Abstract
A pervasive theme in development is that dynamic changes in gene expression drive developmental progression; yet in studies of gene expression, the general RNA decay pathways have historically played second fiddle to transcription. However, recent advances in this field have revealed a surprising degree of mRNA specificity for particular branches of these RNA decay pathways. General cytoplasmic mRNA decay typically initiates with deadenylation, following which the deadenylated mRNA can continue decay from the 3'-end through the action of the exosome, or it can undergo 5'-to-3' decay. Functional characterization of exosome subunits using inducible knock-outs uncovered a surprising complexity of molecular phenotypes and RNA substrates. Decay in the 5'-to-3' direction requires decapping, which is carried out by the decapping complex in Processing bodies (PBs). Recent analyses of decapping mutants have also revealed substrate specificity and roles in translational regulation. In addition, recent studies of specialized pathways such as nonsense-mediated decay and silencing reveal interactions with the general RNA decay pathways.
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