Skip to content
naulon

No retraction, correction or concern found when last checked on Oct 30, 2026.

Upstream open reading frames: Molecular switches in (patho)physiology

Klaus Wethmar, Jeske J. Smink, Achim Leutz

BioEssays · 2010 · Review

doi:10.1002/bies.201000037

Abstract

Conserved upstream open reading frames (uORFs) are found within many eukaryotic transcripts and are known to regulate protein translation. Evidence from genetic and bioinformatic studies implicates disturbed uORF‐mediated translational control in the etiology of human diseases. A genetic mouse model has recently provided proof‐of‐principle support for the physiological relevance of uORF‐mediated translational control in mammals. The targeted disruption of the uORF initiation codon within the transcription factor CCAAT/enhancer binding protein β (C/EBPβ) gene resulted in deregulated C/EBPβ protein isoform expression, associated with defective liver regeneration and impaired osteoclast differentiation. The high prevalence of uORFs in the human transcriptome suggests that intensified search for mutations within 5′ RNA leader regions may reveal a multitude of alterations affecting uORFs, causing pathogenic deregulation of protein expression.

Shown for reading. Its publisher allows quoting it, not republishing it.

References 91

  1. 1.

    Scheper GC, van der Knaap MS, Proud CG. Translation matters: protein synthesis defects in inherited disease. Nat Rev Genet. 2007;8:711-23.

    Not in our library10.1038/nrg2142

  2. 2.

    Mignone F, Gissi C, Liuni S, et al. Untranslated regions of mRNAs. Genome Biol. 2002;3:4.1-4.10.

    Not in our library10.1186/gb-2002-3-3-reviews0004

  3. 3.

    Pickering BM, Willis AE. The implications of structured 5′ untranslated regions on translation and disease. Semin Cell Dev Biol. 2005;16:39-47.

    Not in our library10.1016/j.semcdb.2004.11.006

  4. 4.

    Wilkie GS, Dickson KS, Gray NK. Regulation of mRNA translation by 5′- and 3′-UTR-binding factors. Trends Biochem Sci. 2003;28:182-8.

    Not in our library10.1016/s0968-0004(03)00051-3

  5. 5.

    Chatterjee S, Pal JK. Role of 5′- and 3′-untranslated regions of mRNAs in human diseases. Biol Cell. 2009;101:251-62.

    Not in our library10.1042/bc20080104

  6. 6.

    Jackson RJ, Hellen CU, Pestova TV. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol. 2010;11:113-27.

    Not in our library10.1038/nrm2838

  7. 7.

    Le Quesne JP, Spriggs KA, Bushell M, et al. Dysregulation of protein synthesis and disease. J Pathol. 2010;220:140-51.

    Not in our library10.1002/path.2627

  8. 8.

    Wethmar K, Begay V, Smink JJ, et al. C/EBPbetaDeltauORF mice – a genetic model for uORF-mediated translational control in mammals. Genes Dev. 2010;24:15-20.

    Not in our library10.1101/gad.557910

  9. 9.

    Kozak M. Pushing the limits of the scanning mechanism for initiation of translation. Gene. 2002;299:1.

    Not in our library10.1016/s0378-1119(02)01056-9

  10. 10.

    Kozak M. How do eucaryotic ribosomes select initiation regions in messenger RNA? Cell. 1978;15:1109-23.

    Not in our library10.1016/0092-8674(78)90039-9

  11. 11.

    Kozak M. An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 1987;15:8125-48.

    Not in our library10.1093/nar/15.20.8125

  12. 12.

    Hinnebusch AG. Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol. 2005;59:407-50.

    Not in our library10.1146/annurev.micro.59.031805.133833

  13. 13.

    Mueller PP, Hinnebusch AG. Multiple upstream AUG codons mediate translational control of GCN4. Cell. 1986;45:201-7.

    Not in our library10.1016/0092-8674(86)90384-3

  14. 14.

    Kozak M. Effects of intercistronic length on the efficiency of reinitiation by eucaryotic ribosomes. Mol Cell Biol. 1987;7:3438-45.

    Not in our library10.1128/mcb.7.10.3438-3445.1987

  15. 15.

    Kozak M. Constraints on reinitiation of translation in mammals. Nucleic Acids Res. 2001;29:5226-32.

    Not in our library10.1093/nar/29.24.5226

  16. 16.

    Iacono M, Mignone F, Pesole G. uAUG and uORFs in human and rodent 5′untranslated mRNAs. Gene. 2005;349:97.

    Not in our library10.1016/j.gene.2004.11.041

  17. 17.

    Matsui M, Yachie N, Okada Y, et al. Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse. FEBS Lett. 2007;581:4184-8.

    Not in our library10.1016/j.febslet.2007.07.057

  18. 18.

    Calvo SE, Pagliarini DJ, Mootha VK. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci USA. 2009;106:7507-12.

    Not in our library10.1073/pnas.0810916106

  19. 19.

    Neafsey DE, Galagan JE. Dual modes of natural selection on upstream open reading frames. Mol Biol Evol. 2007;24:1744-51.

    Not in our library10.1093/molbev/msm093

  20. 20.

    Ingolia NT, Ghaemmaghami S, Newman JR, et al. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324:218-23.

    Not in our library10.1126/science.1168978

  21. 21.

    Mendell JT, Sharifi NA, Meyers JL, et al. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet. 2004;36:1073-8.

    Not in our library10.1038/ng1429

  22. 22.

    Rahmani F, Hummel M, Schuurmans J, et al. Sucrose control of translation mediated by an upstream open reading frame-encoded peptide. Plant Physiol. 2009;150:1356-67.

    Not in our library10.1104/pp.109.136036

  23. 23.

    Gaba A, Jacobson A, Sachs MS. Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay. Mol Cell. 2005;20:449-60.

    Not in our library10.1016/j.molcel.2005.09.019

  24. 24.

    Hanfrey C, Franceschetti M, Mayer MJ, et al. Translational regulation of the plant S-adenosylmethionine decarboxylase. Biochem Soc Trans. 2003;31:424-7.

    Not in our library10.1042/bst0310424

  25. 25.

    Oyama M, Itagaki C, Hata H, et al. Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res. 2004;14:2048-52.

    Not in our library10.1101/gr.2384604

  26. 26.

    Oyama M, Kozuka-Hata H, Suzuki Y, et al. Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics. 2007;6:1000-6.

    Not in our library10.1074/mcp.m600297-mcp200

  27. 27.

    Child SJ, Miller MK, Geballe AP. Translational control by an upstream open reading frame in the HER-2/neu transcript. J Biol Chem. 1999;274:24335-41.

    Not in our library10.1074/jbc.274.34.24335

  28. 28.

    Rajkowitsch L, Vilela C, Berthelot K, et al. Reinitiation and recycling are distinct processes occurring downstream of translation termination in yeast. J Mol Biol. 2004;335:71-85.

    Not in our library10.1016/j.jmb.2003.10.049

  29. 29.

    Calkhoven CF, Muller C, Leutz A. Translational control of C/EBPalpha and C/EBPbeta isoform expression. Genes Dev. 2000;14:1920-32.

    Not in our library

  30. 30.

    Kozak M. An analysis of vertebrate mRNA sequences: intimations of translational control. J Cell Biol. 1991;115:887-903.

    Not in our library10.1083/jcb.115.4.887

  31. 31.

    Calkhoven CF, Muller C, Leutz A. Translational control of gene expression and disease. Trends Mol Med. 2002;8:577-83.

    Not in our library10.1016/s1471-4914(02)02424-3

  32. 32.

    Johnson PF. Molecular stop signs: regulation of cell-cycle arrest by C/EBP transcription factors. J Cell Sci. 2005;118:2545-55.

    Not in our library10.1242/jcs.02459

  33. 33.

    Nerlov C. The C/EBP family of transcription factors: a paradigm for interaction between gene expression and proliferation control. Trends Cell Biol. 2007;17:318-24.

    Not in our library10.1016/j.tcb.2007.07.004

  34. 34.

    Ramji DP, Foka P. CCAAT/enhancer-binding proteins: structure, function and regulation. Biochem J. 2002;365:561-75.

    Not in our library10.1042/bj20020508

  35. 35.

    Smink JJ, Begay V, Schoenmaker T, et al. Transcription factor C/EBPbeta isoform ratio regulates osteoclastogenesis through MafB. EMBO J. 2009;28:1769-81.

    Not in our library10.1038/emboj.2009.127

  36. 36.

    Smink JJ, Leutz A. Rapamycin and the transcription factor C/EBPbeta as a switch in osteoclast differentiation: implications for lytic bone diseases. J Mol Med. 2010;88:227-33.

    Not in our library10.1007/s00109-009-0567-8

  37. 37.

    Zahnow CA. CCAAT/enhancer-binding protein beta: its role in breast cancer and associations with receptor tyrosine kinases. Expert Rev Mol Med. 2009;11:e12.

    Not in our library10.1017/s1462399409001033

  38. 38.

    Mink S, Haenig B, Klempnauer KH. Interaction and functional collaboration of p300 and C/EBPbeta. Mol Cell Biol. 1997;17:6609-17.

    Not in our library10.1128/mcb.17.11.6609

  39. 39.

    Erickson RL, Hemati N, Ross SE, et al. p300 coactivates the adipogenic transcription factor CCAAT/enhancer-binding protein alpha. J Biol Chem. 2001;276:16348-55.

    Not in our library10.1074/jbc.m100128200

  40. 40.

    Nerlov C, Ziff EB. CCAAT/enhancer binding protein-alpha amino acid motifs with dual TBP and TFIIB binding ability co-operate to activate transcription in both yeast and mammalian cells. EMBO J. 1995;14:4318-28.

    Not in our library10.1002/j.1460-2075.1995.tb00106.x

  41. 41.

    Muller C, Bremer A, Schreiber S, et al. Nucleolar retention of a translational C/EBP[alpha] isoform stimulates rDNA transcription and cell size. EMBO J. 2010;29:897-909.

    Not in our library10.1038/emboj.2009.404

  42. 42.

    Descombes P, Schibler U. A liver-enriched transcriptional activator protein, LAP, and a transcriptional inhibitory protein, LIP, are translated from the same mRNA. Cell. 1991;67:569-79.

    Not in our library10.1016/0092-8674(91)90531-3

  43. 43.

    Calkhoven CF, Bouwman PR, Snippe L, et al. Translation start site multiplicity of the CCAAT/enhancer binding protein alpha mRNA is dictated by a small 5′ open reading frame. Nucleic Acids Res. 1994;22:5540-7.

    Not in our library10.1093/nar/22.25.5540

  44. 44.

    Lincoln AJ, Monczak Y, Williams SC, et al. Inhibition of CCAAT/enhancer-binding protein alpha and beta translation by upstream open reading frames. J Biol Chem. 1998;273:9552-60.

    Not in our library10.1074/jbc.273.16.9552

  45. 45.

    Buck M, Turler H, Chojkier M. LAP (NF-IL-6), a tissue-specific transcriptional activator, is an inhibitor of hepatoma cell proliferation. EMBO J. 1994;13:851-60.

    Not in our library10.1002/j.1460-2075.1994.tb06328.x

  46. 46.

    Nerlov C, Graf T. PU.1 induces myeloid lineage commitment in multipotent hematopoietic progenitors. Genes Dev. 1998;12:2403-12.

    Not in our library10.1101/gad.12.15.2403

  47. 47.

    Hata K, Nishimura R, Ueda M, et al. A CCAAT/enhancer binding protein beta isoform, liver-enriched inhibitory protein, regulates commitment of osteoblasts and adipocytes. Mol Cell Biol. 2005;25:1971-9.

    Not in our library10.1128/mcb.25.5.1971-1979.2005

  48. 48.

    Calkhoven CF, Snippe L, Ab G. Differential stimulation by CCAAT/enhancer-binding protein alpha isoforms of the estrogen-activated promoter of the very-low-density apolipoprotein II gene. Eur J Biochem. 1997;249:113-20.

    Not in our library10.1111/j.1432-1033.1997.t01-2-00113.x

  49. 49.

    Freytag SO, Paielli DL, Gilbert JD. Ectopic expression of the CCAAT/enhancer-binding protein alpha promotes the adipogenic program in a variety of mouse fibroblastic cells. Genes Dev. 1994;8:1654-63.

    Not in our library10.1101/gad.8.14.1654

  50. 50.

    Kowenz-Leutz E, Leutz A. A C/EBP beta isoform recruits the SWI/SNF complex to activate myeloid genes. Mol Cell. 1999;4:735-43.

    Not in our library10.1016/s1097-2765(00)80384-6

  51. 51.

    Lin FT, MacDougald OA, Diehl AM, et al. A 30-kDa alternative translation product of the CCAAT/enhancer binding protein alpha message: transcriptional activator lacking antimitotic activity. Proc Natl Acad Sci USA. 1993;90:9606-10.

    Not in our library10.1073/pnas.90.20.9606

  52. 52.

    Ossipow V, Descombes P, Schibler U. CCAAT/enhancer-binding protein mRNA is translated into multiple proteins with different transcription activation potentials. Proc Natl Acad Sci USA. 1993;90:8219-23.

    Not in our library10.1073/pnas.90.17.8219

  53. 53.

    Sears RC, Sealy L. Multiple forms of C/EBP beta bind the EFII enhancer sequence in the Rous sarcoma virus long terminal repeat. Mol Cell Biol. 1994;14:4855-71.

    Not in our library10.1128/mcb.14.7.4855-4871.1994

  54. 54.

    Nerlov C. C/EBPs: recipients of extracellular signals through proteome modulation. Curr Opin Cell Biol. 2008;20:180-5.

    Not in our library10.1016/j.ceb.2008.02.002

  55. 55.

    Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 1986;44:283-92.

    Not in our library10.1016/0092-8674(86)90762-2

  56. 56.

    Kozak M. At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. J Mol Biol. 1987;196:947-50.

    Not in our library10.1016/0022-2836(87)90418-9

  57. 57.

    Corradetti MN, Guan KL. Upstream of the mammalian target of rapamycdo all roads pass through mTOR? Oncogene. 2006;25:6347-60.

    Not in our library10.1038/sj.onc.1209885

  58. 58.

    Jundt F, Raetzel N, Muller C, et al. A rapamycin derivative (everolimus) controls proliferation through down-regulation of truncated CCAAT enhancer binding protein {beta} and NF-{kappa}B activity in Hodgkin and anaplastic large cell lymphomas. Blood. 2005;106:1801-7.

    Not in our library10.1182/blood-2004-11-4513

  59. 59.

    Zahnow CA, Cardiff RD, Laucirica R, et al. A role for CCAAT/enhancer binding protein beta-liver-enriched inhibitory protein in mammary epithelial cell proliferation. Cancer Res. 2001;61:261-9.

    Not in our library

  60. 60.

    Berenson JR, Yellin O. New drugs in multiple myeloma. Curr Opin Support Palliat Care. 2008;2:204-10.

    Not in our library10.1097/spc.0b013e3283090475

  61. 61.

    Chan S, Scheulen ME, Johnston S, et al. Phase II study of temsirolimus (CCI-779), a novel inhibitor of mTOR, in heavily pretreated patients with locally advanced or metastatic breast cancer. J Clin Oncol. 2005;23:5314-22.

    Not in our library10.1200/jco.2005.66.130

  62. 62.

    Xiong W, Hsieh C-C, Kurtz AJ, et al. Regulation of CCAAT/enhancer-binding protein-{beta} isoform synthesis by alternative translational initiation at multiple AUG start sites. Nucleic Acids Res. 2001;29:3087-98.

    Not in our library10.1093/nar/29.14.3087

  63. 63.

    Timchenko NA, Welm AL, Lu X, et al. CUG repeat binding protein (CUGBP1) interacts with the 5′ region of C/EBPbeta mRNA and regulates translation of C/EBPbeta isoforms. Nucleic Acids Res. 1999;27:4517-25.

    Not in our library10.1093/nar/27.22.4517

  64. 64.

    Eiring AM, Harb JG, Neviani P, et al. miR-328 functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts. Cell. 2010;140:652-65.

    Not in our library10.1016/j.cell.2010.01.007

  65. 65.

    Kim K, Kim JH, Lee J, et al. MafB negatively regulates RANKL-mediated osteoclast differentiation. Blood. 2007;109:3253-9.

    Not in our library10.1182/blood-2006-09-048249

  66. 66.

    Lamb J, Ramaswamy S, Ford HL, et al. A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell. 2003;114:323-34.

    Not in our library10.1016/s0092-8674(03)00570-1

  67. 67.

    Mo X, Kowenz-Leutz E, Xu H, et al. Ras induces mediator complex exchange on C/EBP beta. Mol Cell. 2004;13:241-50.

    Not in our library10.1016/s1097-2765(03)00521-5

  68. 68.

    Sebastian T, Malik R, Thomas S, et al. C/EBPbeta cooperates with RB:E2F to implement Ras(V12)-induced cellular senescence. EMBO J. 2005;24:3301-12.

    Not in our library10.1038/sj.emboj.7600789

  69. 69.

    Zhang DE, Zhang P, Wang ND, et al. Absence of granulocyte colony-stimulating factor signaling and neutrophil development in CCAAT enhancer binding protein alpha-deficient mice. Proc Natl Acad Sci USA. 1997;94:569-74.

    Not in our library10.1073/pnas.94.2.569

  70. 70.

    D'Alo F, Johansen LM, Nelson EA, et al. The amino terminal and E2F interaction domains are critical for C/EBP{alpha}-mediated induction of granulopoietic development of hematopoietic cells. Blood. 2003;102:3163.

    Not in our library10.1182/blood-2003-02-0479

  71. 71.

    Johansen LM, Iwama A, Lodie TA, et al. c-Myc is a critical target for C/EBPalpha in granulopoiesis. Mol Cell Biol. 2001;21:3789-806.

    Not in our library10.1128/mcb.21.11.3789-3806.2001

  72. 72.

    Porse BT, Pedersen TA, Xu X, et al. E2F repression by C/EBPalpha is required for adipogenesis and granulopoiesis in vivo. Cell. 2001;107:247-58.

    Not in our library10.1016/s0092-8674(01)00516-5

  73. 73.

    Nerlov C. C/EBP[alpha] mutations in acute myeloid leukemias. Nat Rev Cancer. 2004;4:394.

    Not in our library10.1038/nrc1363

  74. 74.

    Leroy H, Roumier C, Huyghe P, et al. CEBPA point mutations in hematological malignancies. Leukemia. 2005;19:329-34.

    Not in our library10.1038/sj.leu.2403614

  75. 75.

    Sellick GS, Spendlove HE, Catovsky D, et al. Further evidence that germline CEBPA mutations cause dominant inheritance of acute myeloid leukaemia. Leukemia. 2005;19:1276-8.

    Not in our library10.1038/sj.leu.2403788

  76. 76.

    Smith ML, Cavenagh JD, Lister TA, et al. Mutation of CEBPA in familial acute myeloid leukemia. N Engl J Med. 2004;351:2403-7.

    Not in our library10.1056/nejmoa041331

  77. 77.

    Kirstetter P, Schuster MB, Bereshchenko O, et al. Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells. Cancer Cell. 2008;13:299-310.

    Not in our library10.1016/j.ccr.2008.02.008

  78. 78.

    Koschmieder S, D'Alo F, Radomska H, et al. CDDO induces granulocytic differentiation of myeloid leukemic blasts through translational up-regulation of p42 CCAAT enhancer binding protein alpha. Blood. 2007;110:3695-705.

    Not in our library10.1182/blood-2006-11-058941

  79. 79.

    Yamanaka R, Kim GD, Radomska HS, et al. CCAAT/enhancer binding protein epsilon is preferentially up-regulated during granulocytic differentiation and its functional versatility is determined by alternative use of promoters and differential splicing. Proc Natl Acad Sci USA. 1997;94:6462-7.

    Not in our library10.1073/pnas.94.12.6462

  80. 80.

    Lekstrom-Himes JA. The role of C/EBP(epsilon) in the terminal stages of granulocyte differentiation. Stem Cells. 2001;19:125-33.

    Not in our library10.1634/stemcells.19-2-125

  81. 81.

    Bedi R, Du J, Sharma AK, et al. Human C/EBP-epsilon activator and repressor isoforms differentially reprogram myeloid lineage commitment and differentiation. Blood. 2009;113:317-27.

    Not in our library10.1182/blood-2008-02-139741

  82. 82.

    Yamanaka R, Barlow C, Lekstrom-Himes J, et al. Impaired granulopoiesis, myelodysplasia, and early lethality in CCAAT/enhancer binding protein epsilon-deficient mice. Proc Natl Acad Sci USA. 1997;94:13187-92.

    Not in our library10.1073/pnas.94.24.13187

  83. 83.

    Wiestner A, Schlemper RJ, van der Maas AP, et al. An activating splice donor mutation in the thrombopoietin gene causes hereditary thrombocythaemia. Nat Genet. 1998;18:49-52.

    Not in our library10.1038/ng0198-49

  84. 84.

    Liu L, Dilworth D, Gao L, et al. Mutation of the CDKN2A 5′ UTR creates an aberrant initiation codon and predisposes to melanoma. Nat Genet. 1999;21:128-32.

    Not in our library10.1038/5082

  85. 85.

    Wen Y, Liu Y, Xu Y, et al. Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis. Nat Genet. 2009;41:228-33.

    Not in our library10.1038/ng.276

  86. 86.

    Zhou W, Song W. Leaky scanning and reinitiation regulate BACE1 gene expression. Mol Cell Biol. 2006;26:3353-64.

    Not in our library10.1128/mcb.26.9.3353-3364.2006

  87. 87.

    Spevak CC, Park E-H, Geballe AP, et al. her-2 upstream open reading frame effects on the use of downstream initiation codons. Biochem Biophys Res Commun. 2006;350:834.

    Not in our library10.1016/j.bbrc.2006.09.128

  88. 88.

    Williams SC, Baer M, Dillner AJ, et al. CRP2 (C/EBP beta) contains a bipartite regulatory domain that controls transcriptional activation, DNA binding and cell specificity. EMBO J. 1995;14:3170-83.

    Not in our library10.1002/j.1460-2075.1995.tb07319.x

  89. 89.

    Pei DQ, Shih CH. An “attenuator domain” is sandwiched by two distinct transactivation domains in the transcription factor C/EBP. Mol Cell Biol. 1991;11:1480-7.

    Not in our library10.1128/mcb.11.3.1480-1487.1991

  90. 90.

    Kowenz-Leutz E, Twamley G, Ansieau S, et al. Novel mechanism of C/EBP beta (NF-M) transcriptional control: activation through derepression. Genes Dev. 1994;8:2781-91.

    Not in our library10.1101/gad.8.22.2781

  91. 91.

    Lee S, Miller M, et al. CCAAT/enhancer binding protein beta DNA binding is auto-inhibited by multiple elements that also mediate association with p300/CBP. J Biol Chem. 2010;285:21399-410.

    Not in our library10.1074/jbc.m110.128413

Cited by papers we hold 6

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.