Cg10543 protein is involved in the regulation of transcription of ecdysone-dependent genes

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access

Abstract

Despite increasing data on the properties of replication origins, molecular mechanisms underlying origin recognition complex (ORC) positioning in the genome are still poorly understood. It has been suggested that the key factors determining the positioning of ORC in the genome are DNA-binding proteins that form various DNA regulatory elements, including insulators, promoters, and enhancers, thereby linking the replication program to different levels of transcriptional regulation. Previously, we demonstrated that the Su(Hw) protein is the first example of such a protein. Subsequent studies identified a number of other DNA-binding proteins, including CG10543, which may be responsible for the formation of corresponding regulatory elements and the recruitment of transcriptional and replication complexes to their binding sites. It has been shown that the Drosophila CG10543 protein interacts with the deubiquitinating (DUB) module of the SAGA complex. The binding sites of the CG10543 protein are predominantly located in the promoter regions of active genes and colocalize with the SAGA and dSWI/SNF chromatin modification and remodeling complexes, as well as with the ORC replication complex. To investigate the role of the CG10543 protein in transcriptional regulation, an RNA-Seq experiment was conducted in Drosophila S2 cells under normal conditions and upon RNA interference of the CG10543 protein. It was shown that the CG10543 protein affects the transcription of 469 genes, with a significant portion of these genes (23%) being ecdysone-dependent genes. Ecdysone is the main steroid hormone in Drosophila, responsible for Drosophila metamorphosis and has a significant effect on the expression of many genes during development. We demonstrated that CG10543 sites colocalize with the CBP protein and the histone mark H3K27Ac, which are characteristic of active regulatory elements. The CG10543 protein also colocalizes with the CP190 protein, suggesting a potential mechanism of transcriptional regulation through the formation of long-range interactions between regulatory elements.

About the authors

N. E. Vorobyova

Institute of Gene Biology, Russian Academy of Sciences

Moscow, 119334 Russia

J. V. Nikolenko

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

Moscow, 119991 Russia

A. N. Krasnov

Institute of Gene Biology, Russian Academy of Sciences

Email: krasnov@genebiology.ru
Moscow, 119334 Russia

References

  1. Orphanides G., Reinberg D. (2002) A unified theory of gene expression. Cell. 108, 439–451.
  2. van Bemmel J.G., Pagie L., Braunschweig U., Brugman W., Meuleman W., Kerkhoven R.M., van Steensel B. (2010) The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PLoS One. 5, e15013.
  3. Rando O.J., Chang H.Y. (2009) Genome-wide views of chromatin structure. Annu. Rev. Biochem. 78, 245–271.
  4. Tchurikov N.A., Krasnov A.N., Ponomarenko N.A., Golova Y.B., Chernov B.K. (1998) Forum domain in Drosophila melanogaster cut locus possesses looped domains inside. Nucl. Acids Res. 26, 3221–3227.
  5. Mechali M. (2010) Eukaryotic DNA replication origins: many choices for appropriate answers. Nat. Rev. Mol. Cell Biol. 11, 728–738.
  6. Masai H., Matsumoto S., You Z., Yoshizawa-Sugata N., Oda M. (2010) Eukaryotic chromosome DNA replication: where, when, and how? Annu. Rev. Biochem. 79, 89–130.
  7. MacAlpine H.K., Gordan R., Powell S.K., Hartemink A.J., MacAlpine D.M. (2010) Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res. 20, 201–211.
  8. Deal R.B., Henikoff J.G., Henikoff S. (2010) Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science. 328, 1161–1164.
  9. Euskirchen G.M., Auerbach R.K., Davidov E., Gianoulis T.A., Zhong G., Rozowsky J., Bhardwaj N., Gerstein M.B., Snyder M. (2011) Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet. 7, e1002008.
  10. Eaton M.L., Prinz J.A., MacAlpine H.K., Tretyakov G., Kharchenko P.V., MacAlpine D.M. (2011) Chromatin signatures of the Drosophila replication program. Genome Res. 21, 164–174.
  11. MacAlpine D.M., Rodriguez H.K., Bell S.P. (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev. 18, 3094–3105.
  12. Balasov M., Huijbregts R.P., Chesnokov I. (2007) Role of the Orc6 protein in origin recognition complex-dependent DNA binding and replication in Drosophila melanogaster. Mol. Cell Biol. 27, 3143–3153.
  13. Kim J.C., Nordman J., Xie F., Kashevsky H., Eng T., Li S., MacAlpine D.M., Orr-Weaver T.L. (2011) Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes Dev. 25, 1384–1398.
  14. Мазина М.Ю., Воробьева Н.Е., Краснов А.Н. (2013) Способность Su(Hw) создавать платформу для формирования ориджинов репликации не зависит от типа окружающего хроматина. Цитология. 55, 218–224.
  15. Vorobyeva N.E., Erokhin M., Chetverina D., Krasnov A.N., Mazina M.Y. (2021) Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation. Sci. Rep. 11, 16963.
  16. Vorobyeva N.E., Krasnov A.N., Erokhin M., Chetverina D., Mazina M. (2024) Su(Hw) interacts with Combgap to establish long-range chromatin contacts. Epigenetics Chromatin. 17, 17.
  17. Фурсова Н.А., Николенко Ю.В., Сошникова Н.В., Мазина М.Ю., Воробьева Н.Е., Краснов А.Н. (2018) Белок CG9890 с доменами цинковых пальцев – новый компонент ENY2-содержащих комплексов дрозофилы. Acta Naturae. 10, 110–114.
  18. Николенко Ю.В., Куршакова М.М., Копытова Д.В., Вдовина Ю.А., Воробьева Н.Е., Краснов А.Н. (2024) Белки AEF1 и CG10543 дрозофилы, содержащие домены цинковых пальцев, колокализуются с комплексами SAGA, SWI/SNF и ORC на промоторах генов и участвуют в регуляции транскрипции. Молекуляр. биология. 58, 619‒626.
  19. Николенко Ю.В., Куршакова М.М., Копытова Д.В., Вдовина Ю.А., Воробьева Н.Е., Краснов А.Н. (2024) Белок CG9609 дрозофилы, содержащий домены цинковых пальцев, взаимодействует c деубиквитинирующим (DUB) модулем комплекса SAGA и участвует в регуляции транскрипции. Молекуляр. биология. 58, 612–618.
  20. Thummel C.S. (1996) Flies on steroids – Drosophila metamorphosis and the mechanisms of steroid hormone action. Trends Genet. 12, 306–310.
  21. Ou Q., King-Jones K. (2013) What goes up must come down: transcription factors have their say in making ecdysone pulses. Curr. Top. Dev. Biol. 103, 35–71.
  22. Shlyueva D., Stelzer C., Gerlach D., Yanez-Cuna J.O., Rath M., Boryn L.M., Arnold C.D., Stark A. (2014) Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin. Mol. Cell. 54, 180–192.
  23. Mazina M.Y., Kovalenko E.V., Derevyanko P.K., Nikolenko J.V., Krasnov A.N., Vorobyeva N.E. (2018) One signal stimulates different transcriptional activation mechanisms. Biochim. Biophys. Acta. 1861, 178–189.
  24. Mazina M.Y., Nikolenko J.V., Fursova N.A., Nedil’ko P.N., Krasnov A.N., Vorobyeva N.E. (2015) Early-late genes of the ecdysone cascade as models for transcriptional studies. Cell Cycle. 14, 3593–3601.
  25. Мазина М.Ю., Кочерыжкина Е.В., Николенко Ю.В., Краснов А.Н., Георгиева С.Г., Воробьева Н.Е. (2017) Ядерные рецепторы ECR, USP, E75, DHR3 и ERR регулируют транскрипцию генов экдизонового каскада. Доклады Академии наук. 473, 736–738.
  26. Krasnov A.N., Evdokimova A.A., Mazina M.Y., Erokhin M., Chetverina D., Vorobyeva N.E. (2023) Coregulators reside within Drosophila ecdysone-inducible loci before and after ecdysone treatment. Int. J. Mol. Sci. 24(14), 11844.
  27. Cheng D., Dong Z., Lin P., Shen G., Xia Q. (2022) Transcriptional activation of ecdysone-responsive genes requires H3K27 acetylation at enhancers. Int. J. Mol. Sci. 23(18), 10791.
  28. Trapnell C., Hendrickson D.G., Sauvageau M., Goff L., Rinn J.L., Pachter L. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46–53.
  29. Ramirez F., Ryan D.P., Gruning B., Bhardwaj V., Kilpert F., Richter A.S., Heyne S., Dundar F., Manke T. (2016) DeepTools2: a next generation web server for deep-sequencing data analysis. Nucl. Acids Res. 44, W160‒165.
  30. McKay D.J., Lieb J.D. (2013) A common set of DNA regulatory elements shapes Drosophila appendages. Dev. Cell. 27, 306‒318.
  31. Bag I., Chen S., Rosin L.F., Chen Y., Liu C.Y., Yu G.Y., Lei E.P. (2021) M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity. Nat. Commun. 12, 4170.
  32. Sabirov M., Popovich A., Boyko K., Nikolaeva A., Kyrchanova O., Maksimenko O., Popov V., Georgiev P., Bonchuk A. (2021) Mechanisms of CP190 interaction with architectural proteins in Drosophila melanogaster. Int. J. Mol. Sci. 22(22), 12400.
  33. Chen D., Lei E.P. (2019) Function and regulation of chromatin insulators in dynamic genome organization. Curr. Opin. Cell Biol. 58, 61–68.
  34. Kahn T.G., Savitsky M., Kuong C., Jacquier C., Cavalli G., Chang J.M., Schwartz Y.B. (2023) Topological screen identifies hundreds of Cp190- and CTCF-dependent Drosophila chromatin insulator elements. Sci. Adv. 9, eade0090.
  35. Cavalheiro G.R., Girardot C., Viales R.R., Pollex T., Cao T.B.N., Lacour P., Feng S., Rabinowitz A., Furlong E.E.M. (2023) CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles. Sci. Adv. 9, eade1085.
  36. Kaushal A., Dorier J., Wang B., Mohana G., Taschner M., Cousin P., Waridel P., Iseli C., Semenova A., Restrepo S., Guex N., Aiden E.L., Gambetta M.C. (2022) Essential role of Cp190 in physical and regulatory boundary formation. Sci. Adv. 8, eabl8834.
  37. Mazina M.Y., Ziganshin R.H., Magnitov M.D., Golovnin A.K., Vorobyeva N.E. (2020) Proximity-dependent biotin labelling reveals CP190 as an EcR/Usp molecular partner. Sci. Rep. 10, 4793.
  38. Wood A.M., Van Bortle K., Ramos E., Takenaka N., Rohrbaugh M., Jones B.C., Jones K.C., Corces V.G. (2011) Regulation of chromatin organization and inducible gene expression by a Drosophila insulator. Mol. Cell. 44, 29–38.
  39. Ahanger S.H., Gunther K., Weth O., Bartkuhn M., Bhonde R.R., Shouche Y.S., Renkawitz R. (2014) Ectopically tethered CP190 induces large-scale chromatin decondensation. Sci. Rep. 4, 3917.
  40. Bartkuhn M., Straub T., Herold M., Herrmann M., Rathke C., Saumweber H., Gilfillan G.D., Becker P.B., Renkawitz R. (2009) Active promoters and insulators are marked by the centrosomal protein 190. EMBO J. 28, 877–888.
  41. Kwon S.Y., Grisan V., Jang B., Herbert J., Badenhorst P. (2016) Genome-wide mapping targets of the metazoan chromatin remodeling factor NURF reveals nucleosome remodeling at enhancers, core promoters and gene insulators. PLoS Genet. 12, e1005969.
  42. Chen S., Rosin L.F., Pegoraro G., Moshkovich N., Murphy P.J., Yu G., Lei E.P. (2022) NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucl. Acids Res. 50, 7906–7924.
  43. Bohla D., Herold M., Panzer I., Buxa M.K., Ali T., Demmers J., Kruger M., Scharfe M., Jarek M., Bartkuhn M., Renkawitz R. (2014) A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. PLoS One. 9, e107765.
  44. Ali T., Kruger M., Bhuju S., Jarek M., Bartkuhn M., Renkawitz R. (2017) Chromatin binding of Gcn5 in Drosophila is largely mediated by CP190. Nucl. Acids Res. 45, 2384‒2395.
  45. Vo Ngoc L., Kassavetis G.A., Kadonaga J.T. (2019) The RNA polymerase II core promoter in Drosophila. Genetics. 212, 13–24.
  46. Haberle V., Stark A. (2018) Eukaryotic core promoters and the functional basis of transcription initiation. Nat. Rev. Mol. Cell. Biol. 19, 621–637.
  47. Sloutskin A., Shir-Shapira H., Freiman R.N., Juven-Gershon T. (2021) The core promoter is a regulatory hub for developmental gene expression. Front. Cell Dev. Biol. 9, 666508.

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

Copyright (c) 2025 Russian Academy of Sciences