Chromatin - General introduction

Now that the whole Arabidopsis genome is sequenced, the challenge is to learn the function of all plant genes. This will give a better understanding of the mechanisms of plant life.

The role of chromatin organization in regulation of gene expression in Arabidopsis roots

Especially of interest are the mechanisms of plant cell development and differentiation. Recent data from various biological systems indicates that the way the genomic DNA is organized in the cell nucleus is very important. This organization contributes to the regulation of expression of genes during growth and development. Depending on the position in the nucleus, DNA can be present in more condensed or less condensed structures called heterochromatin and euchromatin respectively. Genes that are located in heterochromatin are usually silenced, and whether certain regions are heterochromatic is regulated during development. Such mechanism controlling gene silencing plays an important role in suppressing cancer and in terminal differentiation.

Arabidopsis thaliana has two very important properties which make it a very suitable system for studying the role of chromatin organization in gene regulation. First, it has a relatively simple chromosome organization with heterochromatin blocks in the pericentromeric regions of all five chromosomes, and in the NORs of the chromosomes 2 and 4, which are visible as bright spots (chromocenters) in DAPI stained interphase nuclei (see figure 1A). Heterochromatin regions can be quantified by FISH (fluorescence in situ hybridisation) using the two (peri)centromeric repeats (see figure 1B). Second, Arabidopsis roots display a stereotype cell division pattern with well-defined lineage relationships from embryogenesis onwards. The root is an indeterminate growing organ by which the cells along the root axis are of graded developmental age with the youngest cells near the meristem (including the stem cells) and the oldest cells at the junction with the hypocotyl (see figure 2). The root can therefore be divided in a small zone were the stem cells are located and subsequent zones with (1) dividing differentiating cells (2) differentiated cells that can be reprogrammed and (3) differentiated cells that have lost the ability to obtain another cell fate.

Figure 1.  DAPI staining (A and B) and fluorescence in situ hybridisation (FISH) with pAL1 probe (red signal) and T1J24 probe (green signal) of Arabidopsis interphase nuclei. The DAPI pattern shows 8 bright heterochromatic chromocentres, which are recognised by the two pericentromeric probes.
Figure 1. DAPI staining (A and B) and fluorescence in situ hybridisation (FISH) with pAL1 probe (red signal) and T1J24 probe (green signal) of Arabidopsis interphase nuclei. The DAPI pattern shows 8 bright heterochromatic chromocentres, which are recognised by the two pericentromeric probes.
Figure 2. Organisation of tissues in the Arabidopsis root.
Figure 2. Organisation of tissues in the Arabidopsis root.
Several genes are already known to play a role in the DNA organization of the nucleus, and homologous genes have been found in a wide range of eukaryotes. This showed that mechanisms controlling chromatin organization are well conserved in eukaryotes. Plants with mutations in chromatin remodelling genes can help to understand the role of DNA organization in development. Such plant mutants are searched in a genome wide manner and investigated in detail. As the aim is to understand the mechanism controlling the organization in the nucleus, special technologies that allow studies on nuclear organisation in living cells will be developed. New applications of the light microscope in combination with fluorescence detection are going to be important in these investigations. We will look in detail to the nucleus during development of cells in the Arabidopsis root in order to understand how and when a cell decides to divide and develop. In these investigations, we will learn how cells and nuclei cope with their genomic information to come to proper decisions. Since the mechanisms controlling nuclear organization are conserved from animals to plants, Arabidopsis can be used as a model to obtain insight in such general mechanisms that are also relevant for human nuclear organization. This has an impact for e.g. tumour biology and in vitro formation of human organs.