(Geisler et al. 2012). This might be a general feature of genes induced by environmental stimuli since antisense RNAs stabilized in xrn1Δ and dcp2Δ strains are often an- tisense to induced genes (Van Djik et al. 2011; Geisler et al. 2012), An important and unresolved future issue will be determining why degradation of this antisense RNA is required for efﬁcient gene induction. In other cases, transcripts that overlap the promoter, or even the ORF, can alter the transcription of the associated mRNA (e.g., Martens et al. 2004; Thiebaut et al. 2008; Huang et al. 2010; Toesca et al. 2011). Finally, since some of these RNAs are associated with ribosomes and can con- tain short ORFs, it seems likely that some of these RNAs encode short polypeptides (Olivas et al. 1997; Thompson and Parker 2007; Wilson and Masel 2011). Because many of these RNAs are most easily detected in strains defective in RNA degradation pathways, it is thought that many such RNAs are highly unstable. This set of RNAs is subject to a variety of different and overlapping RNA degradation pathways. For example, many intergenic, antisense, and promoter-associated transcripts increase in levels and/or show increased stability in xrn1Δ, dcp1Δ, or dcp2Δ strains, suggesting that they are subject to degradation by decapping and Xrn1 action (Thompson and Parker 2007; Berretta et al. 2008; Van Dijk et al. 2011; Geisler et al. 2012). A signiﬁcant number of intergenic RNAs are also increased in strains defective in NMD, suggesting that these RNAs might enter translation and then be recog- nized as aberrant RNAs and degraded by NMD (Thompson and Parker 2007; Toesca et al. 2011). Some of these RNAs also appear to be degraded in a mechanism dependent on RNaseP (Marvin et al. 2011). Numerous studies have also shown that intergenic, in- tragenic, promoter-associated, and antisense RNAs increase in levels in strains defective in the nuclear exosome, most commonly the Rrp6 subunit, leading to the suggestion that these RNAs are subject to nuclear 39 to 59 degradation (Wyers et al. 2005; Davis and Ares 2006; Thompson and Parker 2007; Milligan et al. 2008; Lardenois et al. 2011). However, examination of RNA decay rates has shown that while the steady-state levels of RNA actually increase for many RNAs in rrp6Δ strains, the actual decay rates increase and appear dependent on Xrn1 (Thompson and Parker 2007), although some reports indicate an increased half-life in rrp6Δ strains (Wyers et al. 2005). One possibility is that rrp6Δ strains show increased transcription, but this model is inconsistent with nuclear run-on and RNA polymerase II chromatin immunoprecipitation experiments (Wyers et al. 2005; Rougemaille et al. 2007). An alternative is that the nuclear degradation of such transcripts occurs extremely rapidly and cannot be measured at steady state, an issue that remains to be rigorously resolved in future work. The reduction in cryptic unstable transcript and pro- moter-associated RNA levels by the nuclear exosome is facilitated by the TRAMP complexes (Lacava et al. 2005; Wyers et al. 2005; Egecioglu et al. 2006; Houseley et al. 690 R. Parker 2007; San Paolo et al. 2009; Callahan and Butler 2010). The TRAMP complexes consist of one of two related RNA- binding proteins, Air1 and Air2, the Mtr4 RNA helicase, and one of two noncanonical poly(A) polymerases, Trf4 or Trf5 (Lacava et al. 2005; Vanacova et al. 2005; Wyers et al. 2005). Analogous to the situation in bacteria, the TRAMP complex can promote 39 to 59 degradation of RNAs by the addition of poly(A) tails to their 39 end, which is then thought to promote the targeting of those RNAs to the exosome (Kadaba et al. 2004; Lacava et al. 2005; Vanacova et al. 2005; Wyers et al. 2005). However, in some cases the TRAMP complex can also promote exosome-mediated RNA degrada- tion independently of polyadenylation activity and may in that case serve as a scaffolding complex to recruit the exo- some to the RNA (Houseley et al. 2007; Rougemaille et al. 2007; San Paolo et al. 2009). The TRAMP complexes also serve important roles in targeting the exosome for degrada- tion or processing of small nucleolar RNAs (snoRNAs), snRNAs, tRNA, and other RNA species (see below). The targeting of RNAs to the TRAMP and exosome complexes appears to be modulated in part by the Nrd1 and Nab3 RNA-binding proteins. The Nrd1 and Nab3 pro- teins bind to speciﬁc elements in nascent transcripts (Creamer et al. 2011; Jamonnak et al. 2011; Wlotzka et al. 2011) and can direct termination of transcription for snoRNAs, snRNAs, some mRNAs, and numerous intergenic transcripts (Arigo et al. 2006; Thiebaut et al. 2006; Carroll et al. 2007; Rondon et al. 2009; Kim and Levin 2011). Nrd1 and Nab3 associate with the carboxy-terminal doman of RNA polymerase II when phosphorylated at serine 5 and serine 7 (Gudipati et al. 2008; Vasiljeva et al. 2008; Kim et al. 2010) and may act preferentially on shorter transcripts as serine 5 and 7 phosphorylation can be lost with ongoing elongation (Komarnitsky et al. 2000; Schroeder et al. 2000). Nrd1 and Nab3 then appear to recruit the exosome to de- grade intergenic transcripts or to promote processing of snoRNAs and snRNAs (Arigo et al. 2006; Thiebaut et al. 2006; Grzechnik and Kufel 2008; Vasiljeva et al. 2008). This effect is not limited to RNA polymerase II transcripts as Nab3 and Nrd1 can also target RNA polymerase III tran- scripts for polyadenylation and degradation (Wlotzka et al. 2011). Decay of tRNA, rRNAs, snRNAs, and snoRNAs Most functional noncoding RNAs such as rRNAs, tRNAs, snRNAs, and snoRNAs are quite stable, although they are probably degraded at some rate even under optimal growth conditions. However, these RNAs are clearly subject to increased turnover during nutrient limitations (see below) and are also subject to a variety of quality control systems to ensure their proper biogenesis and function. tRNAs Three mechanisms can target tRNAs for degradation. First, when tRNAs have defects in their maturation and/or