Three-dimensional organization of chromatin across the plant cell cycle
Final Report Abstract
DNA is the carrier of all genetic information. Beyond the genomic sequence, its peculiar three-dimensional structure largely varies during the cell cycle. Its different conformations and organization inside the nucleus are now recognized to affect epigenetic regulation. It is becoming increasingly important to understand the mechanisms that drive the spatial organization of the genome. In this project, we set out to uncover the conformational differences of barley chromosomes between different stages of the cell cycle. We used chromosome conformation capture sequencing (Hi-C) and super-resolution microscopy, assisted with polymer simulations, to propose and build a coherent model of metaphase chromosomes. Our varied microscopy methods offer broad possibilities for verifying our model in different species. We also applied the mechanisms of condensation, which we identified during this project, to describe the organization of holocentric chromosomes, approaching general rules of chromosome condensation that could reflect differences between species and increasing genome sizes during evolution.
Publications
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2020. Mitotic chromosome organization: General rules meet species-specific variability. Comput Struct Biotechnol J 18:1311-1319
Beseda T, Capal P, Kubalova I, Schubert V, Dolezel J, Simkova H
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2020. Prospects and limitations of expansion microscopy in chromatin ultrastructure determination. Chromosome Res 28:355-368
Kubalová I, Černohorská Schmidt M, Huranová M, Weisshart K, Houben A, Schubert V
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2021. A protocol to expand plant nuclei. Methods Cell Biol 161:197-216
Kubalová I, Černohorská Schmidt M, Huranová M, Weisshart K, Houben A, Schubert V
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2021. Comparing super-resolution microscopy techniques to analyze chromosomes. Int J Mol Sci 22
Kubalová I, Nemeckova A, Weisshart K, Hribova E, Schubert V
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2021. Hordeum vulgare L. Poaceae - Expansion microscopy. Chromosome Biology Calendar 2021. 4th Edition. IPK Gatersleben, Germany
Kubalová I, Černohorská Schmidt M, Huranová M, Weisshart K, Houben A, Schubert V
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2021. Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds. Chromosoma 130:15-25
Hoang PTN, Rouillard JM, Macas J, Kubalová I, Schubert V, Schubert I
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A simple model explains the cell cycle-dependent assembly of centromeric nucleosomes in holocentric species. (2021) Nucleic Acids Research
Amanda Souza Câmara, Veit Schubert, Martin Mascher, Andreas Houben
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Helical metaphase chromatid coiling is conserved (2021)
Ivona Kubalová, Amanda Souza Câmara, Petr Cápal, Tomáš Beseda, Jean-Marie Rouillard, Gina Marie Krause, Helena Toegelová, Axel Himmelbach, Nils Stein, Andreas Houben, Jaroslav Doležel, Martin Mascher, Hana Šimková, Veit Schubert
