Skip to main content

Advertisement

SpringerLink
Log in

Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins

  • Original Article
  • Published:
Cellular and Molecular Life Sciences Aims and scope Submit manuscript

Abstract

The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling the silenced and active states of genes in multicellular organisms, respectively. In Drosophila, PcG/TrxG proteins are recruited to the chromatin via binding to specific DNA sequences termed polycomb response elements (PREs). While precise mechanisms of the PcG/TrxG protein recruitment remain unknown, the important role is suggested to belong to sequence-specific DNA-binding factors. At the same time, it was demonstrated that the PRE DNA-binding proteins are not exclusively localized to PREs but can bind other DNA regulatory elements, including enhancers, promoters, and boundaries. To gain an insight into the PRE DNA-binding protein regulatory network, here, using ChIP-seq and immuno-affinity purification coupled to the high-throughput mass spectrometry, we searched for differences in abundance of the Combgap, Zeste, Psq, and Adf1 PRE DNA-binding proteins. While there were no conspicuous differences in co-localization of these proteins with other functional transcription factors, we show that Combgap and Zeste are more tightly associated with the Polycomb repressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap–Adf1, Psq–Dsp1, and Pho–Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste, and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

Data availability

All relevant data are within the paper and its Supporting Information. The ChIP-seq data generated for this work are accessible through the GEO Series accession number GSE200213. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [96] partner repository with the dataset identifier PXD029459 and https://doi.org/10.6019/PXD029459.

References

  1. Chetverina DA, Elizar’ev PV, Lomaev DV, Georgiev PG, Erokhin MM (2017) Control of the gene activity by polycomb and trithorax group proteins in Drosophila. Genetika 53(2):133–154

    CAS  PubMed  Google Scholar 

  2. Chetverina DA, Lomaev DV, Erokhin MM (2020) Polycomb and Trithorax group proteins: the long road from mutations in Drosophila to use in medicine. Acta Naturae 12(4):66–85. https://doi.org/10.32607/actanaturae.11090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kassis JA, Kennison JA, Tamkun JW (2017) Polycomb and Trithorax group genes in Drosophila. Genetics 206(4):1699–1725. https://doi.org/10.1534/genetics.115.185116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Kuroda MI, Kang H, De S, Kassis JA (2020) Dynamic competition of Polycomb and Trithorax in transcriptional programming. Annu Rev Biochem. https://doi.org/10.1146/annurev-biochem-120219-103641

    Article  PubMed  PubMed Central  Google Scholar 

  5. Schuettengruber B, Bourbon HM, Di Croce L, Cavalli G (2017) Genome regulation by Polycomb and Trithorax: 70 years and counting. Cell 171(1):34–57. https://doi.org/10.1016/j.cell.2017.08.002

    Article  CAS  PubMed  Google Scholar 

  6. Chetverina DA, Lomaev DV, Georgiev PG, Erokhin MM (2021) Genetic impairments of PRC2 activity in oncology: problems and prospects. Russ J Genet 57(3):258–272. https://doi.org/10.1134/S1022795421030042

    Article  CAS  Google Scholar 

  7. Erokhin M, Chetverina O, Gyorffy B, Tatarskiy VV, Mogila V, Shtil AA, Roninson IB, Moreaux J, Georgiev P, Cavalli G, Chetverina D (2021) Clinical correlations of Polycomb repressive complex 2 in different tumor types. Cancers. https://doi.org/10.3390/cancers13133155

    Article  PubMed  PubMed Central  Google Scholar 

  8. Fagan RJ, Dingwall AK (2019) COMPASS Ascending: Emerging clues regarding the roles of MLL3/KMT2C and MLL2/KMT2D proteins in cancer. Cancer Lett 458:56–65. https://doi.org/10.1016/j.canlet.2019.05.024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mittal P, Roberts CWM (2020) The SWI/SNF complex in cancer—biology, biomarkers and therapy. Nat Rev Clin Oncol 17(7):435–448. https://doi.org/10.1038/s41571-020-0357-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Piunti A, Shilatifard A (2021) The roles of Polycomb repressive complexes in mammalian development and cancer. Nat Rev Mol Cell Biol 22(5):326–345. https://doi.org/10.1038/s41580-021-00341-1

    Article  CAS  PubMed  Google Scholar 

  11. Francis NJ, Saurin AJ, Shao Z, Kingston RE (2001) Reconstitution of a functional core polycomb repressive complex. Mol Cell 8(3):545–556

    Article  CAS  Google Scholar 

  12. Saurin AJ, Shao Z, Erdjument-Bromage H, Tempst P, Kingston RE (2001) A Drosophila Polycomb group complex includes Zeste and dTAFII proteins. Nature 412(6847):655–660. https://doi.org/10.1038/35088096

    Article  CAS  PubMed  Google Scholar 

  13. Shao Z, Raible F, Mollaaghababa R, Guyon JR, Wu CT, Bender W, Kingston RE (1999) Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98(1):37–46. https://doi.org/10.1016/S0092-8674(00)80604-2

    Article  CAS  PubMed  Google Scholar 

  14. Czermin B, Melfi R, McCabe D, Seitz V, Imhof A, Pirrotta V (2002) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111(2):185–196

    Article  CAS  Google Scholar 

  15. Muller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B, Miller EL, O’Connor MB, Kingston RE, Simon JA (2002) Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111(2):197–208

    Article  CAS  Google Scholar 

  16. Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, Biggin M, Pirrotta V (2006) Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 38(6):700–705. https://doi.org/10.1038/ng1817

    Article  CAS  PubMed  Google Scholar 

  17. Tolhuis B, de Wit E, Muijrers I, Teunissen H, Talhout W, van Steensel B, van Lohuizen M (2006) Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat Genet 38(6):694–699. https://doi.org/10.1038/ng1792

    Article  CAS  PubMed  Google Scholar 

  18. Geisler SJ, Paro R (2015) Trithorax and Polycomb group-dependent regulation: a tale of opposing activities. Development 142(17):2876–2887. https://doi.org/10.1242/dev.120030

    Article  CAS  PubMed  Google Scholar 

  19. Erokhin M, Georgiev P, Chetverina D (2018) Drosophila DNA-binding proteins in Polycomb repression. Epigenomes 2(1):1. https://doi.org/10.3390/epigenomes2010001

    Article  CAS  Google Scholar 

  20. Kassis JA, Brown JL (2013) Polycomb group response elements in Drosophila and vertebrates. Adv Genet 81:83–118. https://doi.org/10.1016/B978-0-12-407677-8.00003-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Bauer M, Trupke J, Ringrose L (2015) The quest for mammalian Polycomb response elements: are we there yet? Chromosoma. https://doi.org/10.1007/s00412-015-0539-4

    Article  PubMed  PubMed Central  Google Scholar 

  22. Loubiere V, Delest A, Thomas A, Bonev B, Schuettengruber B, Sati S, Martinez AM, Cavalli G (2016) Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nat Genet 48(11):1436–1442. https://doi.org/10.1038/ng.3671

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Pherson M, Misulovin Z, Gause M, Mihindukulasuriya K, Swain A, Dorsett D (2017) Polycomb repressive complex 1 modifies transcription of active genes. Sci Adv 3(8):e1700944. https://doi.org/10.1126/sciadv.1700944

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Schaaf CA, Misulovin Z, Gause M, Koenig A, Gohara DW, Watson A, Dorsett D (2013) Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes. PLoS Genet 9(6):e1003560. https://doi.org/10.1371/journal.pgen.1003560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Erceg J, Pakozdi T, Marco-Ferreres R, Ghavi-Helm Y, Girardot C, Bracken AP, Furlong EE (2017) Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements. Genes Dev 31(6):590–602. https://doi.org/10.1101/gad.292870.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Brown JL, Mucci D, Whiteley M, Dirksen ML, Kassis JA (1998) The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol Cell 1(7):1057–1064

    Article  CAS  Google Scholar 

  27. Fritsch C, Brown JL, Kassis JA, Muller J (1999) The DNA-binding polycomb group protein pleiohomeotic mediates silencing of a Drosophila homeotic gene. Development 126(17):3905–3913

    Article  CAS  Google Scholar 

  28. Brown JL, Fritsch C, Mueller J, Kassis JA (2003) The Drosophila pho-like gene encodes a YY1-related DNA binding protein that is redundant with pleiohomeotic in homeotic gene silencing. Development 130(2):285–294

    Article  CAS  Google Scholar 

  29. Hagstrom K, Muller M, Schedl P (1997) A Polycomb and GAGA dependent silencer adjoins the Fab-7 boundary in the Drosophila bithorax complex. Genetics 146(4):1365–1380

    Article  CAS  Google Scholar 

  30. Strutt H, Cavalli G, Paro R (1997) Co-localization of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. EMBO J 16(12):3621–3632. https://doi.org/10.1093/emboj/16.12.3621

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ray P, De S, Mitra A, Bezstarosti K, Demmers JA, Pfeifer K, Kassis JA (2016) Combgap contributes to recruitment of Polycomb group proteins in Drosophila. Proc Natl Acad Sci USA 113(14):3826–3831. https://doi.org/10.1073/pnas.1520926113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Hodgson JW, Argiropoulos B, Brock HW (2001) Site-specific recognition of a 70-base-pair element containing d(GA)(n) repeats mediates bithoraxoid polycomb group response element-dependent silencing. Mol Cell Biol 21(14):4528–4543. https://doi.org/10.1128/MCB.21.14.4528-4543.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Huang DH, Chang YL, Yang CC, Pan IC, King B (2002) pipsqueak encodes a factor essential for sequence-specific targeting of a polycomb group protein complex. Mol Cell Biol 22(17):6261–6271. https://doi.org/10.1128/mcb.22.17.6261-6271.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hur MW, Laney JD, Jeon SH, Ali J, Biggin MD (2002) Zeste maintains repression of Ubx transgenes: support for a new model of Polycomb repression. Development 129(6):1339–1343

    Article  CAS  Google Scholar 

  35. Orsi GA, Kasinathan S, Hughes KT, Saminadin-Peter S, Henikoff S, Ahmad K (2014) High-resolution mapping defines the cooperative architecture of Polycomb response elements. Genome Res 24(5):809–820. https://doi.org/10.1101/gr.163642.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Dejardin J, Rappailles A, Cuvier O, Grimaud C, Decoville M, Locker D, Cavalli G (2005) Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1. Nature 434(7032):533–538. https://doi.org/10.1038/nature03386

    Article  CAS  PubMed  Google Scholar 

  37. Brown JL, Kassis JA (2010) Spps, a Drosophila Sp1/KLF family member, binds to PREs and is required for PRE activity late in development. Development 137(15):2597–2602. https://doi.org/10.1242/dev.047761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Blastyak A, Mishra RK, Karch F, Gyurkovics H (2006) Efficient and specific targeting of Polycomb group proteins requires cooperative interaction between Grainyhead and Pleiohomeotic. Mol Cell Biol 26(4):1434–1444. https://doi.org/10.1128/MCB.26.4.1434-1444.2006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Gehring WJ (1970) A recessive lethal (l(4)29) with a homeotic effect in D. melanogaster. Dros Inform Serv 45:103

    Google Scholar 

  40. Klymenko T, Papp B, Fischle W, Kocher T, Schelder M, Fritsch C, Wild B, Wilm M, Muller J (2006) A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. Genes Dev 20(9):1110–1122. https://doi.org/10.1101/gad.377406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Mohd-Sarip A, Venturini F, Chalkley GE, Verrijzer CP (2002) Pleiohomeotic can link polycomb to DNA and mediate transcriptional repression. Mol Cell Biol 22(21):7473–7483. https://doi.org/10.1128/MCB.22.21.7473-7483.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Wang L, Brown JL, Cao R, Zhang Y, Kassis JA, Jones RS (2004) Hierarchical recruitment of polycomb group silencing complexes. Mol Cell 14(5):637–646. https://doi.org/10.1016/j.molcel.2004.05.009

    Article  CAS  PubMed  Google Scholar 

  43. Frey F, Sheahan T, Finkl K, Stoehr G, Mann M, Benda C, Muller J (2016) Molecular basis of PRC1 targeting to Polycomb response elements by PhoRC. Genes Dev 30(9):1116–1127. https://doi.org/10.1101/gad.279141.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Brown JL, Sun MA, Kassis JA (2018) Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho. Proc Natl Acad Sci USA 115(8):E1839–E1848. https://doi.org/10.1073/pnas.1716299115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML (2019) A comprehensive Drosophila melanogaster transcription factor interactome. Cell Rep 27(3):955-970 e957. https://doi.org/10.1016/j.celrep.2019.03.071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 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(3):423–436. https://doi.org/10.1016/j.jmb.2011.07.052

    Article  CAS  PubMed  Google Scholar 

  47. Schwendemann A, Lehmann M (2002) Pipsqueak and GAGA factor act in concert as partners at homeotic and many other loci. Proc Natl Acad Sci USA 99(20):12883–12888. https://doi.org/10.1073/pnas.202341499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Huang DH, Chang YL (2004) Isolation and characterization of CHRASCH, a polycomb-containing silencing complex. Methods Enzymol 377:267–282. https://doi.org/10.1016/S0076-6879(03)77016-5

    Article  CAS  PubMed  Google Scholar 

  49. Strubbe G, Popp C, Schmidt A, Pauli A, Ringrose L, Beisel C, Paro R (2011) Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proc Natl Acad Sci USA 108(14):5572–5577. https://doi.org/10.1073/pnas.1007916108

    Article  PubMed  PubMed Central  Google Scholar 

  50. Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov AV, Moresco JJ, Blokhina T, Wolle D, Aoki T, Ryabykh V, Yates JR 3rd, Shidlovskii YV, Georgiev P, Schedl P, Chetverina D (2017) The GAGA factor regulatory network: identification of GAGA factor associated proteins. PLoS ONE 12(3):e0173602. https://doi.org/10.1371/journal.pone.0173602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Poux S, Melfi R, Pirrotta V (2001) Establishment of Polycomb silencing requires a transient interaction between PC and ESC. Genes Dev 15(19):2509–2514. https://doi.org/10.1101/gad.208901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Chetverina D, Erokhin M, Schedl P (2021) GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci. https://doi.org/10.1007/s00018-021-03776-z

    Article  PubMed  PubMed Central  Google Scholar 

  53. Gaskill MM, Gibson TJ, Larson ED, Harrison MM (2021) GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo. Elife. https://doi.org/10.7554/eLife.66668

    Article  PubMed  PubMed Central  Google Scholar 

  54. Judd J, Duarte FM, Lis JT (2021) Pioneer-like factor GAF cooperates with PBAP (SWI/SNF) and NURF (ISWI) to regulate transcription. Genes Dev 35(1–2):147–156. https://doi.org/10.1101/gad.341768.120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Nakayama T, Shimojima T, Hirose S (2012) The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions. Development 139(24):4582–4590. https://doi.org/10.1242/dev.083246

    Article  CAS  PubMed  Google Scholar 

  56. Shimojima T, Okada M, Nakayama T, Ueda H, Okawa K, Iwamatsu A, Handa H, Hirose S (2003) Drosophila FACT contributes to Hox gene expression through physical and functional interactions with GAGA factor. Genes Dev 17(13):1605–1616. https://doi.org/10.1101/gad.1086803

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Gutierrez-Perez I, Rowley MJ, Lyu X, Valadez-Graham V, Vallejo DM, Ballesta-Illan E, Lopez-Atalaya JP, Kremsky I, Caparros E, Corces VG, Dominguez M (2019) Ecdysone-induced 3D chromatin reorganization involves active enhancers bound by pipsqueak and Polycomb. Cell Rep 28(10):2715-2727 e2715. https://doi.org/10.1016/j.celrep.2019.07.096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Schuettengruber B, Ganapathi M, Leblanc B, Portoso M, Jaschek R, Tolhuis B, van Lohuizen M, Tanay A, Cavalli G (2009) Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol 7(1):e13. https://doi.org/10.1371/journal.pbio.1000013

    Article  CAS  PubMed  Google Scholar 

  59. Lehmann M, Siegmund T, Lintermann KG, Korge G (1998) The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain. J Biol Chem 273(43):28504–28509. https://doi.org/10.1074/jbc.273.43.28504

    Article  CAS  PubMed  Google Scholar 

  60. Cutler G, Perry KM, Tjian R (1998) Adf-1 is a nonmodular transcription factor that contains a TAF-binding Myb-like motif. Mol Cell Biol 18(4):2252–2261. https://doi.org/10.1128/MCB.18.4.2252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Dejardin J, Cavalli G (2004) Chromatin inheritance upon Zeste-mediated Brahma recruitment at a minimal cellular memory module. EMBO J 23(4):857–868. https://doi.org/10.1038/sj.emboj.7600108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Horard B, Tatout C, Poux S, Pirrotta V (2000) Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor. Mol Cell Biol 20(9):3187–3197

    Article  CAS  Google Scholar 

  63. Benson M, Pirrotta V (1988) The Drosophila zeste protein binds cooperatively to sites in many gene regulatory regions: implications for transvection and gene regulation. EMBO J 7(12):3907–3915

    Article  CAS  Google Scholar 

  64. Pirrotta V, Bickel S, Mariani C (1988) Developmental expression of the Drosophila zeste gene and localization of zeste protein on polytene chromosomes. Genes Dev 2(12B):1839–1850. https://doi.org/10.1101/gad.2.12b.1839

    Article  CAS  PubMed  Google Scholar 

  65. Laney JD, Biggin MD (1992) zeste, a nonessential gene, potently activates Ultrabithorax transcription in the Drosophila embryo. Genes Dev 6(8):1531–1541. https://doi.org/10.1101/gad.6.8.1531

    Article  CAS  PubMed  Google Scholar 

  66. England BP, Admon A, Tjian R (1992) Cloning of Drosophila transcription factor Adf-1 reveals homology to Myb oncoproteins. Proc Natl Acad Sci USA 89(2):683–687. https://doi.org/10.1073/pnas.89.2.683

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Heberlein U, England B, Tjian R (1985) Characterization of Drosophila transcription factors that activate the tandem promoters of the alcohol dehydrogenase gene. Cell 41(3):965–977. https://doi.org/10.1016/s0092-8674(85)80077-5

    Article  CAS  PubMed  Google Scholar 

  68. Erokhin M, Gorbenko F, Lomaev D, Mazina MY, Mikhailova A, Garaev AK, Parshikov A, Vorobyeva NE, Georgiev P, Schedl P, Chetverina D (2021) Boundaries potentiate polycomb response element-mediated silencing. BMC Biol 19(1):113. https://doi.org/10.1186/s12915-021-01047-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Erokhin M, Davydova A, Parshikov A, Studitsky VM, Georgiev P, Chetverina D (2013) Transcription through enhancers suppresses their activity in Drosophila. Epigenet Chromatin 6(1):31. https://doi.org/10.1186/1756-8935-6-31

    Article  CAS  Google Scholar 

  70. Erokhin M, Elizar’ev P, Parshikov A, Schedl P, Georgiev P, Chetverina D (2015) Transcriptional read-through is not sufficient to induce an epigenetic switch in the silencing activity of Polycomb response elements. Proc Natl Acad Sci USA 112(48):14930–14935. https://doi.org/10.1073/pnas.1515276112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Mazina MY, Kovalenko EV, Vorobyeva NE (2021) The negative elongation factor NELF promotes induced transcriptional response of Drosophila ecdysone-dependent genes. Sci Rep 11(1):172. https://doi.org/10.1038/s41598-020-80650-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Mazina MY, Ziganshin RH, Magnitov MD, Golovnin AK, Vorobyeva NE (2020) Proximity-dependent biotin labelling reveals CP190 as an EcR/Usp molecular partner. Sci Rep 10(1):4793. https://doi.org/10.1038/s41598-020-61514-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Mazina MY, Kovalenko EV, Derevyanko PK, Nikolenko JV, Krasnov AN, Vorobyeva NE (2018) One signal stimulates different transcriptional activation mechanisms. Biochim Biophys Acta Gene Regul Mech 2:178–189. https://doi.org/10.1016/j.bbagrm.2018.01.016

    Article  CAS  Google Scholar 

  74. Crosby MA, Miller C, Alon T, Watson KL, Verrijzer CP, Goldman-Levi R, Zak NB (1999) The trithorax group gene moira encodes a brahma-associated putative chromatin-remodeling factor in Drosophila melanogaster. Mol Cell Biol 19(2):1159–1170. https://doi.org/10.1128/MCB.19.2.1159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Mazina MY, Kocheryzhkina EV, Derevyanko PK, Vorobyeva NE (2016) The composition of Swi/Snf chromatin remodeling complex is stable during gene transcription. Tsitologiia 58(4):285–289

    PubMed  Google Scholar 

  76. Mazina MY, Nikolenko YV, Krasnov AN, Vorobyeva NE (2016) SWI/SNF protein complexes participate in the initiation and elongation stages of Drosophila hsp70 gene transcription. Genetika 52(2):164–169

    PubMed  Google Scholar 

  77. Vorobyeva NE, Mazina MU, Golovnin AK, Kopytova DV, Gurskiy DY, Nabirochkina EN, Georgieva SG, Georgiev PG, Krasnov AN (2013) Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of origin recognition complex-binding sites in the Drosophila genome. Nucl Acids Res 41(11):5717–5730. https://doi.org/10.1093/nar/gkt297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Lebedeva LA, Nabirochkina EN, Kurshakova MM, Robert F, Krasnov AN, Evgen’ev MB, Kadonaga JT, Georgieva SG, Tora L (2005) Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation. Proc Natl Acad Sci USA 102(50):18087–18092. https://doi.org/10.1073/pnas.0509063102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Kovalenko EV, Mazina MY, Krasnov AN, Vorobyeva NE (2019) The Drosophila nuclear receptors EcR and ERR jointly regulate the expression of genes involved in carbohydrate metabolism. Insect Biochem Mol Biol 112:103184. https://doi.org/10.1016/j.ibmb.2019.103184

    Article  CAS  PubMed  Google Scholar 

  80. Mazina M, Vorob’eva NE, Krasnov AN (2013) Ability of Su(Hw) to create a platform for ORC binding does not depend on the type of surrounding chromatin. Tsitologiia 55(4):218–224

    CAS  PubMed  Google Scholar 

  81. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Ramirez F, Ryan DP, Gruning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dundar F, Manke T (2016) deepTools2: a next generation web server for deep-sequencing data analysis. Nucl Acids Res 44(W1):W160-165. https://doi.org/10.1093/nar/gkw257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Feng J, Liu T, Qin B, Zhang Y, Liu XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7(9):1728–1740. https://doi.org/10.1038/nprot.2012.101

    Article  CAS  PubMed  Google Scholar 

  84. Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Gruning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D (2018) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucl Acids Res 46(W1):W537–W544. https://doi.org/10.1093/nar/gky379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucl Acids Res 37(Web Server issue):W202–W208. https://doi.org/10.1093/nar/gkp335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Herz HM, Mohan M, Garruss AS, Liang K, Takahashi YH, Mickey K, Voets O, Verrijzer CP, Shilatifard A (2012) Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. Genes Dev 26(23):2604–2620. https://doi.org/10.1101/gad.201327.112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R (2011) Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res 21(2):216–226. https://doi.org/10.1101/gr.114348.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Wani AH, Boettiger AN, Schorderet P, Ergun A, Munger C, Sadreyev RI, Zhuang X, Kingston RE, Francis NJ (2016) Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun 7:10291. https://doi.org/10.1038/ncomms10291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Pherson M, Misulovin Z, Gause M, Dorsett D (2019) Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila. Genome Res 29(4):602–612. https://doi.org/10.1101/gr.243832.118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Bergman CM, Carlson JW, Celniker SE (2005) Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics 21(8):1747–1749. https://doi.org/10.1093/bioinformatics/bti173

    Article  CAS  PubMed  Google Scholar 

  91. Biggin MD, Bickel S, Benson M, Pirrotta V, Tjian R (1988) Zeste encodes a sequence-specific transcription factor that activates the Ultrabithorax promoter in vitro. Cell 53(5):713–722. https://doi.org/10.1016/0092-8674(88)90089-x

    Article  CAS  PubMed  Google Scholar 

  92. Mohrmann L, Kal AJ, Verrijzer CP (2002) Characterization of the extended Myb-like DNA-binding domain of trithorax group protein Zeste. J Biol Chem 277(49):47385–47392. https://doi.org/10.1074/jbc.M202341200

    Article  CAS  PubMed  Google Scholar 

  93. Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB (2006) Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol 2(10):e130. https://doi.org/10.1371/journal.pcbi.0020130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Timmerman C, Suppiah S, Gurudatta BV, Yang J, Banerjee C, Sandstrom DJ, Corces VG, Sanyal S (2013) The Drosophila transcription factor Adf-1 (nalyot) regulates dendrite growth by controlling FasII and Staufen expression downstream of CaMKII and neural activity. J Neurosci 33(29):11916–11931. https://doi.org/10.1523/JNEUROSCI.1760-13.2013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Lang M, Juan E (2010) Binding site number variation and high-affinity binding consensus of Myb-SANT-like transcription factor Adf-1 in Drosophilidae. Nucleic Acids Res 38(19):6404–6417. https://doi.org/10.1093/nar/gkq504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Perez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaino JA (2019) The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res 47(D1):D442–D450. https://doi.org/10.1093/nar/gky1106

    Article  CAS  PubMed  Google Scholar 

  97. Lo SM, Ahuja NK, Francis NJ (2009) Polycomb group protein suppressor 2 of zeste is a functional homolog of posterior sex combs. Mol Cell Biol 29(2):515–525. https://doi.org/10.1128/MCB.01044-08

    Article  CAS  PubMed  Google Scholar 

  98. Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15(8):509–524. https://doi.org/10.1038/nrm3838

    Article  CAS  PubMed  Google Scholar 

  99. 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(16):1686–1701. https://doi.org/10.1101/gad.16651211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Lo Sardo F, Saxena A, Miyoshi K, Siomi H, Siomi MC, Carninci P, Gilmour DS, Corona DF, Orlando V (2011) Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 480(7377):391–395. https://doi.org/10.1038/nature10492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Nazer E, Dale RK, Chinen M, Radmanesh B, Lei EP (2018) Argonaute2 and LaminB modulate gene expression by controlling chromatin topology. PLoS Genet 14(3):e1007276. https://doi.org/10.1371/journal.pgen.1007276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Core L, Adelman K (2019) Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev 33(15–16):960–982. https://doi.org/10.1101/gad.325142.119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Dollinger R, Gilmour DS (2021) Regulation of promoter proximal pausing of RNA polymerase II in metazoans. J Mol Biol 433(14):166897. https://doi.org/10.1016/j.jmb.2021.166897

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Nazer E, Dale RK, Palmer C, Lei EP (2018) Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster. Sci Rep 8(1):15685. https://doi.org/10.1038/s41598-018-34115-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Li J, Gilmour DS (2013) Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J 32(13):1829–1841. https://doi.org/10.1038/emboj.2013.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. King-Jones K, Korge G, Lehmann M (1999) The helix-loop-helix proteins dAP-4 and daughterless bind both in vitro and in vivo to SEBP3 sites required for transcriptional activation of the Drosophila gene Sgs-4. J Mol Biol 291(1):71–82. https://doi.org/10.1006/jmbi.1999.2963

    Article  CAS  PubMed  Google Scholar 

  107. Wong MM, Liu MF, Chiu SK (2015) Cropped, Drosophila transcription factor AP-4, controls tracheal terminal branching and cell growth. BMC Dev Biol 15:20. https://doi.org/10.1186/s12861-015-0069-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Kal AJ, Mahmoudi T, Zak NB, Verrijzer CP (2000) The Drosophila brahma complex is an essential coactivator for the trithorax group protein zeste. Genes Dev 14(9):1058–1071

    Article  CAS  Google Scholar 

  109. Shen X, Mizuguchi G, Hamiche A, Wu C (2000) A chromatin remodelling complex involved in transcription and DNA processing. Nature 406(6795):541–544. https://doi.org/10.1038/35020123

    Article  CAS  PubMed  Google Scholar 

  110. Alfieri C, Gambetta MC, Matos R, Glatt S, Sehr P, Fraterman S, Wilm M, Muller J, Muller CW (2013) Structural basis for targeting the chromatin repressor Sfmbt to Polycomb response elements. Genes Dev 27(21):2367–2379. https://doi.org/10.1101/gad.226621.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Fereres S, Simon R, Mohd-Sarip A, Verrijzer CP, Busturia A (2014) dRYBP counteracts chromatin-dependent activation and repression of transcription. PLoS ONE 9(11):e113255. https://doi.org/10.1371/journal.pone.0113255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Sehadova H, Glaser FT, Gentile C, Simoni A, Giesecke A, Albert JT, Stanewsky R (2009) Temperature entrainment of Drosophila’s circadian clock involves the gene nocte and signaling from peripheral sensory tissues to the brain. Neuron 64(2):251–266. https://doi.org/10.1016/j.neuron.2009.08.026

    Article  CAS  PubMed  Google Scholar 

  113. Amoyel M, Anderson AM, Bach EA (2014) JAK/STAT pathway dysregulation in tumors: a Drosophila perspective. Semin Cell Dev Biol 28:96–103. https://doi.org/10.1016/j.semcdb.2014.03.023

    Article  CAS  PubMed  Google Scholar 

  114. Grau DJ, Antao JM, Kingston RE (2010) Functional dissection of Polycomb repressive complex 1 reveals the importance of a charged domain. Cold Spring Harb Symp Quant Biol 75:61–70. https://doi.org/10.1101/sqb.2010.75.056

    Article  CAS  PubMed  Google Scholar 

  115. Chalkley GE, Moshkin YM, Langenberg K, Bezstarosti K, Blastyak A, Gyurkovics H, Demmers JA, Verrijzer CP (2008) The transcriptional coactivator SAYP is a trithorax group signature subunit of the PBAP chromatin remodeling complex. Mol Cell Biol 28(9):2920–2929. https://doi.org/10.1128/MCB.02217-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Mohrmann L, Langenberg K, Krijgsveld J, Kal AJ, Heck AJ, Verrijzer CP (2004) Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol Cell Biol 24(8):3077–3088. https://doi.org/10.1128/MCB.24.8.3077-3088.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Yin JW, Wang G (2014) The mediator complex: a master coordinator of transcription and cell lineage development. Development 141(5):977–987. https://doi.org/10.1242/dev.098392

    Article  CAS  PubMed  Google Scholar 

  118. Kennison JA, Tamkun JW (1988) Dosage-dependent modifiers of polycomb and antennapedia mutations in Drosophila. Proc Natl Acad Sci USA 85(21):8136–8140. https://doi.org/10.1073/pnas.85.21.8136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. de Ayala G, Alonso A, Gutierrez L, Fritsch C, Papp B, Beuchle D, Muller J (2007) A genetic screen identifies novel polycomb group genes in Drosophila. Genetics 176(4):2099–2108. https://doi.org/10.1534/genetics.107.075739

    Article  CAS  Google Scholar 

  120. Chetverina D, Aoki T, Erokhin M, Georgiev P, Schedl P (2014) Making connections: insulators organize eukaryotic chromosomes into independent cis-regulatory networks. BioEssays 36(2):163–172. https://doi.org/10.1002/bies.201300125

    Article  CAS  PubMed  Google Scholar 

  121. Chetverina D, Fujioka M, Erokhin M, Georgiev P, Jaynes JB, Schedl P (2017) Boundaries of loop domains (insulators): determinants of chromosome form and function in multicellular eukaryotes. BioEssays. https://doi.org/10.1002/bies.201600233

    Article  PubMed  PubMed Central  Google Scholar 

  122. Cubenas-Potts C, Corces VG (2015) Architectural proteins, transcription, and the three-dimensional organization of the genome. FEBS Lett 589(20 Pt A):2923–2930. https://doi.org/10.1016/j.febslet.2015.05.025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Mihaly J, Hogga I, Gausz J, Gyurkovics H, Karch F (1997) In situ dissection of the Fab-7 region of the bithorax complex into a chromatin domain boundary and a Polycomb-response element. Development 124(9):1809–1820

    Article  CAS  Google Scholar 

  124. Kyrchanova O, Kurbidaeva A, Sabirov M, Postika N, Wolle D, Aoki T, Maksimenko O, Mogila V, Schedl P, Georgiev P (2018) The bithorax complex iab-7 Polycomb response element has a novel role in the functioning of the Fab-7 chromatin boundary. PLoS Genet 14(8):e1007442. https://doi.org/10.1371/journal.pgen.1007442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Gruzdeva N, Kyrchanova O, Parshikov A, Kullyev A, Georgiev P (2005) The Mcp element from the bithorax complex contains an insulator that is capable of pairwise interactions and can facilitate enhancer-promoter communication. Mol Cell Biol 25(9):3682–3689. https://doi.org/10.1128/MCB.25.9.3682-3689.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Vorobyeva NE, Erokhin M, Chetverina D, Krasnov AN, Mazina MY (2021) Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation. Sci Rep 11(1):16963. https://doi.org/10.1038/s41598-021-96488-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Chen JD, Chan CS, Pirrotta V (1992) Conserved DNA binding and self-association domains of the Drosophila zeste protein. Mol Cell Biol 12(2):598–608. https://doi.org/10.1128/mcb.12.2.598-608.1992

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Katsani KR, Hajibagheri MA, Verrijzer CP (1999) Co-operative DNA binding by GAGA transcription factor requires the conserved BTB/POZ domain and reorganizes promoter topology. EMBO J 18(3):698–708. https://doi.org/10.1093/emboj/18.3.698

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Attardi LD, Tjian R (1993) Drosophila tissue-specific transcription factor NTF-1 contains a novel isoleucine-rich activation motif. Genes Dev 7(7B):1341–1353. https://doi.org/10.1101/gad.7.7b.1341

    Article  CAS  PubMed  Google Scholar 

  130. Espinas ML, Jimenez-Garcia E, Vaquero A, Canudas S, Bernues J, Azorin F (1999) The N-terminal POZ domain of GAGA mediates the formation of oligomers that bind DNA with high affinity and specificity. J Biol Chem 274(23):16461–16469. https://doi.org/10.1074/jbc.274.23.16461

    Article  CAS  PubMed  Google Scholar 

  131. Pereira A, Paro R (2017) Pho dynamically interacts with Spt5 to facilitate transcriptional switches at the hsp70 locus. Epigenet Chromatin 10(1):57. https://doi.org/10.1186/s13072-017-0166-9

    Article  CAS  Google Scholar 

  132. Harvey R, Schuster E, Jennings BH (2013) Pleiohomeotic interacts with the core transcription elongation factor Spt5 to regulate gene expression in Drosophila. PLoS ONE 8(7):e70184. https://doi.org/10.1371/journal.pone.0070184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Papp B, Muller J (2006) Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev 20(15):2041–2054. https://doi.org/10.1101/gad.388706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Kyrchanova O, Maksimenko O, Stakhov V, Ivlieva T, Parshikov A, Studitsky VM, Georgiev P (2013) Effective blocking of the white enhancer requires cooperation between two main mechanisms suggested for the insulator function. PLoS Genet 9(7):e1003606. https://doi.org/10.1371/journal.pgen.1003606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI (2015) Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev 29(11):1136–1150. https://doi.org/10.1101/gad.260562.115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Experiments of LC–MS fingerprinting were carried out using the equipment provided by the Institute of Bioorganic Chemistry core facility (CKP IBCH). We thank the Center for Precision Genome Editing and Genetic Technologies for Biomedicine, IGB RAS for the use of their equipment. We thank Judith Kassis for providing the CgA22 fly line.

Funding

The work was supported by the Russian Science Foundation (RSF) Grant no.18-74-10091.

Author information

Authors and Affiliations

  1. Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia

    Darya Chetverina, Dmitry Lomaev & Alexandra Golovnina

  2. Group of Dynamics of Transcriptional Complexes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia

    Nadezhda E. Vorobyeva

  3. Group of Hormone-Dependent Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia

    Marina Yu. Mazina

  4. Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia

    Lika V. Fab & Maksim Erokhin

  5. Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia

    Vladic Mogila & Pavel Georgiev

  6. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia

    Rustam H. Ziganshin

Authors
  1. Darya Chetverina
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nadezhda E. Vorobyeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marina Yu. Mazina
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lika V. Fab
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dmitry Lomaev
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Alexandra Golovnina
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Vladic Mogila
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Pavel Georgiev
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Rustam H. Ziganshin
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Maksim Erokhin
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conception and design of the project: DC, PG, ME. Plasmid cloning—DC, NEV, LVF, DL, AG, MYM, VM, ME. Antigen expression, antibodies production, purification and verification—DC, NEV, LVF, DL, MYM, ME. ChIP-seqs and X-ChIP—MYM, NEV, ME. Purification and analysis of protein complexes—ME, LVF, DC. LC–MS—RHZ. Interactome data analysis—DC and ME. IP/Western blotting—NEV, MYM, LVF, AG, ME. Y2H assay—DC, LVF, DL, AG. Data visualization—DC, NEV, MYM, ME. The initial draft of this manuscript was written by—DC and ME, reviewed and edited by—DC, NEV, MYM, VM, PG, RHZ, ME. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Darya Chetverina or Maksim Erokhin.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Ethical approval

Animal handling for the antibody production was carried out strictly according to the procedures outlined in the NIH (USA) Guide for the Care and Use of Laboratory Animals. The protocols used were approved by the Committee on Bioethics of the Institute of Gene Biology, Russian Academy of Sciences. All procedures were performed under the supervision of a licensed veterinarian, under conditions that minimize pain and distress. Rabbits were purchased from a licensed specialized nursery, Manihino. Soviet chinchilla rabbits used in the study are not endangered or protected. Only healthy rabbits, certified by a licensed veterinarian were used. The rabbits were individually housed in standard size, stainless steel rabbit cages, and provided an ad libitum access to alfalfa hay, commercial rabbit food pellets, and water. The appetite and behavior of each rabbit was monitored daily by a licensed veterinarian. Body weight and temperature of each rabbit were evaluated prior to and daily following the immunization. No animals became ill or died at any time prior to the experimental endpoint. At the end of the study period all rabbits were euthanized by intravenous injection of barbiturate anesthetics.

Consent to participate

Not applicable.

Consent to publish

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chetverina, D., Vorobyeva, N.E., Mazina, M.Y. et al. Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins. Cell. Mol. Life Sci. 79, 353 (2022). https://doi.org/10.1007/s00018-022-04383-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00018-022-04383-2

Keywords

Search

Navigation