Messenger RNA (mRNA) turnover is essential for maintaining proper gene expression and cell function. Surplus or aberrant mRNAs—either mis-transcribed, mis-processed, mis-transported, mis-folded, mis-packaged, mis-modified, or mutated—must be identified, sequestered, and degraded in a precise manner. These phenomena, included under the umbrella term mRNA surveillance [1
], require the functional and physical interplay of a network of mRNA metabolic processes. Although much progress has been made towards understanding many of the pathways that comprise the network [3
], the molecular mechanisms by which aberrant or surplus mRNAs are detected and winnowed are still unclear.
The exosome complex and its cofactors have emerged over the last decade as fundamental participants in mRNA surveillance. Structurally, the yeast exosome core is composed of a hexameric ring consisting of RNase PH subunits (Rrp41/Ski6, Rrp42, Rrp43, Rrp45, Rrp46, and Mtr3) and a trimeric cap consisting of S1 domain subunits (Rrp4, Rrp40, and Csl4) [6
]. Two active ribonucleases interact with the core: Rrp6, an RNase D homolog, and Dis3, and RNase II/R homolog. Functionally, these exosome subunits and RNases have been implicated in most if not every aspect of mRNA metabolism including elongation [7
], splicing [9
], 3’ processing [12
], termination [15
], transport [17
], and turnover [19
]. While there is evidence suggesting that the entire core complex participates in mRNA surveillance, there is also evidence indicating that individual subunits “survey” mRNAs independently of the complex [21
]—either alone or as subcomplexes that we have called exozymes [24
]. One recent study that supports the exozyme hypothesis showed that patients with pontocerebellar hypoplasia type 1 have specific, non-lethal mutations in EXOSC3 (Rrp40) [25
]. These mutations have tissue-specific effects, suggesting that Rrp40 regulates a subset of exosome core-surveyed RNAs. Dis3 and Rrp6 have attracted a great deal of attention because they exist in a biochemically defined exozyme [26
], have both exosome-tethered and -independent ribonucleolytic activity [6
] and modulate cell cycle progression [32
]. In light of this functional multivalence, making the biochemical distinction between the core complex and exozymes is necessary for our understanding of how these essential polypeptides recognize and process or degrade distinct RNA substrates.
A critical step in 3’ to 5’ mRNA decay is protein recruitment to the 3’ untranslated region (UTR) of the mRNA substrate [35
]. Several non-exosome RNA binding proteins have been suggested or shown to elicit AU-rich element (ARE)-mediated mRNA turnover through recruitment of the exosome or subunits of the complex [36
]. Several RNase PH subunits preferentially bind AREs, triggering their turnover [39
]. Still, we do not have a complete understanding of which exosome subunits and exozymes directly recognize specific RNA sequence motifs or structures. In this regard, most if not all exosome subunits have bioinformatically predicted or experimentally defined specific RNA interaction domains [41
], some of which are known to bind particular RNA structures [45
]. Moreover, several models have suggested or implied a direct RNA-S1 cap interaction prior to RNA threading through the hexameric RNase PH ring and ultimate catalysis by Dis3 [47
Here, we use bioinformatics to identify novel 3’ UTR instability elements. We characterize two elements that confer Dis3- and exosome subunit-sensitive instability in a reporter system. These cis-acting elements exist almost exclusively within the transcriptomic pool that is stabilized by depleting exosome subunits, suggesting that they are targets for exozyme or exosome recruitment and Dis3-mediated decay.