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Chromosoma

pp 1–9 | Cite as

Heterochromatin restricts the mobility of nuclear bodies

  • Eugene A. Arifulin
  • Dmitry V. Sorokin
  • Anna V. Tvorogova
  • Margarita A. Kurnaeva
  • Yana R. Musinova
  • Oxana A. Zhironkina
  • Sergey A. Golyshev
  • Sergey S. Abramchuk
  • Yegor S. Vassetzky
  • Eugene V. Sheval
Original Article

Abstract

Nuclear bodies are relatively immobile organelles. Here, we investigated the mechanisms underlying their movement using experimentally induced interphase prenucleolar bodies (iPNBs). Most iPNBs demonstrated constrained diffusion, exhibiting infrequent fusions with other iPNBs and nucleoli. Fusion events were actin-independent and appeared to be the consequence of stochastic collisions between iPNBs. Most iPNBs were surrounded by condensed chromatin, while fusing iPNBs were usually found in a single heterochromatin-delimited compartment (“cage”). The experimentally induced over-condensation of chromatin significantly decreased the frequency of iPNB fusion. Thus, the data obtained indicate that the mobility of nuclear bodies is restricted by heterochromatin.

Keywords

Nucleus Chromatin Nuclear body Mobility 

Notes

Acknowledgements

We are grateful to X.W. Wang for the EGFP-NPM1-expressing plasmid and to G.M. Wahl for the histone H2B-EGFP-expressing plasmid. The work of Y.R.M. and Y.V. was partially conducted in the frame of the Koltzov Institute of Developmental Biology government program of basic research №. 0108-2018-0004.

Funding information

The work was supported by the Russian Science Foundation (the light and electron microscopy by the grant 18-14-00195 to E.V.S.; the image processing and trajectory analysis by the grant 17-11-01279 to D.V.S.). The confocal laser scanning microscopy was supported by the Moscow State University Development Program (PNR 5.13), the Russian Foundation for Basic Research (project 18-04-00130), and the President’s grant (MK-716.2018.4).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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References

  1. Albiez H, Cremer M, Tiberi C, Vecchio L, Schermelleh L, Dittrich S, Küpper K, Joffe B, Thormeyer T, von Hase J, Yang S, Rohr K, Leonhardt H, Solovei I, Cremer C, Fakan S, Cremer T (2006) Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosom Res 14:707–733.  https://doi.org/10.1007/s10577-006-1086-x CrossRefGoogle Scholar
  2. Arifulin EA, Musinova YR, Vassetzky YS, Sheval EV (2018) Mobility of nuclear components and genome functioning. Biochem Mosc 83:690–700.  https://doi.org/10.1134/S0006297918060068 CrossRefGoogle Scholar
  3. Bosse JB, Hogue IB, Feric M, Thiberge SY, Sodeik B, Brangwynne CP, Enquist LW (2015) Remodeling nuclear architecture allows efficient transport of herpesvirus capsids by diffusion. Proc Natl Acad Sci U S A 112:E5725–E5733.  https://doi.org/10.1073/pnas.1513876112 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bronshtein I, Kepten E, Kanter I, Berezin S, Lindner M, Redwood AB, Mai S, Gonzalo S, Foisner R, Shav-Tal Y, Garini Y (2015) Loss of lamin A function increases chromatin dynamics in the nuclear interior. Nat Commun 6:8044.  https://doi.org/10.1038/ncomms9044 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bronshtein I, Kanter I, Kepten E, Lindner M, Berezin S, Shav-Tal Y, Garini Y (2016) Exploring chromatin organization mechanisms through its dynamic properties. Nucleus 7:27–33.  https://doi.org/10.1080/19491034.2016.1139272 CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bustin M, Misteli T (2016) Nongenetic functions of the genome. Science 352:aad6933.  https://doi.org/10.1126/science.aad6933 CrossRefPubMedGoogle Scholar
  7. Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18:1119–1130.  https://doi.org/10.1101/gad.292104 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Chang L, Godinez WJ, Kim IH, Tektonidis M, de Lanerolle P, Eils R, Rohr K, Knipe DM (2011) Herpesviral replication compartments move and coalesce at nuclear speckles to enhance export of viral late mRNA. Proc Natl Acad Sci U S A 108:E136–E144.  https://doi.org/10.1073/pnas.1103411108 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–1491.  https://doi.org/10.1016/j.cell.2013.12.001 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Chenouard N, Bloch I, Olivo-Marin J-C (2013) Multiple hypothesis tracking for cluttered biological image sequences. IEEE Trans Pattern Anal Mach Intell 35:2736–3750CrossRefGoogle Scholar
  11. Cremer M, Schmid VJ, Kraus F, Markaki Y, Hellmann I, Maiser A, Leonhardt H, John S, Stamatoyannopoulos J, Cremer T (2017) Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters. Epigenetics Chromatin 10:39.  https://doi.org/10.1186/s13072-017-0146-0 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Daumas F, Destainville N, Millot C, Lopez A, Dean D, Salomé L (2003) Confined diffusion without fences of a g-protein-coupled receptor as revealed by single particle tracking. Biophys J 84:356–366.  https://doi.org/10.1016/S0006-3495(03)74856-5 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Dion V, Gasser SM (2013) Chromatin movement in the maintenance of genome stability. Cell 152:1355–1364.  https://doi.org/10.1016/j.cell.2013.02.010 CrossRefPubMedGoogle Scholar
  14. Dundr M (2012) Nuclear bodies: multifunctional companions of the genome. Curr Opin Cell Biol 24:415–422.  https://doi.org/10.1016/j.ceb.2012.03.010 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Dundr M, Ospina JK, Sung MH, John S, Upender M, Ried T, Hager GL, Matera AG (2007) Actin-dependent intranuclear repositioning of an active gene locus in vivo. J Cell Biol 179:1095–1103.  https://doi.org/10.1083/jcb.20071005 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Foltánková V, Matula P, Sorokin D, Kozubek S, Bártová E (2013) Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body colocalization in DNA lesions. Microsc Microanal 19:360–369.  https://doi.org/10.1017/S1431927612014353 CrossRefPubMedGoogle Scholar
  17. Gilerovitch HG, Bishop GA, King JS, Burry RW (1995) The use of electron microscopic immunocytochemistry with silver-enhanced 1.4-nm gold particles to localize GAD in the cerebellar nuclei. J Histochem Cytochem 43:337–343CrossRefGoogle Scholar
  18. Görisch SM, Wachsmuth M, Ittrich C, Bacher CP, Rippe K, Lichter P (2004) Nuclear body movement is determined by chromatin accessibility and dynamics. Proc Natl Acad Sci U S A 101:13221–13226.  https://doi.org/10.1073/pnas.0402958101 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Hameed FM, Rao M, Shivashankar GV (2012) Dynamics of passive and active particles in the cell nucleus. PLoS One 7:e45843.  https://doi.org/10.1371/journal.pone.0045843 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Iarovaia OV, Rubtsov M, Ioudinkova E, Tsfasman T, Razin SV, Vassetzky YS (2014) Dynamics of double strand breaks and chromosomal translocations. Mol Cancer 13:249.  https://doi.org/10.1186/1476-4598-13-249 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Irianto J, Swift J, Martins RP, McPhail GD, Knight MM, Discher DE, Lee DA (2013) Osmotic challenge drives rapid and reversible chromatin condensation in chondrocytes. Biophys J 104:759–769.  https://doi.org/10.1016/j.bpj.2013.01.006 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kanda T, Sullivan KF, Wahl GM (1998) Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr Biol 8:377–385CrossRefGoogle Scholar
  23. Khanna N, Hu Y, Belmont AS (2014) HSP70 transgene directed motion to nuclear speckles facilitates heat shock activation. Curr Biol 24:1138–1144.  https://doi.org/10.1016/j.cub.2014.03.053 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Kim J, Han KY, Khanna N, Ha T, Belmont AS (2018) Nuclear speckle fusion via long-range directional motion regulates the number and size of speckles. bioRxiv 347955.  https://doi.org/10.1101/347955
  25. Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T (2007) Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 8:104–115.  https://doi.org/10.1038/nrg2041 CrossRefPubMedGoogle Scholar
  26. Levi V, Ruan Q, Plutz M, Belmont AS, Gratton E (2005) Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope. Biophys J 89:4275–4285.  https://doi.org/10.1529/biophysj.105.066670 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Mehta IS, Amira M, Harvey AJ, Bridger JM (2010) Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts. Genome Biol 11:R5.  https://doi.org/10.1186/gb-2010-11-1-r5 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Michalet X (2010) Mean square displacement analysis of single-particle trajectories with localization error: Brownian motion in an isotropic medium. Phys Rev E Stat Nonlinear Soft Matter Phys 82:041914.  https://doi.org/10.1103/PhysRevE.82.041914 CrossRefGoogle Scholar
  29. Muratani M, Gerlich D, Janicki SM, Gebhard M, Eils R, Spector DL (2002) Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nat Cell Biol 4:106–110.  https://doi.org/10.1038/ncb740 CrossRefPubMedGoogle Scholar
  30. Musinova YR, Lisitsyna OM, Golyshev SA, Tuzhikov AI, Polyakov VY, Sheval EV (2011) Nucleolar localization/retention signal is responsible for transient accumulation of histone H2B in the nucleolus through electrostatic interactions. Biochim Biophys Acta 1813:27–38.  https://doi.org/10.1016/j.bbamcr.2010.11.003 CrossRefPubMedGoogle Scholar
  31. Musinova YR, Kananykhina EY, Potashnikova DM, Lisitsyna OM, Sheval EV (2015) A charge-dependent mechanism is responsible for the dynamic accumulation of proteins inside nucleoli. Biochim Biophys Acta 1853:101–110.  https://doi.org/10.1016/j.bbamcr.2014.10.007 CrossRefPubMedGoogle Scholar
  32. Musinova YR, Lisitsyna OM, Sorokin DV, Arifulin EA, Smirnova TA, Zinovkin RA, Potashnikova DM, Vassetzky YS, Sheval EV (2016) RNA-dependent disassembly of nuclear bodies. J Cell Sci 129:4509–4520.  https://doi.org/10.1242/jcs.189142 CrossRefPubMedGoogle Scholar
  33. Pellar GJ, DiMario PJ (2003) Deletion and site-specific mutagenesis of nucleolins carboxy GAR domain. Chromosoma 111:461–469.  https://doi.org/10.1007/s00412-003-0231-y CrossRefPubMedGoogle Scholar
  34. Platani M, Goldberg I, Lamond AI, Swedlow JR (2002) Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4:502–508.  https://doi.org/10.1038/ncb809 CrossRefPubMedGoogle Scholar
  35. Shachar S, Misteli T (2017) Causes and consequences of nuclear gene positioning. J Cell Sci 130:1501–1508.  https://doi.org/10.1242/jcs.199786 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL, Singer RH (2004) Dynamics of single mRNPs in nuclei of living cells. Science 304:1797–1800.  https://doi.org/10.1126/science.1099754 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Sorokin DV, Peterlik I, Tektonidis M, Rohr K, Matula P (2018) Non-rigid contour-based registration of cell nuclei in 2D live cell microscopy images using a dynamic elasticity model. IEEE Trans Med Imaging 37(1):173–184.  https://doi.org/10.1109/TMI.2017.2734169 CrossRefPubMedGoogle Scholar
  38. Soutoglou E, Misteli T (2007) Mobility and immobility of chromatin in transcription and genome stability. Curr Opin Genet Dev 17:435–442.  https://doi.org/10.1016/j.gde.2007.08.004 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Stixová L, Matula P, Kozubek S, Gombitová A, Cmarko D, Raška I, Bártová E (2012) Trajectories and nuclear arrangement of PML bodies are influenced by A-type Lamin deficiency. Biol Cell 104:418–432.  https://doi.org/10.1111/boc.201100053 CrossRefPubMedGoogle Scholar
  40. Ulianov SV, Gavrilov AA, Razin SV (2015) Nuclear compartments, genome folding, and enhancer-promoter communication. Int Rev Cell Mol Biol 315:183–244.  https://doi.org/10.1016/bs.ircmb.2014.11.004 CrossRefPubMedGoogle Scholar
  41. Visvanathan A, Ahmed K, Even-Faitelson L, Lleres D, Bazett-Jones DP, Lamond AI (2013) Modulation of higher order chromatin conformation in mammalian cell nuclei can be mediated by polyamines and divalent cations. PLoS One 8:e67689.  https://doi.org/10.1371/journal.pone.0067689 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Walter A, Chapuis C, Huet S, Ellenberg J (2013) Crowded chromatin is not sufficient for heterochromatin formation and not required for its maintenance. J Struct Biol 184:445–453.  https://doi.org/10.1016/j.jsb.2013.10.004 CrossRefPubMedGoogle Scholar
  43. Wang W, Budhu A, Forgues M, Wang XW (2005) Temporal and spatial control of nucleophosmin by the Ran-Crm1 complex in centrosome duplication. Nat Cell Biol 7:823–830.  https://doi.org/10.1038/ncb1282 CrossRefPubMedGoogle Scholar
  44. Zatsepina OV, Dudnic OA, Todorov IT, Thiry M, Spring H, Trendelenburg MF (1997) Experimental induction of prenucleolar bodies (PNBs) in interphase cells: interphase PNBs show similar characteristics as those typically observed at telophase of mitosis in untreated cells. Chromosoma 105:418–430CrossRefGoogle Scholar
  45. Zhang Q, Kota KP, Alam SG, Nickerson JA, Dickinson RB, Lele TP (2016) Coordinated dynamics of RNA splicing speckles in the nucleus. J Cell Physiol 231:1269–1275.  https://doi.org/10.1002/jcp.25224 CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Eugene A. Arifulin
    • 1
  • Dmitry V. Sorokin
    • 2
  • Anna V. Tvorogova
    • 1
  • Margarita A. Kurnaeva
    • 1
  • Yana R. Musinova
    • 1
    • 3
  • Oxana A. Zhironkina
    • 1
  • Sergey A. Golyshev
    • 1
  • Sergey S. Abramchuk
    • 4
  • Yegor S. Vassetzky
    • 3
    • 5
    • 6
  • Eugene V. Sheval
    • 1
    • 5
    • 7
  1. 1.Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
  2. 2.Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and CyberneticsLomonosov Moscow State UniversityMoscowRussia
  3. 3.Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscowRussia
  4. 4.Faculty of ChemistryLomonosov Moscow State UniversityMoscowRussia
  5. 5.LIA 1066 LFR2O French-Russian Joint Cancer Research LaboratoryVillejuifFrance
  6. 6.UMR8126, CNRS, Institut de Cancérologie Gustave RoussyUniversité Paris-SudVillejuifFrance
  7. 7.Department of Cell Biology and Histology, Faculty of BiologyLomonosov Moscow State UniversityMoscowRussia

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