Ribosomal RNA genes shape chromatin domains associating with the nucleolus

Abstract

Genomic interactions can occur in addition to those within chromosome territories and can be organized around nuclear bodies. Several studies revealed how the nucleolus anchors higher order chromatin structures of specific chromosome regions displaying heterochromatic features. In this review, we comment on advances in this emerging field, with a particular focus on a recent study published by Quinodoz et al., that developed a new method to characterize simultaneous genomic interactions in the same cell. Highlighting studies conducted in animal and plant cells, we then discuss the establishment of inactive chromatin at nucleolus organizer region (NOR)-bearing chromosomes.

Keywords: Chromatin; genome organization; nucleolus; rRNA genes.

Figure 1.

Overlap between NADs and NUP1-regions in Arabidopsis thaliana. (a) Genome-wide view of NAD-genes and the regions enriched at the nuclear periphery (NUP1-enriched regions) in the A. thaliana genome produced by Circos [49]. Considering the concentric circles from the outside inward, the outermost (and first) circle indicates the five chromosomes of A. thaliana. The next two circles are showing the location of NADs-genes (blue) and NUP-enriched regions (green) throughout the genome. (b) Venn diagram of NAD-genes and NUP1-enriched regions corresponding to protein-coding genes in TAIR10. Data from [24,34] were used to generate this figure.

Figure 2.

Gene expression of nucleolus-associated genomic regions in A. thaliana. Box plot representing the global expression of genes located in the short arm of NOR-bearing chromosomes 2 and 4 (NOR-bearing Kr) compare to other chromosomes 1, 3 and 5 (other Kr 1, 3 & 5) or all five chromosomes (all Kr) in A. thaliana. A p value < 0.05 *; p value < 0.01: ** (Wilcoxon rank sum test).