Skip to main content
SpringerLink
Log in

A Method for Testing Random Spatial Models on Nuclear Object Distributions

  • Protocol
  • First Online:
Plant Chromatin Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1675))

Abstract

The cell nucleus is a structurally complex and dynamic organelle ensuring key biological functions. Complex relationships between nuclear structure and functions require a better understanding of the three-dimensional organization of the genome and of the subnuclear compartments. Quantitative image analysis coupled with spatial statistics and modeling is a relevant approach to address these questions. In this chapter, we describe a step-by-step procedure to process images and to test a spatial random model for the distribution of nuclear objects using chromocenters as an example. More elaborate models can be designed on the basis of the random model by introducing additional and more complex constraints to better fit observations and to question determinants of these spatial organizations.

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

Access this chapter

Log in via an institution

Institutional subscriptions

References

  1. Del Prete S, Arpón J, Sakai K, Andrey P, Gaudin V (2014) Nuclear architecture and chromatin dynamics in interphase nuclei of Arabidopsis thaliana. Cytogenet Genome Res 143(1–3):28–50

    Article  PubMed  Google Scholar 

  2. Fang Y, Spector DL (2005) Centromere positioning and dynamics in living Arabidopsis plants. Mol Biol Cell 16(12):5710–5718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ballester M, Kress C, Hue-Beauvais C, Kiêu K, Lehmann G, Adenot P, Devinoy E (2008) The nuclear localization of WAP and CSN genes is modified by lactogenic hormones in HC11 cells. J Cell Biochem 105(1):262–270

    Article  CAS  PubMed  Google Scholar 

  4. Andrey P, Kiêu K, Kress C, Lehmann G, Tirichine L, Liu Z, Biot E, Adenot P-G, Hue-Beauvais C, Houba-Hérin N, Duranthon V, Devinoy E, Beaujean N, Gaudin V, Maurin Y, Debey P (2010) Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol 6(7):e1000853

    Article  PubMed  PubMed Central  Google Scholar 

  5. Ernoult-Lange M, Baconnais S, Harper M, Minshall N, Souquere S, Boudier T, Bénard M, Andrey P, Pierron G, Kress M, Standart N, le Cam E, Weil D (2012) Multiple binding of repressed mRNAs by the P-body protein Rck/p54. RNA 18(9):1702–1715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9(7):671–675

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez J-Y, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682

    Article  CAS  PubMed  Google Scholar 

  8. Poulet A, Arganda-Carreras I, Legland D, Probst AV, Andrey P, Tatout C (2015) NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics 31(7):1144–1146

    Article  CAS  PubMed  Google Scholar 

  9. Andrey P, Maurin Y (2005) Free-D: an integrated environment for three-dimensional reconstruction from serial sections. J Neurosci Methods 145(1–2):233–244

    Article  PubMed  Google Scholar 

  10. Biot E, Crowell E, Burguet J, Höfte H, Vernhettes S, Andrey P (2016) Strategy and software for the statistical spatial analysis of 3D intracellular distributions. Plant J 87(2):230–242

    Article  CAS  PubMed  Google Scholar 

  11. Pecinka A, Schubert V, Meister A, Kreth G, Klatte M, Lysak MA, Fuchs J, Schubert I (2004) Chromosome territory arrangement and homologous pairing in nuclei of Arabidopsis thaliana are predominantly random except for NOR-bearing chromosomes. Chromosoma 113(5):258–269

    Article  CAS  PubMed  Google Scholar 

  12. Baroux C, Pecinka A, Fuchs J, Kreth G, Schubert I, Grossniklaus U (2017) Non-random chromosome arrangement in triploid endosperm nuclei. Chromosoma 126(1):115-124

    Article  CAS  PubMed  Google Scholar 

  13. Tirichine L, Andrey P, Biot E, Maurin Y, Gaudin V (2009) 3D fluorescent in situ hybridization using Arabidopsis leaf cryosections and isolated nuclei. Plant Methods 5:11

    Article  PubMed  PubMed Central  Google Scholar 

  14. She W, Baroux C (2014) Chromatin dynamics during plant sexual reproduction. Front Plant Sci 5:354

    Article  PubMed  PubMed Central  Google Scholar 

  15. Lindhout BI, Fransz P, Tessadori F, Meckel T, Hooykaas PJJ, van der Zaal BJ (2007) Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins. Nucleic Acids Res 35(16):e107

    Article  PubMed  PubMed Central  Google Scholar 

  16. Linkert M, Rueden CT, Allan C, Burel J-M, Moore W, Patterson A, Loranger B, Moore J, Neves C, MacDonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri KW, Swedlow JR (2010) Metadata matters: access to image data in the real world. J Cell Biol 189(5):777–782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Legland D, Arganda-Carreras I, Andrey P (2016) MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics 32(22):3532–3534

    CAS  PubMed  Google Scholar 

  18. R Development Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0

    Google Scholar 

  19. Otsu N (1979) A threshold selection method from gray-level histograms. IEEE Trans Syst Man Cybern 9(1):62–66

    Article  Google Scholar 

  20. Soille P (2003) Morphological image analysis: principles and applications, 2nd edn. Springer, Berlin, Germany

    Google Scholar 

  21. Vincent L, Soille P (1991) Watersheds in digital spaces: an efficient algorithm based on immersion simulation. IEEE Trans Pattern Anal Mach Intell 13(6):583–598

    Article  Google Scholar 

  22. Lorensen WE, Cline HE (1987) Marching cubes: a high resolution 3D surface construction algorithm. ACM Comput Graph 21(4):163–169

    Article  Google Scholar 

  23. Diggle PJ (2014) Statistical analysis of spatial and spatio-temporal point patterns, 3rd edn. Chapman and Hall/CRC Press, Boca Raton

    Google Scholar 

  24. Baddeley A, Diggle PJ, Hardegen A, Lawrence T, Milne RK, Nair G (2014) On tests of spatial pattern based on simulation envelopes. Ecol Monogr 84(3):477–489

    Article  Google Scholar 

  25. Arnold TB, Emerson JW (2011) Nonparametric goodness-of-fit tests for discrete null distributions. R J 3(2):34–39

    Google Scholar 

Download references

Acknowledgements

JA was supported by a PhD fellowship provided by the European Commission Seventh Framework-People-2012-ITN project EpiTRAITS (Epigenetic regulation of economically important plant traits, no-316965). The IJPB benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).

Author information

Authors and Affiliations

  1. Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France

    Javier Arpòn, Valérie Gaudin & Philippe Andrey

Authors
  1. Javier Arpòn
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Valérie Gaudin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Philippe Andrey
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Philippe Andrey .

Editor information

Editors and Affiliations

  1. Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

    Marian Bemer

  2. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

    Célia Baroux

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Arpòn, J., Gaudin, V., Andrey, P. (2018). A Method for Testing Random Spatial Models on Nuclear Object Distributions. In: Bemer, M., Baroux, C. (eds) Plant Chromatin Dynamics. Methods in Molecular Biology, vol 1675. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7318-7_29

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7318-7_29

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7317-0

  • Online ISBN: 978-1-4939-7318-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation