Page 12 domain of RNA polymerase II, thereby coupling transcription, splicing, cleavage and polyadenylation. Finally, molecular changes induced by 212141-51-0 web splicing factor dysregulation may not be confined to the nucleus. Multiple SR proteins facilitate nuclear export of both unspliced and spliced mRNAs128,129. SRSF1 shuttles between the nucleus and cytoplasm and promotes capdependent translation of bound mRNAs in a eukaryotic translation initiation factor 4E -dependent manner130,131. SRSF1 activates the mammalian target of rapamycin signaling pathway, which is required for SRSF1-mediated cell transformation40,42. Splicing itself promotes translation via the deposition of multiprotein exon-junction complexes near exon-exon junctions132. NMD provides a concrete example of a cytoplasmic process that is likely affected by cancerassociated mutations affecting SF3B1, SRSF2, U2AF1 and ZRSR2, even though those proteins localize to the nucleus. NMD is a translation-dependent RNA surveillance process that degrades mRNAs containing premature termination codons. Splicing and NMD are closely linked 
in human cells for several reasons. First, many NMD substrates are generated by alternative splicing, wherein premature termination codons are introduced via inclusion of alternatively spliced sequence containing an in-frame premature stop codon or exclusion of sequence resulting in a frameshift. Second, stop codons are recognized as premature by the NMD machinery if they lie >50 nucleotides upstream of a splice junction133,134. PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19855441 The 50 nucleotide threshold arises because the translating ribosome dislodges EJCs and prevents EJC-facilitated activation of NMD. However, if the ribosome stalls sufficiently upstream of an EJC, then NMD factors are recruited and activated133,134. Third, specific splicing factors including SRSF1, regulator of differentiation 1 and PTB can enhance or repress NMD135137. Human cells express an abundance of mRNAs containing premature termination codons, including the EZH2 poison exon that is promoted by SRSF2 mutations72. A subset of poison exons are among the most evolutionarily conserved elements in the human genome139141. These poison exons enable splicing factors to post-transcriptionally down- or upregulate expression of specific genes, including the genes encoding many splicing factors themselves, likely explaining the extreme sequence conservation of many poison exons139141. Interestingly, in the earliest report of splicing factor mutations, genes involved in NMD were upregulated following overexpression of mutant U2AF18, suggesting a potential link between spliceosomal mutations and overproduction of NMD 
substrates. However, such high levels of NMD substrates have not been observed in subsequent studies of mutations affecting U2AF1 or other splicing factors. The recent discovery of recurrent mutations in UPF1, which Aphrodine encodes a RNA helicase that is central to NMD, in pancreatic adenosquamous carcinoma provided a genetic link between NMD and cancer142. The observed mutations induced abnormal UPF1 splicing and skipping of sequence encoding core domains, potentially resulting in partial or complete loss of UPF1 Author Manuscript Author Manuscript Author Manuscript Author Manuscript Nat Rev Cancer. Author manuscript; available in PMC 2016 November 03. Dvinge et al. Page 13 function, although further work is required to determine how these mutations affect global RNA surveillance. Deficiencies in different NMD factors have been previously.Page 12 domain of RNA polymerase II, thereby coupling transcription, splicing, cleavage and polyadenylation. Finally, molecular changes induced by splicing factor dysregulation may not be confined to the nucleus. Multiple SR proteins facilitate nuclear export of both unspliced and spliced mRNAs128,129. SRSF1 shuttles between the nucleus and cytoplasm and promotes capdependent translation of bound mRNAs in a eukaryotic translation initiation factor 4E -dependent manner130,131. SRSF1 activates the mammalian target of rapamycin signaling pathway, which is required for SRSF1-mediated cell transformation40,42. Splicing itself promotes translation via the deposition of multiprotein exon-junction complexes near exon-exon junctions132. NMD provides a concrete example of a cytoplasmic process that is likely affected by cancerassociated mutations affecting SF3B1, SRSF2, U2AF1 and ZRSR2, even though those proteins localize to the nucleus. NMD is a translation-dependent RNA surveillance process that degrades mRNAs containing premature termination codons. Splicing and NMD are closely linked in human cells for several reasons. First, many NMD substrates are generated by alternative splicing, wherein premature termination codons are introduced via inclusion of alternatively spliced sequence containing an in-frame premature stop codon or exclusion of sequence resulting in a frameshift. Second, stop codons are recognized as premature by the NMD machinery if they lie >50 nucleotides upstream of a splice junction133,134. PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19855441 The 50 nucleotide threshold arises because the translating ribosome dislodges EJCs and prevents EJC-facilitated activation of NMD. However, if the ribosome stalls sufficiently upstream of an EJC, then NMD factors are recruited and activated133,134. Third, specific splicing factors including SRSF1, regulator of differentiation 1 and PTB can enhance or repress NMD135137. Human cells express an abundance of mRNAs containing premature termination codons, including the EZH2 poison exon that is promoted by SRSF2 mutations72. A subset of poison exons are among the most evolutionarily conserved elements in the human genome139141. These poison exons enable splicing factors to post-transcriptionally down- or upregulate expression of specific genes, including the genes encoding many splicing factors themselves, likely explaining the extreme sequence conservation of many poison exons139141. Interestingly, in the earliest report of splicing factor mutations, genes involved in NMD were upregulated following overexpression of mutant U2AF18, suggesting a potential link between spliceosomal mutations and overproduction of NMD substrates. However, such high levels of NMD substrates have not been observed in subsequent studies of mutations affecting U2AF1 or other splicing factors. The recent discovery of recurrent mutations in UPF1, which encodes a RNA helicase that is central to NMD, in pancreatic adenosquamous carcinoma provided a genetic link between NMD and cancer142. The observed mutations induced abnormal UPF1 splicing and skipping of sequence encoding core domains, potentially resulting in partial or complete loss of UPF1 Author Manuscript Author Manuscript Author Manuscript Author Manuscript Nat Rev Cancer. Author manuscript; available in PMC 2016 November 03. Dvinge et al. Page 13 function, although further work is required to determine how these mutations affect global RNA surveillance. Deficiencies in different NMD factors have been previously.