Electron tomography reveals changes in spatial distribution of UBTF1 and UBTF2 isoforms within nucleolar components during rRNA synthesis inhibition.

Tchelidze, Pavel; Kaplan, Herve; Terryn, Christine; Lalun, Nathalie; Ploton, Dominique; Thiry, Marc

doi:10.1016/j.jsb.2019.08.014

Article (Scientific journals)

Electron tomography reveals changes in spatial distribution of UBTF1 and UBTF2 isoforms within nucleolar components during rRNA synthesis inhibition.

Tchelidze, Pavel; Kaplan, Herve; Terryn, Christine et al.

2019 • In Journal of Structural Biology

Peer Reviewed verified by ORBi

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https://hdl.handle.net/2268/240053

DOI
10.1016/j.jsb.2019.08.014

PubMed
31479756

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Keywords :

AMD; Electron tomography; Fibrillar centers; Mitotic NORs; Nucleolar caps; UBTF1/2; rDNA

Abstract :

[en] Upstream binding transcription factor (UBTF) is a co-regulator of RNA polymerase I by constituting an initiation complex on rRNA genes. UBTF plays a role in rDNA bending and its maintenance in "open" state. It exists as two splicing variants, UBTF1 and UBTF2, which cannot be discerned with antibodies raised against UBTF. We investigated the ultrastructural localization of each variant in cells synthesizing GFP-tagged UBTF1 or UBTF2 by using anti-GFP antibodies and pre-embedding nanogold strategy. Detailed 3D distribution of UBTF1 and 2 was also studied by electron tomography. In control cells, the two isoforms are very abundant within fibrillar centers, but their repartition strongly differs. Electron tomography shows that UBTF1 is disposed as fibrils that are folded in coils whereas UBTF2 is localized homogenously, preferentially at their cortical area. As UBTF is a useful marker to trace rDNA genes, we used these data to improve our previous model of 3D organization of active transcribing rDNA gene within fibrillar centers. Finally, when rRNA synthesis is inhibited during actinomycin D treatment or entry in mitosis, UBTF1 and UBTF2 show a similar distribution along extended 3D loop-like structures. Altogether these data suggest new roles for UBTF1 and UBTF2 isoforms in the organization of active and inactive rDNA genes.

Disciplines :

Anatomy (cytology, histology, embryology...) & physiology

Author, co-author :

Tchelidze, Pavel

Kaplan, Herve

Terryn, Christine

Lalun, Nathalie

Ploton, Dominique

Thiry, Marc ; Université de Liège - ULiège > Département des sciences de la vie > Biologie cellulaire

Language :

English

Title :

Electron tomography reveals changes in spatial distribution of UBTF1 and UBTF2 isoforms within nucleolar components during rRNA synthesis inhibition.

Publication date :

2019

Journal title :

Journal of Structural Biology

ISSN :

1047-8477

eISSN :

1095-8657

Publisher :

Elsevier, Atlanta, United States - California

Peer reviewed :

Peer Reviewed verified by ORBi

Commentary :

Available on ORBi :

since 07 October 2019

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Bibliography

Andersen, J.S., Lam, Y.W., Leung, A.K.L., Ong, S.E., Lyon, C.E., Lamond A., Mann, M., 2005. Nucleolar proteome dynamics. Nature 433, 77-83.
Andersen, J.S., Lyon, C.E., Fox, A.H., Leung, A.K.L., Lam, Y.W., Steen, H., Mann, M., Lamond, A., 2002. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12, 1-11.
Banani, S.F., Lee, H.O., Hyman, A.A., Rosen, M.K. 2017. Biomolecular condensates: organizers of cellular biochemistry. Nature Rev. Mol. Cell. Biol. 18, 285-298.
Cavanaugh, A., Hirchler-Laszkiewicz, I., Rothblum, L., 2003. Ribosomal DNA transcription in mammals. In: The Nucleolus, ed. M.O. Olson, Plenum Publisher, pp. 89-129.
Chen, D., Dundr, M., Wang, C., Leung, A., Lamond, A., Misteli, T., Huang, S., 2005. Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins. J. Cell Biol. 168, 41-54.
Cheutin, T., O'Donohue, M.-F., Beorchia, A., Vandelaer, M., Kaplan, H., Defever, B., Ploton, D., Thiry, M., 2002. Three-dimensional organization of active rRNA genes within the nucleolus. J. Cell Sci. 115, 3297-3307.
Copenhaver, G.P., Putnam, C.D., Denton, M.L., Pikaard, C.S., 1994. The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids. Nucleic Acids Res. 22, 2651-2657.
Denissov, S., Lessard, F., Mayer, C., Stefanovsky, V., Van Driel, M., Grummt, I., Moss, T., Stunnenberg, H.G., 2011. A model for the topology of active ribosomal RNA genes. EMBO reports 12, 231-237.
Derenzini, M., Pasquinelli, G., O'Donohue, M.-F., Ploton, D., Thiry, M., 2006. Structural and functional organization of ribosomal genes within the mammalian cell nucleolus. J. Histochem. Cytochem. 54, 131-145.
Derenzini, M., Farabegoli, F., Trere, D., 1993. Localization of DNA in the fibrillar components of the nucleolus: a cytochemical and morphological study. J. Histochem. Cytochem. 41, 829-836.
Dundr, M., Hoffmann-Rohrer, U., Hu, Q., Grummt, I., Rothblum, L.I., Phair, R.D., Misteli, T., 2002. A kinetic framework for a mammalian RNA polymerase in vivo. Science 298, 1623-1626.
Falahati, H., Wieschaus, E., 2017. Independent active and thermodynamic processes govern the nucleolus assembly in vivo. Proc. Natl. Acad. Sci. USA 114, 1335-1340.
Farley, K.I., Surovtseva, Y., Merkel, J., Baserga, S.J., 2015. Determinants of mammalian nucleolar architecture. Chromosoma 124, 323-331.
Feric, M., Vaidya, N., Harmon, T.S., Mitrea, D.M., Zhu, L., Richardson, T.M., Kriwacki, R.W., Pappu, R.V., Brangwynne, C.P., 2016. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1-12.
Gebrane-Younes, J., Fomproix, N., Hernandez-Verdun, D., 1997. When rDNA transcription is arrested during mitosis, UBF is still associated with non-condensed rDNA. J. Cell Sci. 110, 2429-2440.
Goodfellow, S.J., Zomerdjik, J.C.B.M., 2012. Basic mechanisms in RNA polymerase I transcription of the ribosomal RNA genes. Subcell. Biochem. 61, 211-236.
Grob, A., Colleran, C., McStay, B., 2014. Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division. Genes Dev. 28, 220-230.
Grummt, I., 2003. Life on a planet of its own: Regulation of RNA polymerase I transcription in the nucleolus. Genes Dev. 17, 1691-1702.
Hamdane, N., Herdman, C., Mars, J.C., Stefanovsky, V., Tremblay, M.G., Moss, T., 2015. Depletion of the cisplatin targeted HMGB-box factor UBF selectively induces p53-independent apoptotic death in transformed cells. Oncotarget. 6, 27519-27536.
Hamdane, N., Stefanovsky, V.Y., Tremblay, M.G., Németh, A., Paquet, E., Lessard, F., Sanij, E., Hannan, R., Moss, T., 2014. Conditional inactivation of upstream binding factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body. PLOS Genet. 10, e1004505.
Heliot, L., Kaplan, H., Lucas, L., Klein, C., Beorchia, A., Doco-Fenzy, M., Menager, M., Thiry, M., O'Donohue, M.-F., Ploton, D., 1997. Electron tomography of metaphase nucleolar organizers regions: evidence for a twisted-loop organization. Mol. Biol. Cell 8, 2199-2216.
Henras, A.K., Plisson-Chastang, C., O'Donohue, M.-F., Chakraborty, A., Gleizes, P.E., 2015. An overview of pre-ribosomal RNA processing in eukaryotes. WIRES RNA 6, 225- 242.
Herdman, C., Mars, J.C., Stefanovsky, V.Y., Tremblay, M.G., Sabourin-Felix, M., Lindsay, H., Robinson, M.D., Moss, T., 2017. A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription. PLoS Genet. 13, e1006899.
Hernandez-Verdun, D., Roussel, P., Thiry, M., Sirri, V., Lafontaine, D., 2010. The nucleolus: structure/function relationship in RNA metabolism. WIRES RNA 1, 415-431.
Hnisz, D., Shrinivas, K., Young, R.A., Chakraborty, A.K., Sharp, P.A., 2017. A phase separation model for transcriptional control. Cell 169, 13-23.
Klein, C., Cheutin, T., O'Donohue, M.-F., Rothblum, L.I., Kaplan, H., Beorchia, A., Lucas, L., Heliot, L., Ploton, D., 1998. The three-dimensional study of chromosomes and of UBF-immunolabeled NOR's demonstrates their non-random spatial arrangement during mitosis. Mol. Biol. Cell 9, 3147-3159.
Klein, J., Grummt, I., 1999. Cell cycle-dependant regulation of RNA polymerase I transcription: the nucleolar transcription factor UBF is inactive in mitosis and early G1. Proc. Natl. Acad. Sci. USA 96, 6096-6101.
Koberna, K., Malinski, J., Pliss, A., Masata, M., Vecerova, M., Fialova, M., Bednar, J., Raska, I., 2002. Ribosomal genes in focus: new transcripts label the dense fibrillar components and form clusters indicative of “Christmas trees” in situ. J. Cell Biol. 157, 743-748.
Krüger, T., Zentgraf, H., Scheer, U., 2007. Intranucleolar sites of ribosome biogenesis defined by the localization of early binding ribosomal proteins. J. Cell Biol. 177, 573-578.
Kuhn, A., Voit, R., Stefanovsky, V., Evers, R., Bianchi, M., Grummt, I., 1994. Functional difference between the two splice variants of the nucleolar transcription factor UBF: the second HMG box determines specifity of DNA binding and transcriptional activity. EMBO J. 13, 416-424.
Lamaye, F., Galliot, S., Alibardi, L., Lafontaine, D.L., Thiry, M., 2011. Nucleolar structure across evolution: the transition between bi- and tri-compartmentalized nucleoli lies within the class Reptilia. J. Struct. Biol. 174, 352-359.
Mais, C., Wright, J.E., Prieto, J.L., Raggett, S.L., McStay, B. 2005. UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery. Genes Dev. 19, 1-15.
Mangan, H., Gailin, M.O., Mcstay, B., 2017. Integrating the genomic architecture of human nucleolar organizer regions with the biophysical properties of nucleoli. FEBS J 284, 3977-3985.
McStay, B., 2016. Nucleolar organizer regions: genomic 'dark matter' requiring illumination. Genes Dev. 30, 1598-610.
Mars, J.C., Sabourin-Felix, M., Tremblay, M.G., Moss, T., 2018. A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes. G3 (Bethesda) 8, 303–314.
Michel, J., Nolin, F., Wortham, L., Lalun, N., Tchelidze, P., Banchet, V., Terryn, C., Ploton, D., 2019. Various nucleolar stress inducers result in highly distinct changes in water, dry mass and elemental content in cancerous cell compartments: investigation using a nano-analytical approach. Nanotheranostics 3, 179-195.
Mitrea, D.M., Kriwack, R.W. 2016. Phase separation in biology; functional organization of a higher order. Cell comm. Signal. 14, 1-20.
Moss, T., 2004. At the crossroads of growth control; making ribosomal RNA. Curr. Opi. Genet. Dev. 14, 1-8.
Moss, T., Mars, J.C., Tremblay, M.G., Sabourin-Felix, M., 2019. The chromatin landscape of the ribosomal RNA genes in mouse and human. Chromosome Res. 27, 31-40.
Nicolas, E., Parisot, P., Pinto-Monteiro, C., de Walque, R., de Vleeschouwer, C., Lafontaine, D.L.J. 2016. Involvement of human ribosomal proteins in nucleolar structure and p53-dependent nucleolar stress. Nat comm. 7, 11390.
Nolin, F., Michel, J., Wortham, L., Tchelidze, P., Balossier, G., Banchet, V., Bobichon, H., Lalun, N., Terryn, C., Ploton, D., 2013. Changes to cellular water and element content induced by nucleolar stress: investigation by a cryo- correlative nano imaging approach. Cell. Mol. Life Sci. 70, 2383- 2394.
O'Mahony, D.J., Rothblum, L.I. 1991a. Identification of two forms of the RNA polymerase I transcription factor UBF. Proc. Natl. Acad. Sci. USA 88, 3180-3184.
O'Mahony, D.J., Smith, S.D., Xie, W., Rothblum, L.I., 1991b. Analysis of the phosphorylation, DNA-binding and dimerization properties of the RNA polymerase I transcription factors UBF1 and UBF2. Nucleic acids research 20, 1301-1308.
Ploton, D., Thiry, M., Ménager, M., Lepoint, A., Adnet, J.J., Goessens, G. 1987. Behaviour of nucleolus during mitosis. A comparative ultrastructural study of various cancerous cell lines using the Ag-NOR staining procedure. Chromosoma 95, 95-107.
Ponti, D., Bellenchi, G.C., Puca, R., Bastianelli, D., Maroder, M., Ragona, G., Roussel, P., Thiry, M., Mercola, D., Calogero, A., 2014. The transcription factor EGR1 localizes to the nucleolus and is linked to suppression of ribosomal precursor synthesis. PLoS One. 9, e96037.
Puvion-Dutilleul, F., Puvion, E., Bachellerie, J.-P. 1997. Early stages of pre-rRNA formation within the nucleolar ultrastructure of mouse cells studied by in situ hybridization with a 5’ETS leader probe. Chromosoma 105, 496-505.
Puvion-Dutilleul, F., Mazan, S., Nicoloso, M., Pichard, E., Bachellerie, J.-P., Puvion, E., 1992. Alterations of nucleolar ultrastructure and ribosome biogenesis by actinomycin D. Implications for U3 snRNP function. Eur. J. Cell Biol. 58, 149-162.
Puvion-Dutilleul, F., Bachellerie, J.-P., Puvion, E., 1991. Nucleolar organization of HeLa cells as studied by in situ hybridization. Chromosoma 100, 395-409.
Raska I, Koberna K, Malínský J, Fidlerová H, Masata M., 2004. The nucleolus and transcription of ribosomal genes. Biol. Cell.96, 579-594.
Roussel, P., Andre, C., Masson, C., Geraud, G., Hernandez-Verdun, D., 1993. Localization of the RNA polymerase I transcription factor hUBF during the cell cycle. J. Cell Sci. 104, 327-337.
Sanborn, A., Rao, S., Huang, S.C., Durand, N., Huntley, M., Jewett, A., Bochkov, I., Chinnappan, D., Cutkosky, A., Li, J., Geeting, K., Gnirke, A., Melnikov, A., McKenna, D., Stamenova, E., Lander, E., Aiden, E., 2015. Chromatin extrusion explains key features of loop and domain formation in wild-type end engineered genomes. Proc. Natl. Acad. Sci. USA 10, 1-41.
Sanij, E., Diesch, J., Lesmana, A., Poortinga, G., Hein, N., Lidgerwood, G., Cameron, D.P., Ellul, J., Goodall, G.J., Wong, L.H., Dhillon, A.S., Hamdane, N., Rothblum, L.I., Pearson, R.B., Haviv, I., Moss, T., Hannan R.D., 2015. A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes. Genome Res. 25, 201-212.
Sanij, E., Poortinga, G., Sharkey, K., Hung, S., Holloway, T.P., Quin, J., Robb, E., Wong, L.H., Thomas, W.G., Stefanovsky, V., Moss, T., Rothblum, L., Hannan, K.M., McArthur, G.A., Pearson, R.B., Hannan, R.D., 2008. UBF levels determine the number of active ribosomal RNA genes in mammals. J. Cell Biol. 183, 1259-1274.
Scheer, U., Hock, R., 1999. Structure and function of the nucleolus. Curr. Opin. Cell Biol. 11,385-390.
Seither, P1., Iben, S., Thiry, M., Grummt, I., 2001. PAF67, a novel protein that is associated with the initiation-competent form of RNA polymerase I. Biol Chem. 382, 1163-1170.
Shav-Tal, Y., Blechman, J., Darzacq, X., Montagna, C., Dye, B.T., Patton, J.G., Singer, R.H., Zipori, D., 2005. Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol. Biol. Cell 16, 2395-2413.
Stefanovsky, V., Langlois, F., Gagnon-Kugler, T., Rothblum, L.I., Moss, T., 2006. Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling. Mol. Cell 21, 629-639.
Tafforeau, L., Zorbas, C., Langhendries, J.L., Mullineux, S.T., Stamatopoulou, V., Mullier, R., Wacheul, L., Lafontaine, D.L.J. 2013. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of pre-rRNA processing factors. Mol. Cell 51, 539-551.
Tchelidze, P., Benassarou, A., Kaplan, H., O'Donohue, M.-F., Lucas, L., Terryn, C., Rusishvili, L., Mosidze, G., Lalun, N., Ploton, D., 2017. Nucleolar sub-compartments in motion during rRNA synthesis inhibition: Contraction of nucleolar condensed chromatin and gathering of fibrillar centers are concomitant. PLoS One 12, e0187977.
Tchelidze, P., Kaplan, H., Beorchia, A., O'Donohue, M.O., Bobichon, H., Lalun, N., Wortham, L., Ploton, D., 2008. Three-dimensional reconstruction of nucleolar components by electron microscope tomography. Hancock, R., ed. The Nucleus: vol 1: Humana Press
Tchelidze, P., Sauvage, C., Bonnet, N., Kilian, L., Beorchia, A., O'Donohue, M.-F., Ploton, D., Kaplan, H., 2006. Electron tomography of amplified nanogold immunolabelling: Improvement of quality based on alignment of projections with sinograms and use of post-reconstruction deconvolution. J. Struct. Biol. 156, 421-431.
Thiry, M., Lafontaine, D., 2005. Birth of a nucleolus: the evolution of nucleolar compartments. Trends Cell Biol. 15, 194-199.
Thiry, M., Cheutin, T., O'Donohue, M.-F., Kaplan, H., Ploton, D., 2000. Dynamics and three-dimensional localization of ribosomal RNA within the nucleolus. RNA 6, 1750-1761.
Thiry, M., Goessens, G., 1996. The nucleolus during the cell cycle. In: Molecular Biology Intelligence Unit, ed. R.G. Landes Company, Springer-Verlag, Heidelberg, Germany.
Thiry, M., Scheer, U., Goessens, G., 1991a. Localization of nucleolar chromatin by immunocytochemistry and in situ hybridization at the electron microscopic level. Electr. Microsc. Rev. 4, 85-110.
Thiry, M., Thiry-Blaise, L., 1991b. Locating transcribed and non-transcribed rDNA spacer sequences within the nucleolus by in situ hybridization and immunoelectron microscopy. Nucleic Acids Res. 19, 11-15.
Trendelenburg, M.F., Zatsepina, O.V., Waschek, T., Schlegel, W., Tröster, H., Rudolph, D., Schmahl, G., Spring, H., 1996. Multiparameter microscopic analysis of nucleolar structure and ribosomal gene transcription. Histochem. Cell Biol. 106, 167-192.
Vaughan, L., Glänzel, W., Korch, C., Capes-Davis, A., 2017. Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature. Cancer Res. 77, 2784-2788.
Zatsepina, O.V., Voit, R., Grummt, I., Spring, H., Semenov, M., Trendelenburg, M.F., 1993. The RNA polymerase I specific transcription factor UBF is associated with transcriptionally active and inactive ribosomal genes. Chromosoma 102, 599-611.