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Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

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Abstract

The spatial chromatin organisation and molecular interactions within and between chromatin domains and chromosome territories (CTs) are essential for fundamental processes such as replication, transcription and DNA repair via homologous recombination. To analyse the distribution and interaction of whole CTs, centromeres, (sub)telomeres and ~100-kb interstitial chromatin segments in endopolyploid nuclei, specific FISH probes from Arabidopsis thaliana were applied to 2–64C differentiated leaf nuclei. Whereas CTs occupy a distinct and defined volume of the nucleus and do not obviously intermingle with each other in 2–64C nuclei, ~100-kb sister chromatin segments within these CTs become more non-cohesive with increasing endopolyploidy. Centromeres, preferentially located at the nuclear periphery, may show ring- or half-moon like shapes in 2C and 4C nuclei. Sister centromeres tend to associate up to the 8C level. From 16C nuclei on, they become progressively separated. The higher the polyploidy level gets, the more separate chromatids are present. Due to sister chromatid separation in highly endopolyploid nuclei, the centromeric histone variant CENH3, the 180-bp centromeric repeats and pericentromeric heterochromatin form distinct subdomains at adjacent but not intermingling positions. The (sub)telomeres are frequently associated with each other and with the nucleolus and less often with centromeres. The extent of chromatid separation and of chromatin decondensation at subtelomeric chromatin segments varies between chromosome arms. A mainly random distribution and similar shapes of CTs even at higher ploidy levels indicate that in general no substantial CT reorganisation occurs during endopolyploidisation. Non-cohesive sister chromatid regions at chromosome arms and at the (peri)centromere are accompanied by a less dense chromatin conformation in highly endopolyploid nuclei. We discuss the possible function of this conformation in comparison to transcriptionally active regions at insect polytene chromosomes.

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Acknowledgements

We thank Jörg Fuchs for flow sorting of nuclei, Martina Kühne, Andrea Kunze, Joachim Bruder and Rita Schubert for excellent technical assistance, Ingo Schubert and Andreas Houben for critical reading of the manuscript.

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  1. Alexandre Berr

    Present address: Institut de Biologie Moléculaire des Plantes (IBMP), Laboratoire Propre du CNRS (UPR2357) conventionné avec l’Université de Strasbourg (UdS), 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France

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  1. Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Gatersleben, Germany

    Veit Schubert, Alexandre Berr & Armin Meister

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  1. Veit Schubert
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  2. Alexandre Berr
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Correspondence to Veit Schubert.

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Communicated by Peter Shaw

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Schubert, V., Berr, A. & Meister, A. Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness. Chromosoma 121, 369–387 (2012). https://doi.org/10.1007/s00412-012-0367-8

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