Dramatic changes in cellular gene expression profiles occur in response to extracellular stimuli, and during differentiation 
. These changes are achieved in part through the actions of transcription factors which allow coordinated regulation of specific gene sets. However, regulation of mRNA stability can facilitate rapid changes in gene expression both independently and in collaboration with transcriptional effects 
Messenger RNA decay rates can be readily modulated by association of specific stabilizing or destabilizing factors with the transcript 
. These regulatory factors include RNA-binding proteins and/or miRNAs and their associated enzymes. For almost all mRNAs, decay initiates with removal of the poly(A) tail by one or more deadenylases 
. This has the dual effects of silencing translation and rendering the transcript susceptible to other decay enzymes. It seems that many regulatory RNA binding proteins and miRNAs are able to modulate the efficiency of deadenylation to accelerate or slow down mRNA turnover. CUGBP1, for example, can bind to the 3′UTR of its target mRNAs and recruit the PARN deadenylase to enhance mRNA decay 
. Binding of HuR, on the other hand, is generally associated with increased mRNA stability 
, but it is not clear whether this is achieved through a direct inhibition of the decay enzymes, or merely by competing for the binding site of instability factors.
Just as transcription profiles vary between cell types, so can mRNA decay rates 
. Such variations are presumably due to differences in activity of RNA-binding proteins and/or miRNAs that target specific sets of transcripts. We wished to examine rates of mRNA decay in C2C12 muscle cells for three reasons: (i) Previous studies have uncovered changes in mRNA stability that are essential for differentiation in this cell type 
. (ii) Recent results from our lab and others have suggested that changes in mRNA decay rates in muscle cells may be responsible for aspects of pathogenesis in myotonic dystrophy (DM) 
. (iii) Several muscle cell responses require rapid reprogramming of gene expression, including the response to insulin 
, injury 
, membrane depolarization 
and exercise 
. Although the overall changes in gene expression have been characterized for many of these responses, the contribution of mRNA decay is unknown. Our goal in the first experiments described here was to establish mRNA decay rates on a genome-wide scale in C2C12 cells, characterize the sequence elements that influence mRNA turnover in this cell type and compare the results with those in other cell types.
CUGBP1 is an RNA-binding protein whose abundance and/or localization is altered in several neuromuscular diseases, including myotonic dystrophy, Fragile X Tremor/Ataxia Syndrome (FXTAS) and Oculopharyngeal Muscular Dystrophy (OPMD). In addition to its well-defined role as a regulator of splicing, CUGBP1 also influences mRNA turnover through association with GU-rich elements (GREs) in the 3′UTR of its target mRNAs 
. Binding of CUGBP1 to 3′UTR elements results in recruitment of deadenylases such as PARN which can mediate rapid poly(A) shortening. This can induce translational silencing and/or mRNA decay. Thus CUGBP1 is a potent mRNA destabilizing factor. In the later experiments described below, we have determined the full complement of mRNAs associated with CUGBP1 in muscle cells by RNA immunoprecipitation followed by microarray (RIP-Chip).
Overall, we discovered that many unstable mRNAs expressed in muscle contain AU-rich and/or GU-rich elements in their 3′UTRs. AU-rich elements (AREs) are known to influence decay of short-lived mRNAs in many cell types, while the GREs were similar to those recently identified as CUGBP1 binding sites in unstable mRNAs expressed in T-cells 
and in Xenopus 
. By comparing our results with those recently reported on mRNA decay in pluripotent and differentiating Embryonic Stem (ES) cells 
, we found that GREs are significant in different cell types, whereas some AREs show cell-specific activities. The set of mRNAs associated with CUGBP1 in myoblasts was also enriched for GU-rich 3′UTR sequences, but not AU-rich ones. These CUGBP1-bound mRNAs tend to have short half lives and encode factors involved in processes such as cell cycle regulation, protein localization, signaling, apoptosis and RNA processing. Interestingly, several CUGBP1-associated mRNAs are bound by HuR and/or Pum1 in other cell types suggesting the existence of coordinated or competitive binding of RNA-binding proteins to achieve appropriate regulation. Finally, several CUGBP1 target transcripts were significantly stabilized in a CUGBP1 KD cell line. Taken together, our results strongly implicate CUGBP1 as a key regulator of mRNA decay in muscle cells.