The Nucleolus: In Genome Maintenance and Repair

Abstract

The nucleolus is the subnuclear membrane-less organelle where rRNA is transcribed and processed and ribosomal assembly occurs. During the last 20 years, however, the nucleolus has emerged as a multifunctional organelle, regulating processes that go well beyond its traditional role. Moreover, the unique organization of rDNA in tandem arrays and its unusually high transcription rates make it prone to unscheduled DNA recombination events and frequent RNA:DNA hybrids leading to DNA double strand breaks (DSBs). If not properly repaired, rDNA damage may contribute to premature disease onset and aging. Deregulation of ribosomal synthesis at any level from transcription and processing to ribosomal subunit assembly elicits a stress response and is also associated with disease onset. Here, we discuss how genome integrity is maintained within nucleoli and how such structures are functionally linked to nuclear DNA damage response and repair giving an emphasis on the newly emerging roles of the nucleolus in mammalian physiology and disease.

Keywords: DNA repair; nucleolus; nucleus; ribosomal DNA.

Figure 1

The function of nucleolus. In normal state, the RNA Pol I machinery transcribes a polycistronic pre-rRNA molecule, which is subsequently processed to mature rRNAs (18S, 5.8S, and 28S) of the small and large ribosomal subunit. Outside the nucleolus, RNA Pol III transcribes the fourth rRNA (5S), while RNA Pol II transcribes the ribosomal protein genes to be translated in the cytoplasm. Ribosomal proteins of the large (RPLs) and the small (RPSs) subunit enter the nucleolus to associate with rRNAs and assemble the ribosomal subunits, which are then exported to the cytoplasm.

Figure 2

The nucleolar response to DNA damage. (a) DSBs in the rDNA cause nucleolar segregation and nucleolar cap formation. While DSBs outside the nucleolus result in a global nuclear response, DNA damage inside the nucleolus elicits only a localized response. DNA damage kinases, ATM and DNA-PK, inhibit RNA Pol I to cease transcription and subsequent rRNA processing and ribosomal assembly. Ribosomal proteins and possibly nucleolar proteins activate the P53 pathway. Damaged DNA is predominantly repaired by NHEJ, while HR, when activated, contributes to rDNA instability. (b) DSBs outside the nucleolus also induce nucleolar segregation and cap formation. RNA Pol I is inhibited by ATM and DNA-PK kinases while nucleolar proteins translocate to the damaged site in the nucleoplasm to participate in DNA repair as well as to the cytoplasm to activate the stress response.

Figure 3

The crosstalk between the DNA and rDNA maintenance pathways and rRNA biogenesis regulates the stress response. DNA damage dramatically affects the nucleolar architecture and function through a network of interactions and translocations where rRNA biogenesis factors participate in DNA repair. Vice versa, DNA maintenance factors participate in and regulate rDNA transcription. In addition, nucleolar factors directly regulate the stress response. Genome maintenance pathways, nucleolar transcription and rRNA processing form a complex network that converges to the stress response, activation of which ultimately leads to aging and/or age-related disease or progeria, whereas evasion leads to cancer.