Insights into chromatin structure and dynamics in plants

Abstract

The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.

Figure 1

Organizational network of chromatin in the cell. Scheme depicting different aspects of chromatin regulation. PTM, post-translational modification. Chromosome territories within the nucleus, shown in different colours, are composed of chromatin fibres, which, in turn, contain packed nucleosomes.

Figure 2

Rabl chromosome organization in wheat root tissue. (a) Centromeres (green) and telomeres (red) are labelled by fluorescence in situ hybridization (FISH) and are located at opposite sides of the nuclei; (b) Diagrammatic interpretation of the organization in (a); (c) Introgressed pair of rye chromosomes in wheat labelled by genomic in situ hybridization (GISH) with total rye genomic probe confirms a Rabl organization of individual CTs. (d) Single rye arm translocation into wheat localized by GISH. In (c) and (d) the RH panel in each case shows a nucleus from a seedling treated with 5-AC, whereas the LH panel shows a control untreated seedling. The 5-AC treatment has disrupted the CT organization, but the CTs remain in a Rabl configuration. Bar = 10 µm.

Figure 3

Decondensation of the Sad1 gene locus in oat root visualized using different coloured probes for the 5' and 3' ends of the gene. (a) Diagram of the labelling scheme used; the 5' portion is labelled in green, the 3' portion in red; (b) Examples of G2 nuclei from tissue labelled with the two probes. In the epidermal cells, where Sad1 is actively transcribed, the red and green ends of the gene can be seen to be separated, whereas they overlap to a much greater extent in the cortex cells, where Sad1 is not transcribed. Bar = 5 m; (c) A gallery of Sad1 double labelled sites from different nuclei. Bar = 1 µm.

Figure 4

Vernalization in Arabidopsis involves Polycomb-mediated epigenetic silencing of FLOWERING LOCUS C (FLC) and physical clustering of FLC alleles. (a) Schematic representation of changes in FLC expression during vernalization; (b) FLC nuclear position was monitored in root nuclei using a FLC-lacO transgene. The lacO array was inserted downstream of the polyadenylation site of FLC; (c–d) Representative fluorescence images of Arabidopsis root cells in plants grown in warmth conditions (non-vernalized, NV) (c) and plants grown in cold for 2 weeks (vernalized, +V) (d). (scale bars: 5 μm).