The Untranslated Regions of mRNAs in Cancer
2019; Elsevier BV; Volume: 5; Issue: 4 Linguagem: Inglês
10.1016/j.trecan.2019.02.011
ISSN2405-8033
AutoresSamantha L. Schuster, Andrew C. Hsieh,
Tópico(s)RNA and protein synthesis mechanisms
ResumoThe UTRs of mRNAs represent important mediators of post-transcriptional gene regulation. UTR control of mRNA metabolism and translation can be usurped in cancer. Somatic alterations in UTRs are emerging as potential gene-specific drivers of cancer etiology. Protein–RNA and RNA–RNA interactions within regulatory elements of the UTRs may present novel therapeutic opportunities in cancer. The 5′ and 3′ untranslated regions (UTRs) regulate crucial aspects of post-transcriptional gene regulation that are necessary for the maintenance of cellular homeostasis. When these processes go awry through mutation or misexpression of certain regulatory elements, the subsequent deregulation of oncogenic gene expression can drive or enhance cancer pathogenesis. Although the number of known cancer-related mutations in UTR regulatory elements has recently increased markedly as a result of advances in whole-genome sequencing, little is known about how the majority of these genetic aberrations contribute functionally to disease. In this review we explore the regulatory functions of UTRs, how they are co-opted in cancer, new technologies to interrogate cancerous UTRs, and potential therapeutic opportunities stemming from these regions. The 5′ and 3′ untranslated regions (UTRs) regulate crucial aspects of post-transcriptional gene regulation that are necessary for the maintenance of cellular homeostasis. When these processes go awry through mutation or misexpression of certain regulatory elements, the subsequent deregulation of oncogenic gene expression can drive or enhance cancer pathogenesis. Although the number of known cancer-related mutations in UTR regulatory elements has recently increased markedly as a result of advances in whole-genome sequencing, little is known about how the majority of these genetic aberrations contribute functionally to disease. In this review we explore the regulatory functions of UTRs, how they are co-opted in cancer, new technologies to interrogate cancerous UTRs, and potential therapeutic opportunities stemming from these regions. Post-transcriptional processes account for ∼60% of the variation in protein expression [1Schwanhüusser B. et al.Global quantification of mammalian gene expression control.Nature. 2011; 473: 337-342Crossref PubMed Scopus (2434) Google Scholar], and as such are vital for our complete understanding of proteome diversity. The 5′ and 3′UTRs are mRNA domains that control crucial post-transcriptional gene regulation (see Glossary) processes. As regions that are transcribed, but seldom translated, the 5′ and 3′UTRs contain a myriad of regulatory elements involved in pre-mRNA processing, mRNA stability, and translation initiation. Moreover, emerging evidence suggests that the UTRs are either directly mutated or co-opted in diseases such as cancer [2Mularoni L. et al.OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations.Genome Biol. 2016; 17: 128Crossref PubMed Scopus (20) Google Scholar, 3Weinhold N. et al.Genome-wide analysis of noncoding regulatory mutations in cancer.Nat. Genet. 2014; 46: 1160-1165Crossref PubMed Scopus (204) Google Scholar] (Table 1). Nevertheless, most studies of cancer genomics have focused only on genetic aberrations of protein-coding regions of the genome [4Bailey M.H. et al.Comprehensive characterization of cancer driver genes and mutations.Cell. 2018; 173: 371-385Abstract Full Text Full Text PDF PubMed Scopus (64) Google Scholar, 5Cancer Genome Atlas Research Network Comprehensive molecular characterization of urothelial bladder carcinoma.Nature. 2014; 507: 315-322Crossref PubMed Scopus (1200) Google Scholar]. This is largely because of the high cost of whole-genome sequencing in comparison with targeted exome sequencing, which historically under-captures UTRs. Although studies focused on coding sequences (CDSs) have undoubtedly increased our understanding of many cancers, these approaches have found actionable mutations in only 57% of tumors [4Bailey M.H. et al.Comprehensive characterization of cancer driver genes and mutations.Cell. 2018; 173: 371-385Abstract Full Text Full Text PDF PubMed Scopus (64) Google Scholar]. The 5′ and 3′UTRs represent genomic regions that may harbor yet undiscovered driver mutations of cancer pathogenesis at the post-transcriptional level.Table 1Regulatory Elements of the 5′ and 3′UTRs, Their Relevance to Cancer, and Tools for their IdentificationUTR regulatory elementGenes modulated by cis-elements in cancerTransacting regulatory machinery implicated in cancerTechnologies for cis-element identificationaAbbreviations: HITS-CLIP, high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation; m6A-Seq, N6-methyl-adenosine immunoprecipitation and deep sequencing; MeRIP-Seq, methylated RNA immunoprecipitation and deep sequencing; Roar, 'ratio of a ratio' alternative polyadenylation analysis; 3′READS, 3′-region extraction and deep sequencing; WTTS-Seq, whole-transcriptome termini site sequencing.Upstream ORFsCDKN2AbKnown somatic UTR mutation in cancer., CDKN1BbKnown somatic UTR mutation in cancer., TMPRSS2–ERG, KRAS, NPM1, ERCC5bKnown somatic UTR mutation in cancer.eIF2αComputational search for AUG/Kozak sequenceMass spectrometry (small peptides)Ribosome profiling 148Ingolia N.T. et al.Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.Science. 2009; 324: 218-223Crossref PubMed Scopus (1484) Google ScholarInternal ribosome entry sitesp120, p53, p27hnRNP A1 153Holmes B. et al.Mechanistic target of rapamycin (mTOR) inhibition synergizes with reduced internal ribosome entry site (IRES)-mediated translation of cyclin D1 and c-MYC mRNAs to treat glioblastoma.J. Biol. Chem. 2016; 291: 14146-14159Crossref PubMed Scopus (10) Google ScholarBicistronic assayCircular RNA reporter assay5′-Hairpin cap-blockingreporter assaymiRNA binding siteE2F1bKnown somatic UTR mutation in cancer.miR-21, miR-17-92, miRNA-34amiRNA and mRNA expression analysis 158Li Z. Tzeng C.-M. Integrated analysis of miRNA and mRNA expression profiles to identify miRNA targets.Methods Mol. Biol. 2018; 1720: 141-148Crossref PubMed Scopus (0) Google ScholarBiotin pulldown + RNA-Seq 159Tan S.M. Lieberman J. Capture and identification of miRNA targets by biotin pulldown and RNA-seq.Methods Mol. Biol. 2016; 1358: 211-228Crossref PubMed Scopus (1) Google ScholarAlternative poly(A) signalsJUN, NRAS, MGMTCSTF64, CFIm253′READS 160Hoque M. et al.Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing.Nat. Methods. 2013; 10: 133-139Crossref PubMed Scopus (164) Google ScholarWTTS-Seq 161Zhou X. et al.Accurate profiling of gene expression and alternative polyadenylation with whole transcriptome termini site sequencing (WTTS-Seq).Genetics. 2016; 203: 683-697Crossref PubMed Scopus (8) Google ScholarRoar 162Grassi E. et al.Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.BMC Bioinform. 2016; 17: 423Crossref PubMed Scopus (8) Google Scholarm6ASOX2, NANOGMETTL3, METTL14, ALKBH5, FTOm6A-Seq 107Dominissini D. et al.Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.Nature. 2012; 485: 201-206Crossref PubMed Scopus (814) Google ScholarMeRIP-Seq 104Meyer K.D. et al.Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons.Cell. 2012; 149: 1635-1646Abstract Full Text Full Text PDF PubMed Scopus (760) Google ScholarModified HITS-CLIP 126Ke S. et al.A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation.Genes Dev. 2015; 29: 2037-2053Crossref PubMed Scopus (0) Google Scholara Abbreviations: HITS-CLIP, high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation; m6A-Seq, N6-methyl-adenosine immunoprecipitation and deep sequencing; MeRIP-Seq, methylated RNA immunoprecipitation and deep sequencing; Roar, 'ratio of a ratio' alternative polyadenylation analysis; 3′READS, 3′-region extraction and deep sequencing; WTTS-Seq, whole-transcriptome termini site sequencing.b Known somatic UTR mutation in cancer. Open table in a new tab Despite the crucial role of the UTRs in controlling gene regulation, some studies argue that UTRs are not functionally important in cancer because regulatory region mutations rarely have effect sizes as large as protein-coding mutations [6Hornshøj H. et al.Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.NPJ Genomic Med. 2018; 3: 1Crossref PubMed Scopus (0) Google Scholar, 7Fredriksson N.J. et al.Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.Nat. Genet. 2014; 46: 1258-1263Crossref PubMed Scopus (129) Google Scholar]. However, many other studies have found evidence for the functional and clinical relevance of UTR mutations in cancer, both in genome-wide and gene-specific analyses. Whole-genome sequencing has identified areas of recurrent mutations across the UTRs of many cancer-related genes, arguing for extensive deregulation of UTR function in disease [2Mularoni L. et al.OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations.Genome Biol. 2016; 17: 128Crossref PubMed Scopus (20) Google Scholar, 3Weinhold N. et al.Genome-wide analysis of noncoding regulatory mutations in cancer.Nat. Genet. 2014; 46: 1160-1165Crossref PubMed Scopus (204) Google Scholar, 8Puente X.S. et al.Non-coding recurrent mutations in chronic lymphocytic leukaemia.Nature. 2015; 526: 519-524Crossref PubMed Scopus (262) Google Scholar]. In addition to whole-genome studies, many targeted analyses have been performed on particular UTR regulatory elements, providing evidence for functional mutations in 5′ and 3′UTRs [9Zeraati M. et al.Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression.Sci. Rep. 2017; 7: 708Crossref PubMed Scopus (4) Google Scholar, 10Schulz J. et al.Loss-of-function uORF mutations in human malignancies.Sci. Rep. 2018; 8: 2395Crossref PubMed Scopus (5) Google Scholar, 11Wethmar K. et al.Comprehensive translational control of tyrosine kinase expression by upstream open reading frames.Oncogene. 2016; 35: 1736-1742Crossref PubMed Scopus (11) Google Scholar, 12Ziebarth J.D. et al.Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes.PLoS One. 2012; 7e47137Crossref PubMed Scopus (18) Google Scholar]. In this review, we explore the regulatory functions of UTRs, how they can be hijacked in cancer, recent advances in technology for studying UTR elements, and exciting potential therapeutic opportunities stemming from these regions. The 5′ and 3′UTRs primarily function through a dynamic interplay between sequence and structural motifs, collectively called cis-regulatory elements, and RNA-binding protein (RBP) or small RNA trans-acting factors (Figure 1A, Key Figure). Together, they can shape the cellular proteome by tuning the metabolism and translation of specific mRNAs. Importantly, deregulation of cis-regulatory elements can drive cancer pathogenesis by inducing oncogenic gene expression. We highlight below a series of sequence-based and structural cis-elements implicated in cancer. Examples of cis-elements in the 5′UTR associated with cancer include the 5′-terminal oligopyrimidine (5′TOP) motif [13Meyuhas O. Kahan T. The race to decipher the top secrets of TOP mRNAs.Biochim. Biophys. Acta Gene Regul. Mech. 2015; 1849: 801-811Crossref Scopus (65) Google Scholar], the pyrimidine-rich translational element (PRTE) [14Hsieh A.C. et al.The translational landscape of mTOR signalling steers cancer initiation and metastasis.Nature. 2012; 485: 55-61Crossref PubMed Scopus (586) Google Scholar] or TOP-like sequence [15Thoreen C.C. et al.A unifying model for mTORC1-mediated regulation of mRNA translation.Nature. 2012; 485: 109-113Crossref PubMed Scopus (600) Google Scholar], the cytosine-enriched regulator of translation (CERT) [16Truitt M.L. et al.Differential requirements for eIF4E dose in normal development and cancer.Cell. 2015; 162: 59-71Abstract Full Text Full Text PDF PubMed Scopus (78) Google Scholar], the G-quadruplex structure [17Wolfe A.L. et al.RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer.Nature. 2014; 513: 65-70Crossref PubMed Scopus (182) Google Scholar], and the eukaryotic initiation factor 3 (eIF3)-binding stem-loop structure [18Lee A.S.Y. et al.eIF3 targets cell-proliferation messenger RNAs for translational activation or repression.Nature. 2015; 522: 111-114Crossref PubMed Google Scholar]. Each of these elements is present in a subset of mRNAs, enabling targeted control of select gene networks. The 5′TOP and PRTE/TOP-like motifs are similar sequence-specific elements found in distinct parts of the 5′UTR that mediate translation initiation of mRNAs associated with protein synthesis, proliferation, metabolism, and metastasis downstream of oncogenic mTOR signaling [13Meyuhas O. Kahan T. The race to decipher the top secrets of TOP mRNAs.Biochim. Biophys. Acta Gene Regul. Mech. 2015; 1849: 801-811Crossref Scopus (65) Google Scholar, 14Hsieh A.C. et al.The translational landscape of mTOR signalling steers cancer initiation and metastasis.Nature. 2012; 485: 55-61Crossref PubMed Scopus (586) Google Scholar, 19Cunningham J.T. et al.Protein and nucleotide biosynthesis are coupled by a single rate-limiting enzyme, PRPS2, to drive cancer.Cell. 2014; 157: 1088-1103Abstract Full Text Full Text PDF PubMed Scopus (78) Google Scholar]. Interestingly, a subset of genes that possess the PRTE can predict prostate cancer aggressiveness [20Sheridan C.M. et al.YB-1 and MTA1 protein levels and not DNA or mRNA alterations predict for prostate cancer recurrence.Oncotarget. 2015; 6: 7470-7480Crossref PubMed Scopus (12) Google Scholar]. The CERT is another sequence-based element, which was identified within the 5′UTR of mRNAs sensitive to haploinsufficiency of the translation initiation factor eIF4E. Importantly, a series of reactive oxygen species (ROS) regulators, such as FTH1, possess the CERT and are necessary to buffer ROS production during tumor initiation [16Truitt M.L. et al.Differential requirements for eIF4E dose in normal development and cancer.Cell. 2015; 162: 59-71Abstract Full Text Full Text PDF PubMed Scopus (78) Google Scholar]. Together, these examples demonstrate that 5′UTR motifs are important for deregulation of gene expression in cancer; however, the mechanisms by which these cis-regulatory elements drive gene-specific mRNA translation have yet to be fully elucidated. In particular, with the exception of TOP mRNAs [21Philippe L. et al.La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region.Nucleic Acids Res. 2018; 46: 1457-1469Crossref PubMed Scopus (3) Google Scholar], additional work is needed to identify and validate novel trans-interacting factors that mediate specificity. In addition to sequence-specific motifs, structural elements present within the 5′UTR can regulate mRNA translation in cancer. For example, it has been shown in T cell acute lymphoblastic leukemia models that a series of G-quadruplex-containing mRNAs are essential for the enhanced translation of oncogenes, transcription factors, and epigenetic regulators in an eIF4A-dependent manner [17Wolfe A.L. et al.RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer.Nature. 2014; 513: 65-70Crossref PubMed Scopus (182) Google Scholar]. In addition, a 5′UTR stem-loop that can bind eIF3 has been discovered that may explain previous findings that the eIF3 complex is associated with several types of cancers independently of its normal role in preinitiation complex (PIC) assembly (Box 1). Through binding this structural motif, eIF3 can either promote or repress translation. Specifically, it was found to upregulate the proto-oncogene JUN and downregulate the tumor-suppressive BTG1, which together could promote cancer pathogenesis [18Lee A.S.Y. et al.eIF3 targets cell-proliferation messenger RNAs for translational activation or repression.Nature. 2015; 522: 111-114Crossref PubMed Google Scholar]. The mechanism for this differential regulation remains to be determined.Box 1Mechanisms of Canonical mRNA Processing and Cap-Dependent TranslationThe 5′ and 3′UTRs control virtually every aspect of post-transcriptional gene regulation, from pre-mRNA processing to translation initiation. The first regulatory processes to occur on the UTRs are capping and polyadenylation, which take place cotranscriptionally (see Figure 2A in main text). 5′-end capping with N7-7-methyl guanosine is required for cap-dependent translation and stabilizes the mRNA. Polyadenylation is a two-step process of endonucleolytic cleavage of pre-mRNA followed by synthesis of a poly(A) tail directed by the poly(A) site (PAS). The PAS is composed of a combination of cis-elements including the core hexamer AAUAAA 10–30 nt upstream of the cleavage site, a CA dinucleotide sequence, and several U/GU-rich elements [151Shi Y. Manley J.L. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site.Genes Dev. 2015; 29: 889-897Crossref PubMed Scopus (105) Google Scholar]. Not all these elements need to be present around the cleavage site for polyadenylation to occur, but the similarity of the region to these canonical sequences strengthens the PAS, which has consequences for alternative polyadenylation. The PAS cis-elements are recognized by multiple protein complexes, including CPSF (cleavage and polyadenylation specificity factor), CstF (cleavage stimulation factor), and CFI (cleavage factor Im).Once the mRNA is capped, polyadenylated, and exported to the cytoplasm, translation can take place. Many mRNAs in eukaryotic cells are translated in a cap-dependent manner (see Figure 2B in main text). This mode of translation starts with the assembly of the 43S preinitiation complex (PIC), which consists of the 40S small ribosomal subunit, several initiation factors (eIF1, eIF1A, eIF3, and eIF5), and the preformed ternary complex (methionyl-initiator tRNA bound to eIF2:GTP). The eIF4F complex, composed of the cap-binding protein eIF4E, RNA helicase eIF4A, and scaffolding protein eIF4G, binds to the 5′ cap of mRNA and recruits the PIC to this site. Once this complex is assembled, the PIC scans the 5′UTR for an AUG start codon. Unwinding of 5′UTR RNA secondary structure by eIF4A is required during this scanning, making highly structured transcripts more heavily dependent on eIF4A.When the PIC encounters a start codon in the optimal context of the Kozak sequence (A/G)CCAUGG, translation can initiate with the binding of the 60S large ribosomal subunit. Recycling of eIF2:GDP after initiation back into eIF2:GTP is an essential step for subsequent rounds of translation to occur. This process is catalyzed by eIF2B and can be inhibited by phosphorylation of the eIF2α subunit to repress global rates of translation during cellular stress. When cap-dependent translation is inhibited in this context, other methods of translation can play a crucial role in maintaining cellular homeostasis. In addition, alternative forms of translation include IRES and uORF-mediated translation, and others such as the cap-dependent but eIF4E-independent mechanism characterized by usage of a DAP5–eIF3D complex that is involved in the translation of many known oncogenes [152de la Parra C. et al.A widespread alternate form of cap-dependent mRNA translation initiation.Nat. Commun. 2018; 9: 3068Crossref PubMed Scopus (1) Google Scholar]. The 5′ and 3′UTRs control virtually every aspect of post-transcriptional gene regulation, from pre-mRNA processing to translation initiation. The first regulatory processes to occur on the UTRs are capping and polyadenylation, which take place cotranscriptionally (see Figure 2A in main text). 5′-end capping with N7-7-methyl guanosine is required for cap-dependent translation and stabilizes the mRNA. Polyadenylation is a two-step process of endonucleolytic cleavage of pre-mRNA followed by synthesis of a poly(A) tail directed by the poly(A) site (PAS). The PAS is composed of a combination of cis-elements including the core hexamer AAUAAA 10–30 nt upstream of the cleavage site, a CA dinucleotide sequence, and several U/GU-rich elements [151Shi Y. Manley J.L. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site.Genes Dev. 2015; 29: 889-897Crossref PubMed Scopus (105) Google Scholar]. Not all these elements need to be present around the cleavage site for polyadenylation to occur, but the similarity of the region to these canonical sequences strengthens the PAS, which has consequences for alternative polyadenylation. The PAS cis-elements are recognized by multiple protein complexes, including CPSF (cleavage and polyadenylation specificity factor), CstF (cleavage stimulation factor), and CFI (cleavage factor Im). Once the mRNA is capped, polyadenylated, and exported to the cytoplasm, translation can take place. Many mRNAs in eukaryotic cells are translated in a cap-dependent manner (see Figure 2B in main text). This mode of translation starts with the assembly of the 43S preinitiation complex (PIC), which consists of the 40S small ribosomal subunit, several initiation factors (eIF1, eIF1A, eIF3, and eIF5), and the preformed ternary complex (methionyl-initiator tRNA bound to eIF2:GTP). The eIF4F complex, composed of the cap-binding protein eIF4E, RNA helicase eIF4A, and scaffolding protein eIF4G, binds to the 5′ cap of mRNA and recruits the PIC to this site. Once this complex is assembled, the PIC scans the 5′UTR for an AUG start codon. Unwinding of 5′UTR RNA secondary structure by eIF4A is required during this scanning, making highly structured transcripts more heavily dependent on eIF4A. When the PIC encounters a start codon in the optimal context of the Kozak sequence (A/G)CCAUGG, translation can initiate with the binding of the 60S large ribosomal subunit. Recycling of eIF2:GDP after initiation back into eIF2:GTP is an essential step for subsequent rounds of translation to occur. This process is catalyzed by eIF2B and can be inhibited by phosphorylation of the eIF2α subunit to repress global rates of translation during cellular stress. When cap-dependent translation is inhibited in this context, other methods of translation can play a crucial role in maintaining cellular homeostasis. In addition, alternative forms of translation include IRES and uORF-mediated translation, and others such as the cap-dependent but eIF4E-independent mechanism characterized by usage of a DAP5–eIF3D complex that is involved in the translation of many known oncogenes [152de la Parra C. et al.A widespread alternate form of cap-dependent mRNA translation initiation.Nat. Commun. 2018; 9: 3068Crossref PubMed Scopus (1) Google Scholar]. In addition to these distinct cis-regulatory elements, the overall level of secondary structure in the 5′UTR can also affect translational regulation of distinct transcripts in cis. During cap-dependent translation initiation, secondary structure within the 5′UTR is unwound by eIF4A of the eIF4F cap-binding complex to allow the PIC to scan (Box 1). In this way, transcripts with highly structured 5′UTRs are more dependent on the eIF4F complex [22Svitkin Y.V. et al.The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure.RNA. 2001; 7: 382-394Crossref PubMed Scopus (0) Google Scholar, 23Grens A. Scheffler I.E. The 5′- and 3′-untranslated regions of ornithine decarboxylase mRNA affect the translational efficiency.J. Biol. Chem. 1990; 265: 11810-11816PubMed Google Scholar]. Interestingly, many oncogenes possess structured 5′UTRs including hairpins and G-quadruplexes, making the expression of eIF4F components (particularly eIF4A and eIF4E) oncogenic [17Wolfe A.L. et al.RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer.Nature. 2014; 513: 65-70Crossref PubMed Scopus (182) Google Scholar, 24Rubio C.A. et al.Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation.Genome Biol. 2014; 15: 476Crossref PubMed Scopus (51) Google Scholar, 25Ruggero D. et al.The translation factor eIF-4E promotes tumor formation and cooperates with c-Myc in lymphomagenesis.Nat. Med. 2004; 10: 484-486Crossref PubMed Scopus (424) Google Scholar]. Oncogenes may circumvent this dependence and increase their translation efficiency by using alternative transcription start-sites, thereby shortening their 5′UTRs and including fewer structural elements [26Dieudonné F.X. et al.The effect of heterogeneous transcription start sites (TSS) on the translatome: implications for the mammalian cellular phenotype.BMC Genomics. 2015; 16: 986Crossref PubMed Scopus (8) Google Scholar]. The 3′UTR also possesses sequence-based and structural motifs that can modulate mRNA metabolism, including AU-rich elements (AREs), G-rich elements (GREs), and the transforming growth factor (TGF)-β-activated translational (BAT) element. It has been shown that ARE-containing mRNAs are over-represented in cancer and may play a role in mitotic progression [27Hitti E. et al.Systematic analysis of AU-rich element expression in cancer reveals common functional clusters regulated by key RNA-binding proteins.Cancer Res. 2016; 76: 4068-4080Crossref PubMed Google Scholar]. The GRE is enriched in the 3′UTRs of 10 epithelial-to-mesenchymal transition (EMT)-related genes. This element promotes the translation of these genes through interactions with the RNA-binding protein CELF1, which is upregulated in breast cancer tissues and promotes lung metastasis in xenograft models [28Chaudhury A. et al.CELF1 is a central node in post-transcriptional regulatory programmes underlying EMT.Nat. Commun. 2016; 7: 13362Crossref PubMed Scopus (14) Google Scholar]. In addition, the BAT element is a structural motif consisting of a stem-loop with an asymmetrical bulge. This structural element represses translation of two EMT-related genes, DAB2 and ILEI, via the binding of heterologous nuclear protein (hnRNP) E1. TGF-β signaling can phosphorylate hnRNP E1, releasing it from the stem-loop, increasing protein expression of these genes and promoting EMT [29Chaudhury A. et al.TGF-β-mediated phosphorylation of hnRNP E1 induces EMT via transcript-selective translational induction of Dab2 and ILEI.Nat. Cell Biol. 2010; 12: 286-293Crossref PubMed Scopus (169) Google Scholar]. These sequence- and structure-specific motifs demonstrate the functional consequences of UTR-mediated deregulation in cancer. The following sections highlight additional examples of well-studied and emerging UTR cis-elements that can promote cancer phenotypes. Importantly, many fundamental questions about cis-regulatory elements remain. For example, it is unknown if any of these motifs are somatically mutated in cancer. Moreover, the mechanisms of many elements and what drives their selectivity in disease are open questions. Lastly, some of these elements can be found within the same mRNAs, raising the intriguing potential of cis-on-cis interactions that will require novel experimental designs to unlock their regulatory logic. The upstream open reading frame (uORF) is a unique 5′UTR element that can regulate the translation initiation of specific transcripts. It consists of a translatable ORF with a start codon upstream of the primary ORF start codon. Although there is debate as to whether uORFs are translated into functional peptides, the presence of uORFs on mRNA transcripts has been shown to modulate expression of the main downstream ORF (reviewed in [30Hinnebusch A.G. et al.Translational control by 5′-untranslated regions of eukaryotic mRNAs.Science. 2016; 352: 1413-1416Crossref PubMed Scopus (484) Google Scholar, 31Morris D.R. Geballe A.P. Upstream open reading frames as regulators of mRNA translation.Mol. Cell. Biol. 2000; 20: 8635-8642Crossref PubMed Scopus (486) Google Scholar]). Under normal conditions, uORFs decrease protein expression through induction of either translation repression or nonsense-mediated decay (NMD) [32Barbosa C. et al.Gene expression regulation by upstream open reading frames and human disease.PLoS Genet. 2013; 9e1003529Crossref PubMed Scopus (166) Google Scholar]. A phenomenon called 'leaky scanning' determines whether uORFs are recognized or disregarded based on the strength of the uORF AUG sequence context. If a uORF is recognized by the PIC (Box 1), it can repress translation initiation by preventing access to the downstream main ORF or by blocking the scanning of other PICs. If the uORF stop codon is recognized as a premature stop codon, it can trigger NMD, decreasing transcript abundance and protein synthesis (Figure 1B) [32Barbosa C. et al.Gene expression regulation by upstream open reading frames and human disease.PLoS Genet. 2013; 9e1003529Crossref PubMed Scopus (166) Google Scholar]. Germline or somatic mutations that create, delete, or alter uORFs can contribute to cancer phenotypes. For example, a single point mutation that creates a novel uORF in the tumor-suppressor CDKN2A decreases CDKN2A protein levels in hereditary melanoma [33Liu L. et al.Mutation of the CDKN2A 5′ UTR creates an aberrant initiation codon and predisposes to melanoma.Nat. Genet. 1999; 21: 128-132Crossref PubMed Scopus (0) Google Scholar]. Likewise, examination of the CDKN1B 5′UTR in a patient with inherited multiple endocrine neoplasia syndrome uncovered a four nucleotide deletion that induces a frameshift and lengthens the uORF reading frame
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