Long Noncoding RNAs and Stress Response in the Nucleolus

Abstract

Long noncoding RNAs (lncRNAs) perform diverse functions in the regulation of cellular processes. Here we consider a variety of lncRNAs found in the ribosome production center, the nucleolus, and focus on their role in the response to environmental stressors. Nucleolar lncRNAs ensure stress adaptation by cessation of resource-intensive ribosomal RNA (rRNA) synthesis and by inducing the massive sequestration of proteins within the nucleolus. Different cell states like quiescence and cancer are also controlled by specific lncRNAs in the nucleolus. Taken together, recent findings allow us to consider lncRNAs as multifunctional regulators of nucleolar activities, which are responsive to various physiological conditions.

Keywords: PAPAS; SLERT; chromatin; intergenic spacers; lncRNA; noncoding RNA; nucleolus; pRNA; ribosomal RNA; stress.

Figure 1

Scheme of a mouse rRNA gene with associated proteins. The pre-rRNA coding region consists of 18S, 5.8S and 28S rRNA sequences and transcribed ETS and ITS spacers. Individual rDNA repeats are separated by IGSs. Pol I transcription at the 47S promoter is initiated by specific set of proteins, which includes UBF and SL1 complex. The dimers of UBF are also associated with the pre-rRNA coding regions of active rDNA repeats. Transcription ends at multiple terminator elements (T_1–10) that bind TTF-I protein. In addition, TTF1 occupies a terminator-like sequence (T₀) near the rDNA promoter. IGSs also contain repetitive enhancer elements and spacer promoters, which in mice are located about 2 kb upstream of the pre-rRNA transcription start site.

Figure 2

Mechanisms of pRNA and PAPAS action. (a) pRNA is transcribed by Pol I from spacer promoters juxtaposed to active rRNA genes. A hairpin structure of pRNA is recognized by TIP5 protein that allows it to form the Nucleolar Remodeling Complex (NoRC). Glucose starvation increases the activity of SIRT1, which deacetylates TIP5 and thereby enhances its association with pRNA. NoRC shifts a promoter nucleosome into a repressive position to block the 47S promoter and provides chromatin repression by histone deacetylation (removal of H4ac marks) and establishment of H3K9me3 modification. The 5′-end of pRNA forms RNA-DNA triplex with T_o site of the rDNA promoter. The triplex impairs TTF-I binding and recruits DNMT3b, which methylates DNA (indicated as CH3). (b) Quiescence and heat shock activate Pol II-mediated transcription of PAPAS antisense RNAs, which starts from random sites within the rDNA locus. PAPAS is able to anchor by forming DNA:RNA triplex with the enhancer element region in the IGS. Upon quiescence, PAPAS recruits Suv4-20h2, which establishes the repressive H4K20me3 mark at the rDNA. Under heat shock, PAPAS interacts with dephosphorylated CHD4 protein, a component of the NuRD complex that represses rDNA transcription by histone deacetylation and promoter nucleosome shifting.

Figure 3

IGSRNAs and A-body formation in human cells. IGS₂₂RNA and IGS₂₈RNA are transcribed by Pol I from two distinct IGS promoters in response to heat shock and acidosis stress, respectively. These transcripts capture HSP70, VHL and many other nucleoplasmic proteins for their detention in the nucleolus. The electrostatic interactions between cationic amyloid-converting motifs of proteins and negatively charged unstructured IGSRNAs trigger formation of the solid A-body in the nucleolus.