The locations of the sequences corresponding to the primers are shown in Figure ?Figure11 and Table ?Table1.1. intron caused a frameshift generating 18 PTCs, were cloned into pIREShyg2 and stably expressed in a murine cell line, Ba/F3. Results Compared with wild-type c, the mRNA levels of c79 were less than one tenth and decayed faster. Both translation inhibition and Upf1 knockdown led to significantly greater up-regulation of c79 than wild-type c. However, the use of a monocistronic pMT21 vector abolished the up-regulatory effects of translation inhibition and Upf1 knockdown on both wild-type c and c79, suggesting that this NMD is usually attributable to a structural determinant in pIREShyg2. The elimination of the intron and the proximal Dynarrestin 3′ 17 PTCs did not alter the greater effects of translation inhibition on c79, suggesting that the first PTC, which determines 3’UTR length, was sufficient to enhance NMD efficiency. Thus, transcripts of PTC-harboring genes with longer 3’UTR are more efficiently degraded by the vector-dependent NMD than those of wild-type genes with relatively shorter 3’UTR, resulting in minimized expression of truncated mutants. Dynarrestin Conclusions We conclude that pIREShyg2, which sensitizes its bicistronic transcripts to NMD, may be useful for studying NMD but should be avoided when maximum expressions of PTC-harboring genes are required. Background Expression vectors containing an internal ribosome entry site (IRES) element have been widely used as bicistronic vectors that provide co-expression of two unrelated reading frames from a single transcript unit [1-6]. A reading frame in a multiple cloning site Dynarrestin downstream of a promoter is called the first cistron, and the second cistron is usually downstream of an IRES element. pIREShyg2 is usually a Dynarrestin bicistronic expression vector that possesses an intervening sequence NR4A2 (IVS) between the first cistron and an IRES element derived from encephalomyocarditis virus, and a hygromycin resistance gene in the second cistron, which serves as a selection marker for stable transfection. It has been shown that the first cistron gene is expressed at levels comparable to those achieved in a monocistronic vector and initiation of translation is cap-dependent . However, the present study is the first to show that the use of pIREShyg2 affects the mRNA stability of their carrying genes in mammalian cells, potentially leading to their insufficient expression. Nonsense-mediated mRNA decay (NMD) is a post-transcriptional mRNA quality control system that eliminates aberrant mRNAs harboring premature termination codons (PTCs) within protein coding regions in eukaryotes [8-10] to protect the cells from accumulation of harmful or nonfunctional C-terminally truncated polypeptides [11,12]. The degradation occurs in a translation-dependent manner when translation is initiated in an mRNA cap-dependent manner [13,14]. In mammalian cells, two determinants have been identified that distinguish “premature” termination codons from “normal” termination codons and provide a protective advantage to the normal termination codon . One is the presence of an exon-junction complex (EJC) more than 50 nucleotides downstream of a termination codon [16-23]. Induction of NMD requires the association between the EJC and the protein complex bound to the ribosome stalled at a PTC, which contains essential proteins to trigger NMD such as Upf1, eukaryotic release factors, and SMG1 [13,24-28]. Because normal termination codons generally reside either in the final exon or within 50 nucleotides upstream of the 3′-end in the penultimate exon, the transcripts coding wild-type proteins are able to escape NMD [16,29]. Another determinant is the distance between the stop codon and a poly(A) region [30-33]. Normal termination requires the interaction between the terminating ribosomal complex and the poly(A)-binding proteins (PABP), which leads to faster release of a terminating ribosome from mRNA . A ribosomal complex at a PTC fails to interact with PABPs because of the relatively longer distance from the poly(A) region, resulting in prolonged association with mRNA, which stimulates NMD . Recently, it has been reported.