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Northern analysis of CCW12, which falls [http://www.selleckchem.com/products/a-1331852.html www.selleckchem.com/products/a-1331852.html] into a typical mRNA cluster (X), revealed a slight increase following Nab2 depletion and dramatic decrease upon Hrp1 depletion ( Figure?4E). This is consistent with the essential role of Hrp1 in mRNA synthesis and with the mild general increase in mRNA expression observed in a previous analysis of Nab2 depletion ( Schmid et?al., 2012). In contrast, the abundance of two tested CUTs, CUT479 and CUT200, was increased up to 15-fold following depletion of Nab2 or Hrp1 ( Figure?4E). Many of the RNA fragments isolated with Hrp1 or Nab2, including those mapping to CUTs, possessed short nonencoded oligo(A) tails ( Figures 5A�C5C). These are hallmarks of nuclear decay intermediates, suggesting that CUTs bound by Hrp1 and Nab2 were undergoing active degradation. Previous analyses showed that Nab2 [http://en.wikipedia.org/wiki/GUCY1B3 GUCY1B3] binds the surveillance factors Rrp6 and Trf4 (Schmid et?al., 2012) and participates in degradation of intron-containing pre-mRNAs, whereas Hrp1 was implicated in Nrd1-dependent termination coupled to pre-mRNA turnover at the NRD1 and HRP1 loci ( Kuehner and Brow, 2008). We conclude that Hrp1 and Nab2 participate in the nuclear turnover of CUTs, in addition to their roles in the generation of stable mRNAs and perhaps SUTs. These dual roles support a model in which 3�� end processing is a key step in determining transcript fate. Finally, we sought to determine the origin of the 5�� proximal binding of surveillance factors to mRNAs. RNAs carrying nonencoded A-tails were identified for many proteins (Figure?5A) and indicate that transcripts have been released from the polymerase. Generally, stable mRNAs possess long Pab1-bound poly(A) tails that promote export and translation but are deadenylated to ?10�C12 adenosines prior to cytoplasmic turnover by Xrn1 or the Ski complex and exosome. In contrast, short (4�C5 nt) oligo(A) tails mapping throughout a gene arise from the adenylation activity of the TRAMP complex and characterize nuclear surveillance intermediates. In agreement with these roles, (1) A-tails in Xrn1 and Ski2 data sets were ?1�C12 nt long (Figures 5B and 5C), absent from transcript classes such as tRNAs (Figure?5D), and almost exclusively present at the 3�� end of mRNAs (Figure?5E); (2) Pab1 bound to long poly(A) tails (present on 74.2% of recovered fragments) but not oligo(A)[http://www.selleckchem.com/products/eai045.html EAI045 clinical trial] (Figures 5B and 5C); and (3) Mtr4 substrates universally possessed short (4�C5 nt) oligo(A) tails (Figures 5B�C5D), some of which mapped across mRNAs (Figure?5E). Therefore, oligo(A) tails are a universal feature of TRAMP activity and are exclusively associated with nuclear surveillance, whereas the longer A-tails in Xrn1 and Ski2 data sets reflect 3�� poly(A) tails on mRNAs and some other Pol II transcripts. The abundant short oligo(A)-tails in Nab2 data sets (Figure?5B) support a noncanonical role in surveillance.