uORFdbmdasha comprehensive literature database oneukaryotic uORF biologyKlaus Wethmar12 Adriano Barbosa-Silva3 Miguel A Andrade-Navarro3 and

Achim Leutz14

1Max Delbruck Center for Molecular Medicine (MDC) Cell Differentiation and Tumorigenesis Robert-Rossle-Strasse 10 D-13092 Berlin Germany 2Hematology Oncology and Tumor Immunology Helios Klinikum Berlin-Buch Schwanebecker Chaussee 50 D-13125 Berlin Germany 3Max Delbruck Center for Molecular Medicine(MDC) Computational Biology and Data Mining Robert-Rossle-Strasse 10 D-13092 Berlin Germany and4Humoldt-University Department of Biology Invalidenstrasse 43 D-10115 Berlin Germany

Received August 22 2013 Revised September 25 2013 Accepted September 26 2013

ABSTRACT

Approximately half of all human transcripts containat least one upstream translational initiation site thatprecedes the main coding sequence (CDS) and givesrise to an upstream open reading frame (uORF) Wegenerated uORFdb publicly available at httpcbdmmdc-berlindetoolsuorfdb to serve as a compre-hensive literature database on eukaryotic uORFbiology Upstream ORFs affect downstream transla-tion by interfering with the unrestrained progressionof ribosomes across the transcript leader sequenceAlthough the first uORF-related translational activitywas observed gt30 years ago and an increasingnumber of studies link defective uORF-mediatedtranslational control to the development of humandiseases the features that determine uORF-mediated regulation of downstream translation arenot well understood The uORFdb was manuallycurated from all uORF-related literature listed at thePubMed database It categorizes individual publica-tions by a variety of denominators including taxongene and type of study Furthermore the databasecan be filtered for multiple structural and functionaluORF-related properties to allow convenient andtargeted access to the complex field of eukaryoticuORF biology

INTRODUCTION

Ribosome profiling of the yeast mouse and human tran-scriptomes uncovered high rates of translation beyond theborders of annotated main protein-coding sequences(CDSs) (1ndash4) Most of these nonndashprotein-coding transla-tional hot spots are localized within the transcript leadersequence of mRNAs (4) where upstream AUG codons or

alternative upstream initiation codons give rise toupstream open reading frames (uORFs) The presence ofuORFs which may overlap or terminate upstream of themain protein CDS affects downstream initiation effi-ciency and the translation rate of the respective protein(Figure 1)

The regulatory potential of uORFs has first beendescribed in the 1980s (5) however only recentlyribosome profiling and a growing list of physiologicaland medical implications attributed an increased level ofbiological significance to uORF-mediated translationalcontrol (6ndash9) For example germ line mutations resultingin the de novo generation or functional activation ofuORFs in two prominent tumor suppressor genes(CDKN2A and CDKN1B) were associated with the de-velopment of hereditary melanoma and multiple endo-crine neoplasia syndrome (MEN4) respectively (910)

The vast majority of experiments focused on the func-tional analysis of AUG-initiated uORFs by luciferasereporter assays and mostly demonstrated inhibitoryeffects on downstream translation Exceptionally uORFscan also mediate the paradoxical induction of downstreamprotein translation under unfavorable global translationalconditions as intensively studied for the yeast transcriptionfactor GCN4 in response to nutrient stresses (11) A multi-tude of other uORF-related regulatory functions (1213)

To whom correspondence should be addressed Tel +49 30940 62809 or 12199 Fax +49 30940 63298 Email kwethmarmdc-berlinde

Figure 1 Model of a uORF-containing transcript Two uORFs (blueboxes) precede the main ORF of the CDS (white box) Ribosomes mayinitiate at the CDS initiation codon (white flag) after leaky scanningthrough both uORF initiation codons (blue flags) or may reinitiateafter translating the first uORF and leaky scanning through thesecond uORF initiation site Ribosomes translating the secondoverlapping uORF will not be available for translation of the CDS

D60ndashD67 Nucleic Acids Research 2014 Vol 42 Database issue Published online 24 October 2013doi101093nargkt952

The Author(s) 2013 Published by Oxford University PressThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (httpcreativecommonsorglicensesby-nc30) which permits non-commercial re-use distribution and reproduction in any medium provided the original work is properly cited For commercialre-use please contact journalspermissionsoupcom

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eg uORF-directed selection of downstream translationalinitiation sites in mammalian key-regulatory transcriptionfactors (14) or the uORF-mediated integration of smallmolecule concentrations determining downstream transla-tional activity (15ndash18) may hold abundant novel thera-peutic target sites for medical application

Owing to the overwhelming number and transcript-specific variability of uORF-related properties and func-tions the biology of uORFs is far from being understoodWith uORFdb we generated a comprehensive browsableliterature database on eukaryotic uORF biology toprovide a rapid targeted and convenient overview ofthis developing field

LITERATURE REVIEW AND GENERATION OF THEDATABASE

Since February 2010 we applied a Boolean search for lsquoup-stream open readingrsquo or lsquouORFrsquo or lsquouORFsrsquo or lsquoupstreaminitiationrsquo or lsquouAUGrsquo or lsquosmall open readingrsquo or lsquosORFrsquo orlsquoupORFrsquo or lsquoribosome profilingrsquo to the NCBI PubMeddatabase at httpwwwncbinlmnihgovpubmed On 15July 2013 this search returned 981 publications All ab-stracts were curated manually to eliminate non-related ac-cidental hits Furthermore only publications investigatingeukaryotic or viral transcriptsuORFs were included whilebacterial data were omitted

Most importantly during the curation process weidentified a number of numerical structural sequentialand cofactor-related properties that were recurrentlyassociated with uORF-mediated regulatory functionsAll references were screened and indexed for these newlydefined function-related categories Additionally publica-tions were categorized by the type of article by the taxonand by the gene investigated Wherever required full-textarticles were analyzed to extract missing information ac-cording to the uORFdb denominators All informationwas collected to build a publicly available browsabledatabase at httpcbdmmdc-berlindetoolsuorfdb

The initial release of uORFdb provided links to 467uORF-related references covering a wide range ofspeciestaxa and genes (Table 1) The comprehensive lit-erature survey performed to generate uORFdb revealedthat only 100 of the gt10 000 human protein-coding

genes that produce uORF-bearing transcripts have beeninvestigated for uORF-mediated translational controlmechanisms The proportion of analyzed uORF genesfor other species is even lower eg 04 for mouseand yeast and 01 for ratConsidering the universal prevalence of one or

more uORF(s) in 50 of mRNAs in mammaliantranscriptomes together with the recently proven highrate of uORF-mediated translational activity (47) thenumber of reports on functionally important uORFs islikely to rapidly increase within the next decade of research

FEATURES OF THE DATABASE

The uORFdb is intended to facilitate convenient andtargeted access to the complex field of uORF-mediatedtranslational control mechanisms by a web-based querytool Making use of manually curated data derived froma review of all PubMed-listed uORF-related literatureusers may query uORFdb by three options

I) Query uORF bibliography by gene or taxon

A free-text input field at the query page of the webinterface allows flexible search inputs including genename gene symbol gene alias NCBI GeneGenBankID taxon or taxon common name to identify uORF-related references for a specific gene or taxon

II) Query uORF bibliography by uORF-relatedproperties

An individual user-specific literature compilation forone or multiple uORF-related properties can be generatedby simple one-click selections of the respective categorieson the query page

III) Query uORF bibliography by manuscript category

Users may limit returned references to specific manu-script categories including protocols review articles andstudies characterized by the type of the experimentalmethod applied

After querying uORFdb an output page (Figure 2)returns a table summarizing all categories met or ad-dressed by the respective publications Whereverpossible the output table provides the taxon officialgene symbol and accession number for individualuORF-bearing genes or transcripts along with links tothe corresponding records in the NCBIrsquos Entrez Gene orNucleotide databases for further sequence analysis (19)Selection fields next to each reference in the output tableallow users to directly display an individual set of ab-stracts at the PubMed web page for further readingQuery results as well as the complete content ofuORFdb may be downloaded from the output page anddownloads page respectively

TECHNICAL SPECIFICATIONS

The uORFdb is presented as a Web site developed usingPHP programming language (version 532 wwwphp

Table 1 Content of uORFdb v10

Taxon References Genes

Human 166 103Yeast 85 15Mouse 66 43Virus 50 17Arabidopsis 28 14Rat 21 16Others 52 47

The table summarizes the number of references per taxon and thenumber of analyzed genes per taxon contained within the initialrelease of uORFdb Note that reviews and other manuscript categorieswhich are not restricted to specific transcripts or taxa are not repre-sented by this table

Nucleic Acids Research 2014 Vol 42 Database issue D61

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net) On selection of desired filters by the database users aserver-side PHP script builds a correspondent SQL queryand executes it on the MySQL system where uORFdbdata is stored (MySQL Server version 5161) Matchingrecords are fetched from the MySQL query result andpopulated into a HTML table to be displayed at theuserrsquos browserThe following section will provide short explanatory

and summarizing paragraphs on the individual categoriesof uORFdb

DETERMINANTS OF uORF PRESENCE ORABSENCE

Alternative promoters Alternative splicing Tissue-specific uORFsWhile AUG is the best conserved trinucleotide within thetranscript leader sequence of human and mouse (7) thegeneral prevalence of uAUGs is lower than expected bynormal distribution (20) These observations argue for thefunctional importance of uAUGs and for an evolutionary

negative selection respectively In specific cases thepresence or absence of one or several uORF(s) is depend-ent on the transcript variant produced by transcriptioninitiation from alternative promoters or due to alternativesplicing For example the predominant usage of an alter-native promoter within the oncogene MDM-2 in tumorcells results in the production of a transcript variantlacking exon1 and two inhibitory uORFs leading toincreased translation of MDM-2 protein (21) Tissue-spe-cific presence and functional importance of uORFs havebeen reported for a number of human and mouse genesincluding AdipoR1 where a gain of two translational re-pressive uORFs in a splicing-derived alternative transcriptin muscle tissue is implicated in whole-body insulin sensi-tivity and glucose tolerance (22)

Non-AUG uORFs

In a recent study using global translational initiationsequencing (4) 54 of human transcripts displayed oneor more translational initiation site(s) preceding the CDSSurprisingly about three-fourths of upstream translationwas initiated by near-cognate non-AUG initiation

Figure 2 Example of a uORFdb query result At the first release of uORFdb filtering for lsquohumanrsquo data and selecting lsquotissue specificityrsquo from theuORF-related property section returned 12 PubMed IDs linked to the respective abstracts The table summarizes all categories met or addressedwithin the returned publications The green check marks indicate lsquopositiversquo evidence for a regulatory function of the respective uORF-relatedproperty or that the respective manuscript category is met The red X symbol identifies lsquonegativersquo evidence for a regulatory function of the respectiveuORF-related property (eg PMID 8027046 contains evidence that the overlap of the uORF with the CDS does not influence CDS translation)Users may sort the output table for a category of choice by clicking on the column header (a white arrowhead indicates active sorting) By checkingthe selection fields on the left users may select an individual set of abstracts for bulk display via the lsquoPubMedrsquo button above the table A yellowfunnel sign in the header of the table marks active filters Links to NCBI Gene or GenBank entries allow further sequence analysis and query resultsmay be downloaded for local use via a link below the table

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codons further relativizing the classical lsquofirst-AUGrsquo-roleNevertheless uAUG codons appeared to be functionallymost effective in repressing CDS translation To date onlytwo publications analyzing human BIRC2 and yeastGCN4 have been focusing on non-AUG uORF functionsat the individual transcript level (2324)

STRUCTURAL AND SEQUENCE-DEPENDENTuORF PROPERTIES

Number Length Distance from 50-cap Distancefrom uORF-stop to CDS CDS overlap RNA second-ary structure

Many publications investigated the importance of struc-tural and sequence-dependent uORF properties inmediating translational regulation The impact of uORFnumber length and position within the transcript leadersequence has most intensively been studied in the classicalmodel for uORF-mediated translational control the yeastGCN4 transcript (1125) and in a series of mutational ex-periments performed by M Kozak reviewed in (26) Therepression of downstream translation appears to be posi-tively correlated with the number of uORFs per transcriptthe length of the uORF and the distance between the 50-capstructure and the uORF initiation codon Furthermoretranslational repression correlates negatively with thedistance between the uORF-stop and the CDS initiationsite and is even more profound when the uORF overlapsthe CDS initiation codon Together the experimentssuggest a dynamic regulatory model where indispensableinitiation cofactors detach gradually from ribosomes duringthe elongation phase of uORF translation but may bereloaded to allow reinitiation at the CDS

FUNCTIONAL CONSEQUENCES OFuORF-MEDIATED TRANSLATIONAL CONTROL

CDS repression CDS induction Start site selection

Most uORFs analyzed to date repress translation of thesubsequent initiation site(s) and inhibitdiminish transla-tion of the main protein Post-uORF initiation at the CDSinitiation codon may occur after leaky scanning of ribo-somes across the uORF initiation codon or by reinitiationif the uORF-stop codon precedes the CDS (26) Despite agenerally repressive function on downstream translationseveral exceptions have been described including humanDDIT3 (15) mouse Atf4 and yeast GCN4 (11) wheretranslation of specific uORFs or a certain alignment ofsubsequent uORFs mediate enhanced CDS initiationFurthermore uORF-directed start site selection canresult in the production of N-terminally distinct proteinisoforms that harbor unique biological functions asdemonstrated for CEBPA and CEBPB transcriptionfactors (142728)

Nonsense-mediated decay mRNA destabilization

Nonsense-mediated decay (NMD) of mRNA is activatedwhen specific cellular surveillance mechanisms detectpremature termination of protein translation (29)Such premature termination events may result from the

use of nonsense codons that arise in mature transcriptsdue to mutations incorrect splicing or aberrant initiationsite selection Upstream ORFs have been suggested toinduce NMD by conferring additional terminationcodons to the 50-leader sequence of certain transcriptsExpression profiling in mammalian cells (30)Caenorhabditis elegans (31) and yeast (32) revealed an en-richment of uORF-containing transcripts in the fractionof mRNAs that were targeted by NMD Similarlyanother mode of termination-dependent RNA destabiliza-tion that is distinct and independent of the common NMDpathway has been reported in yeast (3334)

Ribosome load Ribosome pausingstalling Ribosomeshunting

Mutational deletion of a uORF can result in increasedribosome load on a given transcript associated withincreased translational activity as observed for humanAMD1 (35) and ERBB2 (36) On the contrary ribosomestalling at the uORF termination codon or pausing ofribosomes on inhibitory uORF structures (37) mayhamper CDS translation In specific cases such as theArabidopsis transcription factor GBF6 binding of asmall molecule cofactor (sucrose) to the nascent uORF-peptide induced stalling of ribosomes at the uORF termin-ation codon and resulted in decreased translationalinitiation at the CDS (38) Additional examples ofribosome stalling or pausing due to the interaction ofuORF-peptides with regulatory small molecules entailthe translational repression of mammalian AMD1 bypolyamines (3940) or repression of yeast CPA1 andNeurospora crassa Arg2 by arginine (16)Underlining the multiplicity of uORF-mediated trans-

lational regulation certain uORFs may facilitateenhanced CDS translation by supporting a ribosomeshunt across a highly structured and inhibitory transcriptleader sequence as best studied for Cauliflower mosaicvirus 35S RNA (41)

CO-REGULATORY EVENTS AFFECTING uORFFUNCTIONS

Kozak consensus sequence

Whether or not the ternary preinitiation complex recog-nizes an AUG or non-AUG triplet as a translational startcodon is strongly influenced by the nucleotide context sur-rounding it Extensive sequence analysis (2042) as well asmutational analysis (264344) identified crucial nucleotideresidues in the context of an AUG triplet that createfavorable or unfavorable surroundings for translationalinitiation The optimal surrounding sequence for initi-ation is GCCRCCAUGG (also called optimal Kozak con-sensus sequence R representing a purine base mostimportant residues underlined) Initiation sequencecontexts are frequently classified as strong (both criticalresidues match the consensus sequence) adequateinter-mediate (either residue 3 or+4 matches) or weak (bothcritical residues do not match) (45) If the AUG codonis surrounded by a strong context virtuallyall scanning ribosomes will stop and initiate

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translation When the surrounding context is weak manyribosomes may scan past the AUG codon and insteadinitiate at one further downstream Since the quality ofthe Kozak consensus sequence is not the only determinantof translation initiation efficiency the mere evaluation ofthe surrounding nucleotides does not permit the preciseprediction of initiation

Translational status

Regulation through uORFs may integrate the overall trans-lation status of a cell and adjust the translation rate ofimportant regulatory proteins This was first described ina series of experiments on the yeast transcription factorGCN4 where four subsequent uORFs control the para-doxical translation initiation of the main protein whileglobal translation is shut down (1146ndash48) Briefly underfavorable translational conditions with high levels of theeIF2ndashGTPndashMet-tRNAMet

i ternary complex a fraction ofthe ribosomes that translate the GCN4 uORF1 reinitiateat the inhibitory uORF4 detach from the mRNA at theuORF4-stop codon and thus inhibit translation of GCN4Under starving conditions low availability of the ternarycomplex causes delayed restoration of a functional pre-ini-tiation ribosomal complex after translation of uORF1 Thisresults in leaky scanning across the uORF4 initiation codonand permits translation of the GCN4 CDS only after pro-longed post-termination scanningSimilar mechanisms depending on the translational

status of a cell have been described for the mammaliantranscription factors ATF4 (49) ATF5 (50) CEBPAand CEBPB (14) and the macrophage receptor proteinCD36 (51)

Termination (context)

The sequence context surrounding a uORF terminationcodon may determine the reinitiation efficiency at down-stream initiation sites In particular stable interactionsbetween the terminating ribosome and the RNA orstable base pairing of the RNA alone may cause ribosomalpausing or mediate premature mRNA decay (3452)

uORF RNApeptide sequence Regulatory sequencemotif Cofactorribosome interaction

Specific RNA sequences may influence CDS translationby forming stable secondary structures by binding to aregulatory cofactor or by direct interaction with thetranslating ribosome Furthermore uORF-encodedpeptides may induce ribosome stalling and inhibit down-stream translation on binding of their respective smallmolecule interactors as demonstrated for the sucrosecontrol peptide of Arabidopsis GBF6 (38) or the arginineattenuator peptide of Neurospora ARG2 (53) For othertranscripts including the HHV-5 gp48 mRNA (54) theDNA damage-inducible transcript 3 (DDIT3CHOPCEBPz) (55) and the vasopressin V1b receptor (56) trans-lational repression by uORF-encoded peptides has beendescribed without detailed analysis of the mechanisminvolved A subset of 200 human uORFs was suggestedto encode unique functional peptides based on a highdegree of amino acid sequence conservation (57)Except for the Kozak consensus sequence to date only

few uORF-related co-regulatory RNA sequence motives

have been identified The most prominent example wasdescribed for Drosophila msl-2 where a protein inter-action RNA-motif facilitates binding of the cofactorprotein SXL that enhances uORF initiation and therebyrepresses translation of the CDS (58) In yeast GCN4reinitiation-promoting elements have been identified sur-rounding uORF1 which interact with eukaryotic initi-ation factor 3a to facilitate downstream reinitiation (59)Recently the h-subunit of eIF3 was found to promotereinitiation after translation of a reinitiation-permissiveuORF (60) To what extent lsquospecialized ribosomesrsquointeract with uORFs and other cis-regulatory RNAelements to regulate translation awaits investigation (61)

MEDICAL IMPACT

Disease-related uORFs Acquired mutations SNPs

Defects in uORF-mediated translational control mayresult in the development of human disease Loss of auORF in a mutation-related alternative splicing productof the thrombopoietin gene drives enhanced translation ofthrombopoietin and causes hereditary thrombocytosis(62) The roles of uORF-related mutations in CDKN2Aand CDKN1B for cancer development were mentionedabove (910) Marie Unna hereditary hair loss is causedby a variety of mutations altering a uORF within thehairless homolog (HR) transcript resulting in increasedexpression of hairless homolog protein (8) AdditionaluORF-altering mutations were identified by computa-tional analysis of the Human Gene Mutation Database(7) Diseases with a confirmed implication of uORF mu-tations include Cystic fibrosis (CFTR) (63) the van derWoude syndrome (IRF6) hereditary pancreatitis(SPINK1) familial hypercholesterolemia (LDLR) andsome others (7) Furthermore the expression of the betasecretase BACE1 related to Alzheimerrsquos disease (64) orthe transmembrane receptor tyrosine kinase ERBB2related to breast cancer (65) is at least partially controlledby uORFs Whether deregulated uORF-mediated transla-tional control is the crucial pathogenic event in these lattercases remains to be established

Despite few unequivocal cases at this time it is evidentthat uORF mutations may be involved in a wide variety ofdiseases including malignancies metabolic or neurologicdisorders and inherited syndromes Considering thatmany important regulatory proteins including cellsurface receptors tyrosine kinases and transcriptionfactors act in a dose-dependent fashion and possesuORFs we speculate that a substantial number of as yetunexplained pathologies will be traced back to uORF mu-tations altering expression levels of such key regulatorygenes

MANUSCRIPT CATEGORIES

Mouse models Ribosome profiling Bioinformaticsarraysscreens Proteomics

To date two genetically altered mouse models havebeen generated confirming the pathogenic role of loss-of-uORF mutations in HR resulting in Marie Unna

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hereditary hypotrichosis in humans (66) and validating thephysiological importance of the CEBPB uORF in cellulardifferentiation and proliferation (6) respectively

Recent progress in computational and sequencing-based technologies and the development of the ribosomeprofiling method (3) have generated a large amount ofinformation on uORF localization initiation codonusage and uORF function in response to altered transla-tional conditions (2) Nevertheless it is yet not possible topredict whether a uORF is translated or has a regulatoryrole from sequence information only

Proteomic studies have identified a number of poten-tially functional uORF-encoded peptides in human cells(6768) In the human K562 cell line 40 of small ORF-encoded peptides detected by mass spectrometryoriginated from transcript leader sequences (69)

OUTLOOK AND FURTHER DEVELOPMENTOF uORFdb

The uORFdb is intended to grow concomitantly to thepublication of novel uORF-related literature in respectto the number of references listed and the amount ofcategorized uORF-related properties We aim to con-stantly improve the quality and completeness of indexingapplied to individual references and invite users to sendfeedback additions and corrections via the contact pageof the uORFdb Web site

ACKNOWLEDGEMENTS

The authors thank Julia Schulz for critical reading of themanuscript

FUNDING

Deutsche Krebshilfe eV Bonn Germany [110525 toKW and AL] Funding for open access chargeDeutsche Krebshilfe eV Bonn Germany [110525 toKW and AL]

Conflict of interest statement None declared

REFERENCES

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2 HsiehAC LiuY EdlindMP IngoliaNT JanesMRSherA ShiEY StumpfCR ChristensenC BonhamMJet al (2012) The translational landscape of mTOR signallingsteers cancer initiation and metastasis Nature 485 55ndash61

3 IngoliaNT GhaemmaghamiS NewmanJR and WeissmanJS(2009) Genome-wide analysis in vivo of translation withnucleotide resolution using ribosome profiling Science 324218ndash223

4 LeeS LiuB HuangSX ShenB and QianSB (2012) Globalmapping of translation initiation sites in mammalian cells atsingle-nucleotide resolution Proc Natl Acad Sci USA 109E2424ndashE2432

5 KozakM (1984) Selection of initiation sites by eucaryoticribosomes effect of inserting AUG triplets upstream from thecoding sequence for preproinsulin Nucleic Acids Res 123873ndash3893

6 WethmarK BegayV SminkJJ ZaragozaK WiesenthalVDorkenB CalkhovenCF and LeutzA (2010)CEBPbetaDeltauORF micendasha genetic model for uORF-mediatedtranslational control in mammals Genes Dev 24 15ndash20

7 CalvoSE PagliariniDJ and MoothaVK (2009) Upstreamopen reading frames cause widespread reduction of proteinexpression and are polymorphic among humans Proc Natl AcadSci USA 106 7507ndash7512

8 WenY LiuY XuY ZhaoY HuaR WangK SunMLiY YangS ZhangXJ et al (2009) Loss-of-functionmutations of an inhibitory upstream ORF in the human hairlesstranscript cause Marie Unna hereditary hypotrichosis NatGenet 41 228ndash233

9 OcchiG RegazzoD TrivellinG BoarettoF CiatoDBobisseS FerasinS CetaniF PardiE KorbonitsM et al(2013) A novel mutation in the upstream open reading frame ofthe CDKN1B gene causes a MEN4 phenotype PLoS Genet 9e1003350

10 LiuL DilworthD GaoL MonzonJ SummersA LassamNand HoggD (1999) Mutation of the CDKN2A 50 UTR createsan aberrant initiation codon and predisposes to melanoma NatGenet 21 128ndash132

11 HinnebuschAG (2005) Translational regulation of GCN4 andthe general amino acid control of yeast Annu Rev Microbiol59 407ndash450

12 SomersJ PoyryT and WillisAE (2013) A perspective onmammalian upstream open reading frame function IntJ Biochem Cell Biol 45 1690ndash1700

13 MorrisDR and GeballeAP (2000) Upstream open readingframes as regulators of mRNA translation Mol Cell Biol 208635ndash8642

14 CalkhovenCF MullerC and LeutzA (2000) Translationalcontrol of CEBPalpha and CEBPbeta isoform expression GenesDev 14 1920ndash1932

15 ChenYJ TanBC ChengYY ChenJS and LeeSC (2010)Differential regulation of CHOP translation by phosphorylatedeIF4E under stress conditions Nucleic Acids Res 38 764ndash777

16 HoodHM NeafseyDE GalaganJ and SachsMS (2009)Evolutionary roles of upstream open reading frames in mediatinggene regulation in fungi Annu Rev Microbiol 63 385ndash409

17 IvanovIP AtkinsJF and MichaelAJ (2010) A profusion ofupstream open reading frame mechanisms in polyamine-responsive translational regulation Nucleic Acids Res 38353ndash359

18 MizeGJ and MorrisDR (2001) A mammalian sequence-dependent upstream open reading frame mediates polyamine-regulated translation in yeast RNA 7 374ndash381

19 NCBI Resources Coordinators (2013) Database resources of theNational Center for Biotechnology Information Nucleic AcidsRes 41 D8ndashD20

20 IaconoM MignoneF and PesoleG (2005) uAUG and uORFsin human and rodent 50untranslated mRNAs Gene 349 97ndash105

21 BrownCY MizeGJ PinedaM GeorgeDL and MorrisDR(1999) Role of two upstream open reading frames in thetranslational control of oncogene mdm2 Oncogene 185631ndash5637

22 AshwalR HemiR TiroshA GordinR YissacharE Cohen-DayagA RosenbergA KarasikA BluherM and KanetyH(2011) Differential expression of novel adiponectin receptor-1transcripts in skeletal muscle of subjects with normal glucosetolerance and type 2 diabetes Diabetes 60 936ndash946

23 WarnakulasuriyarachchiD UngureanuNH and HolcikM(2003) The translation of an antiapoptotic protein HIAP2 isregulated by an upstream open reading frame Cell Death Differ10 899ndash904

24 CairnsVR DeMariaCT PoulinF SanchoJ LiuP ZhangJCampos-RiveraJ KareyKP and EstesS (2011) Utilization ofnon-AUG initiation codons in a flow cytometric method forefficient selection of recombinant cell lines Biotechnol Bioeng108 2611ndash2622

25 AbastadoJP MillerPF JacksonBM and HinnebuschAG(1991) Suppression of ribosomal reinitiation at upstream openreading frames in amino acid-starved cells forms the basis forGCN4 translational control Mol Cell Biol 11 486ndash496

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26 KozakM (2002) Pushing the limits of the scanning mechanismfor initiation of translation Gene 299 1ndash34

27 SminkJJ BegayV SchoenmakerT SterneckE de VriesTJand LeutzA (2009) Transcription factor CEBPbeta isoform ratioregulates osteoclastogenesis through MafB EMBO J 281769ndash1781

28 WethmarK SminkJJ and LeutzA (2010) Upstream openreading frames molecular switches in (patho)physiologyBioessays 32 885ndash893

29 IskenO and MaquatLE (2007) Quality control of eukaryoticmRNA safeguarding cells from abnormal mRNA function GenesDev 21 1833ndash1856

30 MendellJT SharifiNA MeyersJL Martinez-MurilloF andDietzHC (2004) Nonsense surveillance regulates expression ofdiverse classes of mammalian transcripts and mutes genomicnoise Nat Genet 36 1073ndash1078

31 RamaniAK NelsonAC KapranovP BellI GingerasTRand FraserAG (2009) High resolution transcriptome maps forwild-type and nonsense-mediated decay-defective Caenorhabditiselegans Genome Biol 10 R101

32 HeF LiX SpatrickP CasilloR DongS and JacobsonA(2003) Genome-wide analysis of mRNAs regulated by thenonsense-mediated and 50 to 30 mRNA decay pathways in yeastMol Cell 12 1439ndash1452

33 VilelaC LinzB Rodrigues-PousadaC and McCarthyJE(1998) The yeast transcription factor genes YAP1 and YAP2 aresubject to differential control at the levels of both translation andmRNA stability Nucleic Acids Res 26 1150ndash1159

34 VilelaC RamirezCV LinzB Rodrigues-PousadaC andMcCarthyJE (1999) Post-termination ribosome interactions withthe 50UTR modulate yeast mRNA stability EMBO J 183139ndash3152

35 HillJR and MorrisDR (1992) Cell-specific translation ofS-adenosylmethionine decarboxylase mRNA Regulation by the50 transcript leader J Biol Chem 267 21886ndash21893

36 ChildSJ MillerMK and GeballeAP (1999) Translationalcontrol by an upstream open reading frame in the HER-2neutranscript J Biol Chem 274 24335ndash24341

37 KozakM (2001) Constraints on reinitiation of translation inmammals Nucleic Acids Res 29 5226ndash5232

38 RahmaniF HummelM SchuurmansJ Wiese-KlinkenbergASmeekensS and HansonJ (2009) Sucrose control of translationmediated by an upstream open reading frame-encoded peptidePlant Physiol 150 1356ndash1367

39 RaneyA BaronAC MizeGJ LawGL and MorrisDR(2000) In vitro translation of the upstream open reading frame inthe mammalian mRNA encoding S-adenosylmethioninedecarboxylase J Biol Chem 275 24444ndash24450

40 HanfreyC ElliottKA FranceschettiM MayerMJIllingworthC and MichaelAJ (2005) A dual upstreamopen reading frame-based autoregulatory circuit controllingpolyamine-responsive translation J Biol Chem 28039229ndash39237

41 PoogginMM FuttererJ SkryabinKG and HohnT (2001)Ribosome shunt is essential for infectivity of cauliflower mosaicvirus Proc Natl Acad Sci USA 98 886ndash891

42 PesoleG GissiC GrilloG LicciulliF LiuniS and SacconeC(2000) Analysis of oligonucleotide AUG start codon context ineukariotic mRNAs Gene 261 85ndash91

43 KozakM (1987) At least six nucleotides preceding the AUGinitiator codon enhance translation in mammalian cells J MolBiol 196 947ndash950

44 KozakM (1986) Point mutations define a sequence flanking theAUG initiator codon that modulates translation by eukaryoticribosomes Cell 44 283ndash292

45 MeijerHA and ThomasAA (2002) Control of eukaryoticprotein synthesis by upstream open reading frames in the50-untranslated region of an mRNA Biochem J 367 1ndash11

46 HinnebuschAG (1984) Evidence for translational regulation ofthe activator of general amino acid control in yeast Proc NatlAcad Sci USA 81 6442ndash6446

47 HinnebuschAG (1997) Translational regulation of yeast GCN4A window on factors that control initiator-trna binding to theribosome J Biol Chem 272 21661ndash21664

48 MuellerPP and HinnebuschAG (1986) Multiple upstreamAUG codons mediate translational control of GCN4 Cell 45201ndash207

49 HardingHP NovoaI ZhangY ZengH WekR SchapiraMand RonD (2000) Regulated translation initiation controls stress-induced gene expression in mammalian cells Mol Cell 61099ndash1108

50 ZhouD PalamLR JiangL NarasimhanJ StaschkeKA andWekRC (2008) Phosphorylation of eIF2 directs ATF5translational control in response to diverse stress conditionsJ Biol Chem 283 7064ndash7073

51 GriffinE ReA HamelN FuC BushH McCaffreyT andAschAS (2001) A link between diabetes and atherosclerosisglucose regulates expression of CD36 at the level of translationNat Med 7 840ndash846

52 GrantCM and HinnebuschAG (1994) Effect of sequencecontext at stop codons on efficiency of reinitiation in GCN4translational control Mol Cell Biol 14 606ndash618

53 WangZ and SachsMS (1997) Ribosome stalling is responsiblefor arginine-specific translational attenuation in Neurosporacrassa Mol Cell Biol 17 4904ndash4913

54 JanzenDM FrolovaL and GeballeAP (2002) Inhibition oftranslation termination mediated by an interaction of eukaryoticrelease factor 1 with a nascent peptidyl-tRNA Mol Cell Biol22 8562ndash8570

55 JousseC BruhatA CarraroV UranoF FerraraM RonDand FafournouxP (2001) Inhibition of CHOP translation by apeptide encoded by an open reading frame localized in the chop50UTR Nucleic Acids Res 29 4341

56 Rabadan-DiehlC MartinezA VolpiS SubburajuS andAguileraG (2007) Inhibition of vasopressin V1breceptor translation by upstream open readingframes in the 50-untranslated region J Neuroendocrinol 19309ndash319

57 CroweML WangXQ and RothnagelJA (2006) Evidence forconservation and selection of upstream open reading framessuggests probable encoding of bioactive peptides BMC Genomics7 16

58 MedenbachJ SeilerM and HentzeMW (2011) Translationalcontrol via protein-regulated upstream open reading frames Cell145 902ndash913

59 MunzarovaV PanekJ GunisovaS DanyiI SzameczB andValasekLS (2011) Translation reinitiation relies on theinteraction between eIF3aTIF32 and progressively folded cis-acting mRNA elements preceding short uORFs PLoS Genet 7e1002137

60 RoyB VaughnJN KimBH ZhouF GilchristMA andVon ArnimAG (2010) The h subunit of eIF3 promotesreinitiation competence during translation of mRNAs harboringupstream open reading frames RNA 16 748ndash761

61 XueS and BarnaM (2012) Specialized ribosomes a new frontierin gene regulation and organismal biology Nat Rev Mol CellBiol 13 355ndash369

62 WiestnerA SchlemperRJ van der MaasAP and SkodaRC(1998) An activating splice donor mutation in thethrombopoietin gene causes hereditary thrombocythaemia NatGenet 18 49ndash52

63 LukowskiSW BombieriC and TreziseAE (2011) Disruptedposttranscriptional regulation of the cystic fibrosis transmembraneconductance regulator (CFTR) by a 50UTR mutation isassociated with a cftr-related disease Hum Mutat 32E2266ndashE2282

64 ZhouW and SongW (2006) Leaky scanning andreinitiation regulate BACE1 gene expression Mol Cell Biol 263353ndash3364

65 SpevakCC ParkEH GeballeAP PelletierJ and SachsMS(2006) her-2 upstream open reading frame effects on the use ofdownstream initiation codons Biochem Biophys Res Commun350 834ndash841

66 BaekIC KimJK ChoKH ChaDS ChoJW ParkJKSongCW and YoonSK (2009) A novel mutation in Hr causesabnormal hair follicle morphogenesis in hairpoor mouse ananimal model for Marie Unna Hereditary Hypotrichosis MammGenome 20 350ndash358

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67 OyamaM ItagakiC HataH SuzukiY IzumiT NatsumeTIsobeT and SuganoS (2004) Analysis of small human proteinsreveals the translation of upstream open reading frames ofmRNAs Genome Res 14 2048ndash2052

68 OyamaM Kozuka-HataH SuzukiY SembaK YamamotoTand SuganoS (2007) Diversity of translation start sites maydefine increased complexity of the human short ORFeome MolCell Proteomics 6 1000ndash1006

69 SlavoffSA MitchellAJ SchwaidAG CabiliMN MaJLevinJZ KargerAD BudnikBA RinnJL andSaghatelianA (2013) Peptidomic discovery of short open readingframe-encoded peptides in human cells Nat Chem Biol 959ndash64

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67 OyamaM ItagakiC HataH SuzukiY IzumiT NatsumeTIsobeT and SuganoS (2004) Analysis of small human proteinsreveals the translation of upstream open reading frames ofmRNAs Genome Res 14 2048ndash2052

68 OyamaM Kozuka-HataH SuzukiY SembaK YamamotoTand SuganoS (2007) Diversity of translation start sites maydefine increased complexity of the human short ORFeome MolCell Proteomics 6 1000ndash1006

69 SlavoffSA MitchellAJ SchwaidAG CabiliMN MaJLevinJZ KargerAD BudnikBA RinnJL andSaghatelianA (2013) Peptidomic discovery of short open readingframe-encoded peptides in human cells Nat Chem Biol 959ndash64

Nucleic Acids Research 2014 Vol 42 Database issue D67

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