non-coding RNA Review RNA Surveillance by the Nuclear RNA Exosome: Mechanisms and Significance Koichi Ogami 1,* ID , Yaqiong Chen 2 and James L. Manley 2 1 Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan 2 Department of Biological Sciences, Columbia University, New York, NY 10027, USA; [email protected] (Y.C.); [email protected] (J.L.M.) * Correspondence: [email protected]; Tel.: +81-52-836-3665 Received: 8 February 2018; Accepted: 8 March 2018; Published: 11 March 2018 Abstract: The nuclear RNA exosome is an essential and versatile machinery that regulates maturation and degradation of a huge plethora of RNA species. The past two decades have witnessed remarkable progress in understanding the whole picture of its RNA substrates and the structural basis of its functions. In addition to the exosome itself, recent studies focusing on associated co-factors have been elucidating how the exosome is directed towards specific substrates. Moreover, it has been gradually realized that loss-of-function of exosome subunits affect multiple biological processes, such as the DNA damage response, R-loop resolution, maintenance of genome integrity, RNA export, translation, and cell differentiation. In this review, we summarize the current knowledge of the mechanisms of nuclear exosome-mediated RNA metabolism and discuss their physiological significance. Keywords: exosome; RNA surveillance; RNA processing; RNA degradation 1. Introduction Regulation of RNA maturation and degradation is a crucial step in gene expression. The nuclear RNA exosome has a central role in monitoring nearly every type of transcript produced by RNA polymerase I, II, and III (Pol I, II, and III). The exosome guarantees fidelity of the mature 30 ends of certain stable RNA species, such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), telomeric RNAs, small nuclear and nucleolar RNAs (snRNAs and snoRNAs), not only by catalyzing 30 end trimming, but also by degrading transcripts containing an incomplete 30 end [1–3]. Besides, processing of messenger RNA precursors (pre-mRNAs), such as by splicing and 30 end formation, is also under the surveillance of the exosome (Figure1)[4–13]. Intriguingly, recent advances in RNA sequencing techniques have enabled detection of novel Pol II transcripts (Figure1), which are expressed at extremely low levels because of rapid RNA turnover by the exosome. A large fraction of these RNAs can be categorized as long non-coding RNA (lncRNA). The most well-known lncRNA substrates for the exosome are cryptic unstable transcripts (CUTs) in yeast [14–16], and their human counterparts, promoter upstream transcripts (PROMPTs) or upstream antisense RNAs (uaRNAs) [17,18], which arise due to antisense transcription from divergent gene promoters. The exosome removes sense non-coding transcripts, such as prematurely terminated RNAs (ptRNAs) [19], which are prematurely terminated and polyadenylated at a poly(A) signal (PAS) typically located in an intron of a protein-coding gene [20], and transcription start site (TSS)-associated RNAs (tssRNAs), which are infrequent short non-coding RNAs (ncRNA) (20–65 nt) generated as a result of promoter-proximal termination of sense transcription [21]. Transcriptional enhancers are also transcribed bi-directionally, and produce a class of lncRNA called enhancer RNAs (eRNAs). It was reported that exosome-sensitive eRNAs emerge from virtually all active enhancer regions, determined Non-coding RNA 2018, 4, 8; doi:10.3390/ncrna4010008 www.mdpi.com/journal/ncrna Non-coding RNA 2018, 4, 8 2 of 21 Non-Coding RNA 2018, 4, 8 2 of 20 by comprehensiveclass of lncRNA cap called analysis enhancer of gene RNAs expression (eRNAs). (CAGE) It was analysesreported that [22]. exosome Furthermore,-sensitive long eRNAs intergenic RNAsemerge (lincRNAs) from virtually are also all exosome active enhancer targets [ 23regions,], although determined they are by generallycomprehensive more cap stable analysis than uaRNAof and eRNAgene expression [24]. (CAGE) analyses [22]. Furthermore, long intergenic RNAs (lincRNAs) are also Strikingly,exosome targets recent [23], studies although have they been are graduallygenerally more revealing stable thatthan theuaRNA exosome and eRNA is involved [24]. in multiple importantStrikingly, biological recent processes. studies Those have includebeen gradually the DNA revealing damage that response the exosome (DDR), is R-loop involved resolution, in maintenancemultiple important of genome biological integrity, processes. RNA export, Those inclu translation,de the DNA and damage cell differentiation. response (DDR), In R this-loop work, we reviewresolution, and updatemaintenance our current of genome understanding integrity, RNA regarding export, structuraltranslation,insights and cell intodifferentiation. RNA degradation In this work, we review and update our current understanding regarding structural insights into RNA by the exosome and its associated co-factors. We also summarize how abrogation of the functions of degradation by the exosome and its associated co-factors. We also summarize how abrogation of the the exosome impacts cellular processes in mammals. functions of the exosome impacts cellular processes in mammals. Figure 1. Schematic depiction of Polymerase II transcripts generated from enhancers and gene Figure 1. Schematic depiction of Polymerase II transcripts generated from enhancers and gene promoters. Both enhancers and promoters are transcribed bi-directionally and produce various types promoters.of transcripts Both enhancers, including andmessenger promoters RNA are precursors transcribed (pre- bi-directionallymRNA), transcription and produce start site various-associated types of transcripts,RNA (tssRNA), including prematurely messenger RNAterminated precursors RNA (pre-mRNA),(ptRNA), upstream transcription antisense start RNA site-associated (uaRNA) or RNA (tssRNA),promoter prematurely upstream transcript terminated (PROMPT), RNA (ptRNA), and enhancer upstream RNA antisense(eRNA). The RNA exosome (uaRNA) functions or promoter in upstreamnuclear transcript RNA surveillance (PROMPT), to degrade and enhancer these RNAs RNA, as (eRNA).well as misprocessed The exosome messenger functions RNA in nuclear(mRNA) RNA surveillanceprecursors to, degrade such theseas RNAs,intron- asretained well as misprocessedand poly(A) messenger signal-mediated RNA (mRNA) cleavage precursors,, and such as intron-retainedpolyadenylation and-defective poly(A) pre signal-mediated-mRNAs. cleavage, and polyadenylation-defective pre-mRNAs. 2. The Nuclear RNA Exosome: Structure and RNA Degradation Mechanisms 2. The Nuclear RNA Exosome: Structure and RNA Degradation Mechanisms The eukaryotic nuclear RNA exosome is a 3′0–5′0 exonuclease complex, consisting of a 9-protein Thecatalytically eukaryotic inactive nuclear coreRNA complex exosome (EXO- is9) aand 3 –5 twoexonuclease catalytic subunits, complex, Rrp6 consisting (also known of a 9-protein as catalyticallyPM/Scl-100 inactive or EXOSC10) core complex, and (EXO-9) Dis3 (also and twoknown catalytic as Rrp44 subunits, or Rrp6EXOSC11). (also knownEXO-9 asforms PM/Scl-100 a or EXOSC10),double-layered and Dis3barrel (also-like knownstructure as that Rrp44 comprises or EXOSC11). six ribonuclease EXO-9 forms (RNase a double-layered) pleckstrin homology barrel-like structure(PH)-like that proteins comprises (Rrp41, six ribonucleaseRrp42, Rrp43, Rrp45, (RNase) Rrp46 pleckstrin, and Mtr3) homology and three (PH)-like S1/K homology proteins (KH) (Rrp41, Rrp42,“cap Rrp43,” proteins Rrp45, (Rrp4, Rrp46, Rrp40 and, and Mtr3) Csl4) and [3]. three The S1/Ktwo catalytic homology subunits (KH) “cap”occupy proteins opposite (Rrp4,ends of Rrp40, and Csl4)EXO-9 [ 3to]. constitute The two catalyticEXO-11. Rrp6 subunits is placed occupy at the opposite top of the ends S1/KH of EXO-9 cap ring to constitutenear the RNA EXO-11. entry Rrp6 is placedpore, atand the Dis3 top is oftethered the S1/KH to the bottom cap ring of EXO near-9 the near RNA the RNA entry exit pore, pore and [25– Dis327]. Both is tethered Rrp6 and to the Dis3 are 3′–5′ exonucleases, but the latter also has endonucleolytic activity [28–30]. Rrp6 widens the bottom of EXO-9 near the RNA exit pore [25–27]. Both Rrp6 and Dis3 are 30–50 exonucleases, but central channel of core EXO-9 and allosterically stimulates Dis3 activity [26]. Recently, a study the latter also has endonucleolytic activity [28–30]. Rrp6 widens the central channel of core EXO-9 and allosterically stimulates Dis3 activity [26]. Recently, a study focused on the last 100 amino acids of Rrp6, referred to as a “lasso,” and revealed that the lasso binds RNA proximal to the EXO-9 Non-coding RNA 2018, 4, 8 3 of 21 Non-Coding RNA 2018, 4, 8 3 of 20 channelfocused and on enhances the last 100 RNA amino decay acids [31 of]. Rrp6, In humans, referred bothto as Rrp6a “lasso,” and and Dis3 revealed are mostly that the nuclear, lasso binds but Rrp6 showsRNA significant proximal to nucleolar the EXO-9 enrichment channel and [32 enhances,33], whereas RNA decay Dis3 [31]. is excluded In humans, from both the Rrp6 nucleoli and Dis3 [33, 34]. In contrastare mostly to humans, nuclear, yeastbut Rrp6 Rrp6 isshows restricted significant to the nucleus,nucleolar butenrichment Rrp6 and [32,33], Dis3 are whereas both present Dis3 inis the nucleoplasmexcluded from and the nucleolus nucleoli [ 32[33,34].,35]. In contrast to humans, yeast Rrp6 is restricted to the nucleus, but Rrp6Three and additional