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.

Cellular stress leads to the formation of membraneless stress assemblies in eukaryotic cells

“…This has been clarified through the finding that the long noncoding RNA NEAT1 (nuclear para‐speckle assembly transcript 1) drives the formation of nuclear paraspeckles by acting as a template for several proteins including FUS . A similar scaffolding role for rRNAs has been shown for the nucleolus …”

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

“…Nucleolus-associated chromatin domains (NADs), essentially composed of repressed chromatin domains, localize at the nucleolar periphery (Németh et al 2010;van Koningsbruggen et al 2010;Pontvianne et al 2016b). Because rRNA gene nuclear distribution has a critical impact in NADs identity both in plant and animal cells (Quinodoz et al 2018;Picart-Picolo et al 2019, we analyzed NADs composition and 3D organization in 20rDNA L6F6. The fifth generation of the 20rDNA L6 (20rDNA L6F5) was transformed with a transgene ectopically expressing the FIBRILLARIN 2 nucleolar protein fused to the yellow fluorescent protein (FIB2:YFP).…”

Chromatin domains in space and their functional implications

“…A comparison between Arabidopsis LADs and NADs revealed that a tiny fraction of the genome is enriched both at the nuclear periphery and the nucleolus [47]; notably, most of these domains overlap with pericentromeric regions at chromosome 4, and to a less extent with those at chromosome 2 ( Figure 1b). The occurrence of interchangeable perinuclear and nucleolar chromatin domains has been found in animals before [5,48].…”