modiﬁcation, pre-tRNAs can be adenylated by TRAMP com- plexes for targeting to the nuclear exosome (Kadaba et al. 2004, 2006; Vanacova et al. 2005). Similarly, defects in 39-end processing of pre-tRNAs can also lead to adenylation by TRAMP complexes (Copela et al. 2008; Ozanick et al. 2009). Adenylation of defective tRNAs is thought to provide a single-stranded extension of RNA that the nuclear exosome can then load on and then degrade through the structured tRNA. A second mechanism of tRNA decay occurs when tRNAs are defective in their modiﬁcations and/or stability of the combined acceptor and T stems. For example, in trm4Δ trm8Δ strains, which produce undermodiﬁed tRNA[Val(AAC)], the tRNA[Val(AAC)] is degraded more rapidly (Alexandrov et al. 2006). This degradation utilizes the 59 to 39 exonu- cleases Rat1 and Xrn1 (Chernyakov et al. 2008). Moreover, mutations that weaken the stability of the combined acceptor and T stems of the tRNA increase degradation (Whipple et al. 2011). This suggests a model wherein the strength of the tRNA structure at the 59 end dictates whether it can be subject to 59 to 39 degradation. The stability of the 59 stem loop in tRNAs can also affect whether tRNAs receive an additional CCA addition, which can promote their degradation (Wilusz et al. 2011). This occurs when tRNAs have a weak acceptor stem and the ﬁrst two nucleotides of the tRNA are guanosines. In this case, the tRNA appears to adopt an alternative fold whereby the CCA addition enzyme can add a second CCA, which then appears to promote degradation of the tRNA, perhaps by providing a 39 single-stranded region for the recruitment of the exo- some (Wilusz et al. 2011). Strains defective in the CCA ad- dition enzyme also produce tRNAs with shortened 39 ends that are degraded more rapidly (Aebi et al. 1990), although the speciﬁc mechanism is not yet known. One anticipates that the stability of tRNAs will also be inﬂuenced by tRNA- binding proteins (e.g., eEF1 and synthetases) that will limit nuclease accessibility. A ﬁnal mechanism of tRNA cleavage and degradation involves the nuclease Rny1. Rny1 is an RNaseT2 family member that is secreted and targeted to membrane-bound compartments, most notably the vacuole (Macintosh et al. 2001; Thompson and Parker 2009). Rny1 has been shown to cleave tRNAs in the anticodon loop, at least during vari- ous stresses and high cell density (Thompson et al. 2008; Thompson and Parker 2009). Rny1 may be released from membrane compartments to degrade tRNAs during stress, although it remains possible that tRNAs are also imported into the vacuole, or other membrane-bound compartment, by some type of autophagy-related process for degradation by Rny1. rRNA decay To date, three types of RNA degradation have been de- scribed to occur to rRNAs. First, when rRNA processing or assembly into ribosomes is altered by a variety of mutations, the defective rRNA is targeted for degradation by polyade- nylation by TRAMP complexes and recruitment of the nuclear exosome (e.g., Allmang et al. 2000; Kuai et al. 2004; Fang et al. 2005; Lacava et al. 2005; Dez et al. 2006; Kadaba et al. 2006). Polyadenylated rRNA species can also be detected in strains defective in nuclear exosome function, suggesting that a certain percentage of “normal” rRNA transcripts, either due to errors in transcription, processing, or assembly, are subject to this nuclear RNA degradation pathway. Ribosomes that are accurately assembled but fail to function are exported to the cytoplasm and degraded by a process re- ferred to as nonfunctional ribosomal decay. For 25S rRNAs that are defective in peptidyl transferase activity, the 60S subunit appears to be recognized as aberrant prior to assembly into 80S complexes and targeted for degradation by ubiquitination in a process dependent on the ubiquitin ligase Rtt101 and its asso- ciated protein Mms1 (Lariviere et al. 2006; Fujii et al. 2009). The exact nuclease(s) that degrades these defective 25S RNAs is not yet known, although the exosome may have some role (Cole et al. 2009). For the small ribosomal subunit, mutations in the decoding site of the 18S rRNA lead to 40S complexes that can assemble into 80S complexes on the translation start site, but appear to be blocked for subsequent elongation (Lariviere et al. 2006). In this case, the degradation of the defective 18S rRNAs uti- lizes the same Dom34/Hbs1 complex that is involved in the release of ribosomes stalled by defects in the mRNA (NGD; see above), which leads to degradation by the cytoplasmic exo- some as well as Xrn1 (Cole et al. 2009). rRNAs are also subject to degradation during stress or nutrient limitations. For example, in response to oxidative stress or entry into stationary phase, the rRNAs are frag- mented to some extent (Mroczek and Kufel 2008; Thompson et al. 2008). This degradation is at least partially dependent on the Rny1 nuclease, which is concentrated in vacuoles (Thompson and Parker 2009). One possibility is that these stress conditions lead to release of Rny1 from the vacuole and cleavage of cytoplasmic rRNAs (Thompson and Parker 2009). Since the Nuc1 nuclease is also released from mitochondria under these conditions (Buttner et al. 2007), it might also play some role in rRNA degradation during stress. Another possibility is that rRNAs are targeted to vacuoles under these conditions by selective autophagy. Consistent with that model, based on following GFP-tagged ribosomal proteins, ribosomes have been inferred to be targeted to vacuoles dur- ing nitrogen starvation in a process referred to as ribophagy, which requires ubiquitination and de-ubiquitination (Kraft et al. 2008; Ossareh-Nazari et al. 2010). Ribosomes may also be targeted for degradation in the vacuole by a piecemeal microautophagy of the nucleus, wherein regions of the nu- cleus are directly targeted to the vacuole by invagination of the nuclear envelope into the vacuolar lumen (Roberts et al. 2003). snRNAs/snoRNAs Several observations suggest that defects in snRNP or snoRNP assembly lead to degradation of these RNA species. RNA Decay in Yeast 691