Post-transcriptional control of cellular differentiation by the RNA exosome complex

Abstract

Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.

Figure 1.

RNA exosome structure at a resolution of 3.45 Å determined by Lima and colleagues (28) using cryo-electron microscopy. Modified from PDB ID: 6D6Q.

Figure 2.

RNA exosome subunit domain organization. Protein domains were identified from InterPro (https://www.ebi.ac.uk/interpro/search/text/). The relative sizes of subunits are shown, and human disease mutations are depicted as red dots (123,126–128,135,137,140,147,148). The trimeric cap proteins EXOSC1, EXOSC2 and EXOSC3 contain S1 and/or the K homology (KH) domains that mediate RNA binding. The inactive barrel proteins EXOSC4–EXOSC9 contain PH1 and/or PH2 domains that mediate protein–protein binding. EXOSC10 and DIS3 catalytic subunits contain exoribonucleolytic domains, DNA Pol A 3′–5′ exonuclease and ribonuclease B, respectively. EXOSC10 also contains a polycystin 2 N-terminal (PMC2NT) domain that interacts with C1D yeast homolog (33) and a helicase and RNase D C-terminal (HRDC) domain proposed to have RNA-binding activity (34). In DIS3, the CR3 motif composed of three cysteine residues is functionally important (35), PiLT N-terminal domain (PIN) imparts its endonuclease activity (37) and cold shock domains are not functionally characterized in this context.

Figure 3.

RNA exosome controls erythroid differentiation by regulating the balance between erythroid precursor proliferation and differentiation. RNA exosome disruption downregulates Kit mRNA and protein, and therefore RNA exosome confers SCF-mediated receptor tyrosine kinase (c-Kit) signaling, which is vital to maintain the undifferentiated state of erythroid precursor cells (77,78). The repression of genes encoding RNA exosome subunits and the direct repression of Kit transcription constitute an important circuit within the GATA1-dependent genetic network that promotes erythroid differentiation. In addition to abrogating c-Kit expression and signaling, RNA exosome disruption is associated with precocious acquisition of Epo signaling. Epo binds the EpoR to drive erythroid differentiation. Although the full ensemble of transcripts directly regulated by the RNA exosome has not been described in this system, the RNA exosome post-transcriptional mechanism involves degradation of transcripts required for differentiation and accumulation of transcripts, e.g. encoding c-Kit, that support highly proliferative erythroid precursors termed BFU-E. RNA exosome disruption depletes BFU-E.

Figure 4.

Molecular mechanisms underlying RNA exosome control of cellular differentiation and genome integrity. Three modes of RNA exosome function are depicted. Left: Transcription factors regulate expression of genes encoding RNA exosome subunits, thereby altering RNA exosome levels, which remodel transcriptomes via post-transcriptional mechanisms. The transcription factors GATA1 and ZSCAN10 repress and induce RNA exosome subunits, respectively, to regulate differentiation and maintenance of pluripotency (77,78,83). Middle: RNA exosome post-transcriptional activity regulates transcript(s) encoding a differentiation regulatory transcription factor. In human epidermal cells, the RNA exosome degrades GRHL3 transcripts, a TF required for epidermal differentiation. In hESCs, the RNA exosome degrades transcripts that induce differentiation, and its depletion upregulates differentiation-associated factors (20,64). Right: RNA exosome exerts critical activities to maintain genome integrity. By degrading RNA molecules that form R-loop hybrid structures, as described in B cells and mESCs, the RNA exosome counteracts R-loop formation and/or maintenance, thereby regulating genome function (24,25).