Structure and epigenetics of nucleoli in comparison with non-nucleolar compartments

Abstract

The nucleolus is a nuclear compartment that plays an important role in ribosome biogenesis. Some structural features and epigenetic patterns are shared between nucleolar and non-nucleolar compartments. For example, the location of transcriptionally active mRNA on extended chromatin loop species is similar to that observed for transcriptionally active ribosomal DNA (rDNA) genes on so-called Christmas tree branches. Similarly, nucleolus organizer region-bearing chromosomes located a distance from the nucleolus extend chromatin fibers into the nucleolar compartment. Specific epigenetic events, such as histone acetylation and methylation and DNA methylation, also regulate transcription of both rRNA- and mRNA-encoding loci. Here, we review the epigenetic mechanisms and structural features that regulate transcription of ribosomal and mRNA genes. We focus on similarities in epigenetic and structural regulation of chromatin in nucleoli and the surrounding non-nucleolar region and discuss the role of proteins, such as heterochromatin protein 1, fibrillarin, nucleolin, and upstream binding factor, in rRNA synthesis and processing.

Figure 1

Structure and organization of nucleoli and nucleolar organizer regions (NORs). (A) Illustration of nucleolar structure (adapted from Boisvert et al. 2007), showing the fibrillar center (FC), dense fibrillar component (DFC), and granular component (GC). Transcription of ribosomal genes likely proceeds at the border between the FC and DFC. Pre-rRNA is processed and modified by small nucleolar RNPs (snoRNPs) in the DFC. The 5.8S and 28S rRNA associate with 5S RNA in the GC, involving 18S rRNA. Finally, 40S and 60S ribosome subunits in the nucleoplasm are transported to the cytoplasm, where ribosomes with integrated mRNA are assembled. With permission, Boisvert et al. Nat Rev Mol Cell Biol 8:574–585, 2007. (B) Animation of the arrangement of mouse centromeric clusters known as chromocenters (blue) around nucleoli, visualized by an antibody against fibrillarin (red). In the normal (SUV39h wild type) mouse immortalized fibroblasts, nucleoli are larger than in cells with abrogated SUV39h HMT function [SUV39h double null (dn)]. Immortalization likely increases the number of nucleoli. These data show the influence of changes in the histone code on the morphology of nucleoli.

Figure 2

Illustration of epigenetic modifications at rDNA. (A) Micrographs of primary mouse embryonic fibroblasts with single, densely stained nucleoli (Nu). (B) Detail of nucleolus with known epigenetic modifications to rDNA. (C) Scheme of epigenetic regulation of rDNA transcription and silencing. (D) Silver-stained NORs (Ag-NORs) in SUV39h wild-type (wt) and (E) SUV39h double null (dn) fibroblasts. SUV39h deficiency caused changes in the morphology of Ag-NORs. Bar = 1 μm.

Figure 3

An example of selected histone modifications and how HDAC and Dnmts inhibitors change their nucleolar compartment localization. (A1) H3K9me2 in control and 5-azacytidine–treated human small-cell-lung carcinoma A549 cells. (A2) H3K9me2 in centromeric regions of human acrocentric chromosomes 14 and 22 (adapted from Skalníková et al. 2007). (B) H3K4me2 in control and TSA-treated A549 cells. TSA caused an increase in H3K4me2 in the nucleolar compartment (white frame). (C1) Absence of H3K4me2 at centromeres 14 and 22 (red spots). (C2) Association of centromere of human Y chromosome (red spot) with nucleoli. (C3) Absence of H3K9 acetylation at centromeres of human chromosomes (HSA) 9 (red) and 10 (green) in control and TSA-treated A549 cells. Both chromosomes associated with nucleoli even though they are not NOR related. Bar = 1 μm. With permission, Skalníková et al. Physiol Res 56:797–806, 2007.