Beyond rRNA: nucleolar transcription generates a complex network of RNAs with multiple roles in maintaining cellular homeostasis

Abstract

Nucleoli are the major cellular compartments for the synthesis of rRNA and assembly of ribosomes, the macromolecular complexes responsible for protein synthesis. Given the abundance of ribosomes, there is a huge demand for rRNA, which indeed constitutes ∼80% of the mass of RNA in the cell. Thus, nucleoli are characterized by extensive transcription of multiple rDNA loci by the dedicated polymerase, RNA polymerase (Pol) I. However, in addition to producing rRNAs, there is considerable additional transcription in nucleoli by RNA Pol II as well as Pol I, producing multiple noncoding (nc) and, in one instance, coding RNAs. In this review, we discuss important features of these transcripts, which often appear species-specific and reflect transcription antisense to pre-rRNA by Pol II and within the intergenic spacer regions on both strands by both Pol I and Pol II. We discuss how expression of these RNAs is regulated, their propensity to form cotranscriptional R loops, and how they modulate rRNA transcription, nucleolar structure, and cellular homeostasis more generally.

Keywords: RNA pol I; RNA pol II; ncRNAs; nucleolus.

Figure 1.

Diagram of one repeat of the yeast and human rDNA arrays. The top panel depicts the yeast 35S rDNA. The locus contains 35S and 5S rRNA-coding regions and two intergenic spacer regions (IGS1 and IGS2). Positions of Pol I and Pol II promoters (C-pro and E-pro) are indicated. The bottom panel shows the human locus consisting of the 47S 13.3-kb coding region and 30-kb IGS region. Coding and IGS regions are shown with pre-RNA promoters (UCE and CORE), variable size enhancers, the promoter-proximal terminator T0, and terminators T_1–10. Three Pol I promoters (spacer promoter, 47S pre-rRNA promoter, and PNCTR promoter) and possible Pol II promoters are indicated.

Figure 2.

Transcripts from mammalian rDNA spacer promoter are transcribed by Pol I. IGS-rRNA is transcribed by Pol I from spacer promoters (SPs), terminating at the rDNA upstream termination site T0, producing a 2-kb-long transcript. IGS-rRNAs are processed into 100- to 300-nt pRNAs. Unprocessed IGS-rRNAs bind TIP5, abolishing its interaction with TTF1, thereby maintaining the euchromatin rDNA state (see the text). However, pRNAs associate with TIP5 and recruit the chromatin remodeling complex NoRC, repressing 47S pre-rRNA transcription. pRNAs can also form R loops over the promoter/UCE region, which also contributes to repression.

Figure 3.

PNCTR is transcribed by Pol I. Transcription initiates ∼7.5 kb downstream from the pre-rRNA 3′ end and gives rise to a 10-kb-long full-length transcript. A truncated 3-kb transcript is also produced, possibly reflecting a “barrier” formed by antisense Pol II transcription (see the text). When Pol II is inhibited, levels of the 3-kb transcript decrease and 10-kb transcript levels increase. PNCTR is enriched in (UC)n motifs and functions by sequestering the splicing regulator PTBP1 in the perinucleolar compartment (PNC), thereby modulating RNA splicing.

Figure 4.

PAPAS RNAs are transcribed by Pol II. Transcription initiates from uncharacterized promoters likely located in rDNA IGS regions and continues across the 47S-coding and promoter regions. PAPAS transcripts can form R loops at the rDNA promoter/UCE regions, which contributes to repression of 47S transcription. In quiescent cells, PAPAS recruits Suv4-20h2 and establishes the repressive mark at the rDNA. Under stresses (e.g., heat shock, hypotonic stress, serum starvation, or the loss of RPA), PAPAS recruits the CHD4/NuRD complex that represses rDNA transcription.