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Chromatin organisation during Arabidopsis root development

The genetic information is stored in a highly compact manner in every nucleus. About 150 bp of DNA is packed around a histone octamer constituting a nucleosome. Nucleosomes are linked together by histone H1 and further compaction of this "beads on a string" form higher-order chromatin structures. DNA staining reveals two cytologically different chromatin states: weakly stained euchromatin and brightly stained heterochromatin. Euchromatin is gene-rich and decondensed during interphase, whereas heterochromatin is rich in repetitive sequences, low in gene density, and remains mostly condensed throughout the cell cycle. Euchromatin and heterochromatin differ also by their epigenetic modifications. Epigenetic modifications of chromatin are for example methylated cytosine and acetylation or methylation of histones tails. Acetylation of histones is in general a mark of euchromatin, whereas DNA methylation and histone methylation are marks of heterochromatin. To access the chromatin to perform processes such as DNA replication or to modify the expression of a gene, chromatin remodelling is necessary and performed by chromatin modifiers such as Heterochromatin Protein 1. In this thesis, we studied how chromatin is organised through development of the root of Arabidopsis. This model plant has a simple organized root meristem. Further the distribution of eu- and heterochromatin in interphase nuclei is rather simple. This allows us to follow the chromatin organisation of a cell through development from stem cell into a fully differentiated cell. DNA methylation is one of the most abundant epigenetic modifications and varies through development. It is involved in the defence of the genome against transposable elements and retroviruses, in the control of genomic imprinting and in the regulation of gene expression. In Arabidopsis, we showed that Quiescent Center (QC) cells and stem cells are highly methylated contrarily to stem cells in animals. When cells divide their DNA methylation level decreases to increase again when cells differentiate. DRM1 and DRM2, de novo DNA methyltransferases, and HDA1, a histone deacetyltransferase, appear to be involved in establishing the hypermethylated DNA state in nuclei of QC and stem cells. Heterochromatin Protein 1 in animals is a chromatin modifier first discovered as a protein involved in heterochromatin formation. Nowadays it is thought to be a bridging protein, connecting histones through its chromodomain and non-histone chromosomal proteins through its chromoshadow domain. The homologue of Heterochromatin Protein 1 in Arabidopsis is Like Heterochromatin Protein 1 (LHP1). LHP1 was shown to be located in the euchromatic part of interphase nuclei like the animal isoform HP1γ and to form foci in differentiated cells. We showed that these foci are most likely chromatin complexes bound to the DNA and that LHP1 binds probably trimethylated lysine 9 and/or trimethylated lysine 27 of histone H3. HP1 in animal was shown to bind to trimethylated lysine 9 of histone H3 (H3K9m3) and to interact with the H3K9 trimethyltransferase SU( VAR)3-9. In Arabidopsis, we tried to identify among the family of SU( VAR)3-9 homologues, the SUVH proteins, which is responsible for trimethylating H3K9 and might interact with LHP1. We showed that SUVH3, SUVH7 and SUVH9 are tissue specifically expressed and their encoded proteins are located in the euchromatic regions where they most likely form chromatin complexes. SUVH3 and SUVH9 form foci depending on the developmental stage of the cell. SUVH9 might be a candidate for trimethylating histone H3 lysine 9 however neither SUVH3,-7 or -9 are likely to interact with LHP1.