralPubMedCrossRefGoogle Scholar
  13. Ebert A, Lein S, Schotta G, Reuter G (2006) Histone modification and the control of heterochromatic gene silencing in Drosophila. Chromosom Res 14(4):377–392CrossRefGoogle Scholar
  14. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95(25):14863–14868PubMedCentralPubMedCrossRefGoogle Scholar
  15. Elgin SC (1996) Heterochromatin and gene regulation in Drosophila. Curr Opin Genet Dev 6(2):193–202PubMedCrossRefGoogle Scholar
  16. Ernst J, Kellis M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28(8):817–825PubMedCentralPubMedCrossRefGoogle Scholar
  17. Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143(2):212–224PubMedCentralPubMedCrossRefGoogle Scholar
  18. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE (2011) The developmental transcriptome of Drosophila melanogaster. Nature 471(7339):473–479PubMedCentralPubMedCrossRefGoogle Scholar
  19. Greil F, Moorman C, van Steensel B (2006) DamID: mapping of in vivo protein–genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol 410:342–359PubMedCrossRefGoogle Scholar
  20. Hiratani I, Takebayashi S, Lu J, Gilbert DM (2009) Replication timing and transcriptional control: beyond cause and effect—part II. Curr Opin Genet Dev 19(2):142–149PubMedCentralPubMedCrossRefGoogle Scholar
  21. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471(7339):480–485PubMedCentralPubMedCrossRefGoogle Scholar
  22. Kolesnikova TD, Andreeva EN, Pindiurin AV, Anan'ko NG, Beliakin SN, Shloma VV, Iurlova AA, Makunin IV, Pokholkova GV, Volkova EI, Zarutskaia EA, Kokoza EB, Seneshin VF, Beliaeva ES, Zhimulev IF (2006) Contribution of the SuUR gene to the organization of epigenetically repressed regions of Drosophila melanogaster chromosomes. Genetika 42(8):1013–1028PubMedGoogle Scholar
  23. Kolesnikova TD, Posukh OV, Andreyeva EN, Bebyakina DS, Ivankin AV, Zhimulev IF (2013) Drosophila SUUR protein associates with PCNA and binds chromatin in a cell cycle-dependent manner. Chromosoma 122(1–2):55–66. doi: 10.1007/s00412-012-0390-9 Google Scholar
  24. Koryakov DE, Walther M, Ebert A, Lein S, Zhimulev IF, Reuter G (2011) The SUUR protein is involved in binding of SU(VAR)3-9 and methylation of H3K9 and H3K27 in chromosomes of Drosophila melanogaster. Chromosom Res 19(2):235–249. doi: 10.1007/s10577-011-9193-8 CrossRefGoogle Scholar
  25. Kwong C, Adryan B, Bell I, Meadows L, Russell S, Manak JR, White R (2008) Stability and dynamics of polycomb target sites in Drosophila development. PLoS Genet 4(9):e1000178. doi: 10.1371/journal.pgen.1000178 PubMedCentralPubMedCrossRefGoogle Scholar
  26. Luo SD, Shi GW, Baker BS (2011) Direct targets of the D. melanogaster DSXF protein and the evolution of sexual development. Development 138(13):2761–2771PubMedCentralPubMedCrossRefGoogle Scholar
  27. Makunin IV, Volkova EI, Belyaeva ES, Nabirochkina EN, Pirrotta V, Zhimulev IF (2002) The Drosophila suppressor of underreplication protein binds to late-replicating regions of polytene chromosomes. Genetics 160(3):1023–1034PubMedCentralPubMedGoogle Scholar
  28. Markstein M, Pitsouli C, Villalta C, Celniker SE, Perrimon N (2008) Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat Genet 40(4):476–483. doi: 10.1038/ng.101 PubMedCentralPubMedCrossRefGoogle Scholar
  29. Nordman J, Li S, Eng T, Macalpine D, Orr-Weaver TL (2011) Developmental control of the DNA replication and transcription programs. Genome Res 21(2):175–181. doi: 10.1101/gr.114611.110 PubMedCentralPubMedCrossRefGoogle Scholar
  30. 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(Pt 14):2344–2351PubMedCrossRefGoogle Scholar
  31. Pindyurin AV, Boldyreva LV, Shloma VV, Kolesnikova TD, Pokholkova GV, Andreyeva EN, Kozhevnikova EN, Ivanoschuk IG, Zarutskaya EA, Demakov SA, Gorchakov AA, Belyaeva ES, Zhimulev IF (2008) Interaction between the Drosophila heterochromatin proteins SUUR and HP1. J Cell Sci 121(Pt 10):1693–1703. doi: 10.1242/jcs.018655 PubMedCrossRefGoogle Scholar
  32. Reuter G, Spierer P (1992) Position effect variegation and chromatin proteins. Bioessays 14(9):605–612. doi: 10.1002/bies.950140907 PubMedCrossRefGoogle Scholar
  33. Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 21(2):147–163. doi: 10.1101/gr.110098.110 PubMedCentralPubMedCrossRefGoogle Scholar
  34. Roudier F, Ahmed I, Berard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Despres B, Drevensek S, Barneche F, Derozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. Embo J 30(10):1928–1938PubMedCentralPubMedCrossRefGoogle Scholar
  35. Schotta G, Ebert A, Dorn R, Reuter G (2003) Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin Cell Dev Biol 14(1):67–75PubMedCrossRefGoogle Scholar
  36. Schubeler D, Groudine M, Bender MA (2001) The murine beta-globin locus control region regulates the rate of transcription but not the hyperacetylation of histones at the active genes. Proc Natl Acad Sci U S A 98(20):11432–11437PubMedCentralPubMedCrossRefGoogle Scholar
  37. Schwartz YB, Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8(1):9–22. doi: 10.1038/nrg1981 PubMedCrossRefGoogle Scholar
  38. Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL (2012) Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res 22(1):64–75. doi: 10.1101/gr.126003.111 PubMedCentralPubMedCrossRefGoogle Scholar
  39. Siegal ML, Hartl DL (2000) Application of Cre/loxP in Drosophila. Site-specific recombination and transgene coplacement. Methods Mol Biol 136:487–495. doi: 10.1385/1-59259-065-9:487 PubMedGoogle Scholar
  40. Struhl G, Basler K (1993) Organizing activity of wingless protein in Drosophila. Cell 72(4):527–540PubMedCrossRefGoogle Scholar
  41. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA (2011) Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol 12(5):R43PubMedCentralPubMedCrossRefGoogle Scholar
  42. van Steensel B, Henikoff S (2000) Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18(4):424–428PubMedCrossRefGoogle Scholar
  43. Wallrath LL (1998) Unfolding the mysteries of heterochromatin. Curr Opin Genet Dev 8(2):147–153PubMedCrossRefGoogle Scholar
  44. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J (2002) Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 3(11):research0062Google Scholar
  45. Zhimulev IF, Belyaeva ES, Makunin IV, Pirrotta V, Volkova EI, Alekseyenko AA, Andreyeva EN, Makarevich GF, Boldyreva LV, Nanayev RA, Demakova OV (2003) Influence of the SuUR gene on intercalary heterochromatin in Drosophila melanogaster polytene chromosomes. Chromosoma 111(6):377–398PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Daniil A. Maksimov
    • 1
  • Dmitry E. Koryakov
    • 1
  • Stepan N. Belyakin
    • 1
    Email author
  1. 1.Institute of Molecular and Cellular Biology SB RASNovosibirskRussia

Personalised recommendations