Abstract
Recent data suggest that insulators organize chromatin architecture in the nucleus. The best characterized Drosophila insulator, found in the gypsy retrotransposon, contains 12 binding sites for the Su(Hw) protein. Enhancer blocking, along with Su(Hw), requires BTB/POZ domain proteins, Mod(mdg4)-67.2 and CP190. Inactivation of Mod(mdg4)-67.2 leads to a direct repression of the yellow gene promoter by the gypsy insulator. Here, we have shown that such repression is regulated by the level of the EAST protein, which is an essential component of the interchromatin compartment. Deletion of the EAST C-terminal domain suppresses Su(Hw)-mediated repression. Partial inactivation of EAST by mutations in the east gene suppresses the enhancer-blocking activity of the gypsy insulator. The binding of insulator proteins to chromatin is highly sensitive to the level of EAST expression. These results suggest that EAST, one of the main components of the interchromatin compartment, can regulate the activity of chromatin insulators.
Similar content being viewed by others
References
Ali T, Renkawitz R, Bartkuhn M (2016) Insulators and domains of gene expression. Curr Opin Genet Dev 37:17–26. doi:10.1016/j.gde.2015.11.009
Bartkuhn M et al (2009) Active promoters and insulators are marked by the centrosomal protein 190. EMBO J 28:877–888. doi:10.1038/emboj.2009.34
Bezborodova E, Kulikov A, Georgiev P (1997) A new family of genes which, when mutated, suppress the inhibitory effect of the mod(mdg4)1u1 mutation on y2 expression in Drosophila melanogaster. Mol Gen Genet 257:83–90
Bonchuk A, Denisov S, Georgiev P, Maksimenko O (2011) Drosophila BTB/POZ domains of “ttk group” can form multimers and selectively interact with each other. J Mol Biol 412:423–436. doi:10.1016/j.jmb.2011.07.052
Bonchuk A et al (2015) Functional role of dimerization and CP190 interacting domains of CTCF protein in Drosophila melanogaster. BMC Biol 13:63. doi:10.1186/s12915-015-0168-7
Bouwman BA, de Laat W (2015) Architectural hallmarks of the pluripotent genome. FEBS Lett 589:2905–2913. doi:10.1016/j.febslet.2015.04.055
Brasset E, Vaury C (2005) Insulators are fundamental components of the eukaryotic genomes. Heredity (Edinb) 94:571–576. doi:10.1038/sj.hdy.6800669
Buchner K, Roth P, Schotta G, Krauss V, Saumweber H, Reuter G, Dorn R (2000) Genetic and molecular complexity of the position effect variegation modifier mod(mdg4) in Drosophila. Genetics 155:141–157
Cai HN, Levine M (1997) The gypsy insulator can function as a promoter-specific silencer in the Drosophila embryo. EMBO J 16:1732–1741. doi:10.1093/emboj/16.7.1732
Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer MW (2010) Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 140:372–383. doi:10.1016/j.cell.2009.12.054
Chetverina D, Aoki T, Erokhin M, Georgiev P, Schedl P (2014) Making connections: insulators organize eukaryotic chromosomes into independent cis-regulatory networks. Bioessays 36:163–172. doi:10.1002/bies.201300125
Cremer T, Kupper K, Dietzel S, Fakan S (2004) Higher order chromatin architecture in the cell nucleus: on the way from structure to function. Biol Cell 96:555–567. doi:10.1016/j.biolcel.2004.07.002
Davison D, Chapman CH, Wedeen C, Bingham PM (1985) Genetic and physical studies of a portion of the white locus participating in transcriptional regulation and in synapsis-dependent interactions in Drosophila adult tissues. Genetics 110:479–494
Erokhin M, Parshikov A, Georgiev P, Chetverina D (2010) E(y)2/Sus1 is required for blocking PRE silencing by the Wari insulator in Drosophila melanogaster. Chromosoma 119:243–253. doi:10.1007/s00412-009-0253-1
Erokhin M, Davydova A, Kyrchanova O, Parshikov A, Georgiev P, Chetverina D (2011) Insulators form gene loops by interacting with promoters in Drosophila. Development 138:4097–4106. doi:10.1242/dev.062836
Gause M, Morcillo P, Dorsett D (2001) Insulation of enhancer-promoter communication by a gypsy transposon insert in the Drosophila cut gene: cooperation between suppressor of hairy-wing and modifier of mdg4 proteins. Mol Cell Biol 21:4807–4817. doi:10.1128/MCB.21.14.4807-4817.2001
Georgiev P, Kozycina M (1996) Interaction between mutations in the suppressor of Hairy wing and modifier of mdg4 genes of Drosophila melanogaster affecting the phenotype of gypsy-induced mutations. Genetics 142:425–436
Georgieva SG, Nabirochkina EN, Ladygina NG, Georgiev PG, Soldatov AV (2001) Nuclear protein e(y)2 from Drosophila melanogaster participates in transcription control. Genetika 37:24–28
Gerasimova TI, Gdula DA, Gerasimov DV, Simonova O, Corces VG (1995) A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation. Cell 82:587–597
Gerasimova TI, Lei EP, Bushey AM, Corces VG (2007) Coordinated control of dCTCF and gypsy chromatin insulators in Drosophila. Mol Cell 28:761–772. doi:10.1016/j.molcel.2007.09.024
Geyer PK, Corces VG (1992) DNA position-specific repression of transcription by a Drosophila zinc finger protein. Genes Dev 6:1865–1873
Geyer PK, Spana C, Corces VG (1986) On the molecular mechanism of gypsy-induced mutations at the yellow locus of Drosophila melanogaster. EMBO J 5:2657–2662
Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE (2014) Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512:96–100. doi:10.1038/nature13417
Ghosh D, Gerasimova TI, Corces VG (2001) Interactions between the Su(Hw) and Mod(mdg4) proteins required for gypsy insulator function. EMBO J 20:2518–2527. doi:10.1093/emboj/20.10.2518
Gibcus JH, Dekker J (2013) The hierarchy of the 3D genome. Mol Cell 49:773–782. doi:10.1016/j.molcel.2013.02.011
Golovnin A et al (2003) An endogenous Su(Hw) insulator separates the yellow gene from the Achaete-scute gene complex in Drosophila. Development 130:3249–3258
Golovnin A, Melnick E, Mazur A, Georgiev P (2005) Drosophila Su(Hw) insulator can stimulate transcription of a weakened yellow promoter over a distance. Genetics 170:1133–1142. doi:10.1534/genetics.104.034587
Golovnin A et al (2007) Integrity of the Mod(mdg4)-67.2 BTB domain is critical to insulator function in Drosophila melanogaster. Mol Cell Biol 27:963–974. doi:10.1128/MCB.00795-06
Golovnin A, Melnikova L, Volkov I, Kostuchenko M, Galkin AV, Georgiev P (2008) ‘Insulator bodies’ are aggregates of proteins but not of insulators. EMBO Rep 9:440–445. doi:10.1038/embor.2008.32
Golovnin A, Volkov I, Georgiev P (2012) SUMO conjugation is required for the assembly of Drosophila Su(Hw) and Mod(mdg4) into insulator bodies that facilitate insulator complex formation. J Cell Sci 125:2064–2074. doi:10.1242/jcs.100172
Golovnin A, Melnikova L, Shapovalov I, Kostyuchenko M, Georgiev P (2015) EAST organizes Drosophila insulator proteins in the interchromosomal nuclear compartment and modulates CP190 binding to chromatin. PLoS One 10:e0140991. doi:10.1371/journal.pone.0140991
Jack J, Dorsett D, Delotto Y, Liu S (1991) Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer. Development 113:735–747
Johansen KM, Forer A, Yao C, Girton J, Johansen J (2011) Do nuclear envelope and intranuclear proteins reorganize during mitosis to form an elastic, hydrogel-like spindle matrix? Chromosom Res 19:345–365. doi:10.1007/s10577-011-9187-6
Kalverda B, Pickersgill H, Shloma VV, Fornerod M (2010) Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 140:360–371. doi:10.1016/j.cell.2010.01.011
Karess RE, Rubin GM (1984) Analysis of P transposable element functions in Drosophila. Cell 38:135–146
Kuhn-Parnell EJ, Helou C, Marion DJ, Gilmore BL, Parnell TJ, Wold MS, Geyer PK (2008) Investigation of the properties of non-gypsy suppressor of hairy-wing-binding sites. Genetics 179:1263–1273. doi:10.1534/genetics.108.087254
Kurshakova M, Maksimenko O, Golovnin A, Pulina M, Georgieva S, Georgiev P, Krasnov A (2007) Evolutionarily conserved E(y)2/Sus1 protein is essential for the barrier activity of Su(Hw)-dependent insulators in Drosophila. Mol Cell 27:332–338. doi:10.1016/j.molcel.2007.05.035
Kyrchanova O, Georgiev P (2014) Chromatin insulators and long-distance interactions in Drosophila. FEBS Lett 588:8–14. doi:10.1016/j.febslet.2013.10.039
Lei EP, Corces VG (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 38:936–941. doi:10.1038/ng1850
Liang Y, Hetzer MW (2011) Functional interactions between nucleoporins and chromatin. Curr Opin Cell Biol 23:65–70. doi:10.1016/j.ceb.2010.09.008
Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP (2013) Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic Acids Res 41:2963–2980. doi:10.1093/nar/gkt037
Maksimenko O, Georgiev P (2014) Mechanisms and proteins involved in long-distance interactions. Front Genet 5:28. doi:10.3389/fgene.2014.00028
Maksimenko O, Golovnin A, Georgiev P (2008) Enhancer-promoter communication is regulated by insulator pairing in a Drosophila model bigenic locus. Mol Cell Biol 28:5469–5477. doi:10.1128/MCB.00461-08
Matzat LH, Lei EP (2014) Surviving an identity crisis: a revised view of chromatin insulators in the genomics era. Biochim Biophys Acta 1839:203–214. doi:10.1016/j.bbagrm.2013.10.007
Matzat LH, Dale RK, Moshkovich N, Lei EP (2012) Tissue-specific regulation of chromatin insulator function. PLoS Genet 8:e1003069. doi:10.1371/journal.pgen.1003069
Melnikova L, Kostuchenko M, Silicheva M, Georgiev P (2008) Drosophila gypsy insulator and yellow enhancers regulate activity of yellow promoter through the same regulatory element. Chromosoma 117:137–145. doi:10.1007/s00412-007-0132-6
Mohan M et al (2007) The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning. EMBO J 26:4203–4214. doi:10.1038/sj.emboj.7601851
Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, Lei EP (2011) RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev 25:1686–1701. doi:10.1101/gad.16651211
Negre N et al (2010) A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet 6:e1000814. doi:10.1371/journal.pgen.1000814
Pai CY, Lei EP, Ghosh D, Corces VG (2004) The centrosomal protein CP190 is a component of the gypsy chromatin insulator. Mol Cell 16:737–748. doi:10.1016/j.molcel.2004.11.004
Parnell TJ, Viering MM, Skjesol A, Helou C, Kuhn EJ, Geyer PK (2003) An endogenous suppressor of hairy-wing insulator separates regulatory domains in Drosophila. Proc Natl Acad Sci U S A 100:13436–13441. doi:10.1073/pnas.2333111100
Parnell TJ, Kuhn EJ, Gilmore BL, Helou C, Wold MS, Geyer PK (2006) Identification of genomic sites that bind the Drosophila suppressor of Hairy-wing insulator protein. Mol Cell Biol 26:5983–5993. doi:10.1128/MCB.00698-06
Peter A et al (2002) Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep 3:34–38. doi:10.1093/embo-reports/kvf012
Qi H et al (2005) EAST interacts with Megator and localizes to the putative spindle matrix during mitosis in Drosophila. J Cell Biochem 95:1284–1291. doi:10.1002/jcb.20495
Raab JR, Kamakaka RT (2010) Insulators and promoters: closer than we think Nature reviews. Genetics 11:439–446. doi:10.1038/nrg2765
Schwartz YB et al (2012) Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res 22:2188–2198. doi:10.1101/gr.138156.112
Soshnev AA, He B, Baxley RM, Jiang N, Hart CM, Tan K, Geyer PK (2012) Genome-wide studies of the multi-zinc finger Drosophila suppressor of hairy-wing protein in the ovary. Nucleic Acids Res 40:5415–5431. doi:10.1093/nar/gks225
Spana C, Corces VG (1990) DNA bending is a determinant of binding specificity for a Drosophila zinc finger protein. Genes Dev 4:1505–1515
Spector DL (2001) Nuclear domains. J Cell Sci 114:2891–2893
Vaquerizas JM, Suyama R, Kind J, Miura K, Luscombe NM, Akhtar A (2010) Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome. PLoS Genet 6:e1000846. doi:10.1371/journal.pgen.1000846
Vorobyeva NE et al (2013) Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of origin recognition complex-binding sites in the Drosophila genome. Nucleic Acids Res 41:5717–5730. doi:10.1093/nar/gkt297
Wasser M, Chia W (2000) The EAST protein of drosophila controls an expandable nuclear endoskeleton. Nat Cell Biol 2:268–275. doi:10.1038/35010535
Wasser M, Chia W (2003) The Drosophila EAST protein associates with a nuclear remnant during mitosis and constrains chromosome mobility. J Cell Sci 116:1733–1743
Wasser M, Chia W (2007) The extrachromosomal east protein of Drosophila can associate with polytene chromosomes and regulate gene expression. PLoS One 2:e412. doi:10.1371/journal.pone.0000412
Acknowledgments
We are grateful to N.A. Gorgolyuk for his help in preparing the manuscript and to A. Parshikov for the injection of embryos. This study was supported by the Russian Science Foundation (http://www.rscf.ru) (project №14–14–01067). Experiments were performed using the equipment of IGB RAS facilities supported by the Ministry of Science and Education of the Russian Federation (grant no. 16.552.11.7067).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Funding
This study was funded by the Russian Science Foundation (http://www.rscf.ru) (project №14–14–01067).
Conflict of interest
The authors declare that they have no conflict of interest.
Human and animal rights and informed consent
All applicable international, national, and institutional guidelines for the care and use of animals were followed. This article does not contain any studies with human participants performed by any of the authors.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Suppl. Fig. 1
(PDF 789 kb)
Suppl. Fig. 2
(PDF 483 kb)
Suppl. Fig. 3
(PDF 386 kb)
Suppl. Fig. 4
(PDF 601 kb)
Suppl. Fig. 5
(PDF 898 kb)
Suppl. Table 1
(PDF 65 kb)
Suppl. Table 2
(PDF 67 kb)
Rights and permissions
About this article
Cite this article
Melnikova, L., Shapovalov, I., Kostyuchenko, M. et al. EAST affects the activity of Su(Hw) insulators by two different mechanisms in Drosophila melanogaster . Chromosoma 126, 299–311 (2017). https://doi.org/10.1007/s00412-016-0596-3
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00412-016-0596-3