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198 Copyright © 1998, Elsevier Science Ltd. All rights reserved. 0968 – 0004/98/$19.00 PII: S0968-0004(98)01208-0

577–5824 Sakaguchi, S. et al. (1996) Nature 380,

528–5315 Colinge, J. et al. (1994) Nature 370, 295–2976 Tobler, I. et al. (1996) Nature 380, 639–6427 Weissmann, C. (1996) Curr. Biol. 6, 13598 Chesebro, B. (1998) Science 279, 42–439 James, T. L. et al. (1997) Proc. Natl. Acad. Sci.

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13 Brown, D. R., Schulz-Schaeffer, W. J., Schmidt,B. and Kretzschmar, H. A. (1997) Exp. Neurol.146, 104–112

14 Karlin, K. D. and Tyeklar, Z., eds (1993)Bioinorganic Chemistry of Copper, Chapmanand Hall

ROGER C. PRINCE

Exxon Research and Engineering Company,Annandale, NJ 08801, USA.

DIANE E. GUNSON

Novartis Pharmaceutical Corporation, 59Route 10, East Hanover, NJ 07936, USA.

‘Time, that takes survey of all the world,

Must have a stop.’

Shakespeare, Henry IV, Part One

In all eukaryotic cells in which the phe-nomenon has been examined, mecha-nisms exist for eliminating mRNAs inwhich translation terminates prema-turely1,2. These mechanisms could haveevolved as safeguards that protect cellsfrom the potentially deleterious effectsof inefficient or inaccurate splicing.Splicing errors are common and couldresult in the nuclear export and cyto-plasmic translation of intron-containingRNAs3. In the majority of cases, RNAsthat erroneously contain introns would belikely to harbor either an intron-derivednonsense codon or a frameshift that gen-erates an exon-derived nonsense codon4.However, translation of intron-containingRNAs could result in the production ofnonfunctional, dominant negative orgain-of-function proteins.

Distinguishing termination codons thatreduce mRNA abundance from those that do not

The discovery of nonsense-mediatedsafeguard mechanisms raises a ques-tion: what distinguishes a normal termi-nation codon (which does not generallyelicit a reduction in mRNA abundance)from a premature termination codon(which generally does elicit a reductionin mRNA abundance)? In mammaliancells, the distinction between the twoappears to lie neither in the sequence ofthe termination codon (UAA, UAG orUGA) nor in the nucleotides that flankthe termination codon, but rather in the

position of the termination codon rela-tive to the 39-most exon–exon junction5–9.On the basis of studies of transcripts thatencode triose phosphate isomerase, themajor urinary protein or b-globin5,6,8–10,we have defined a rule for termination-codon position: only those terminationcodons located more than 50–55 nucleo-tides upstream of the 39-mostexon–exon junction (meas-ured after splicing) mediate a reduction in mRNA abun-dance. We propose two poss-ible mechanisms by whichpremature termination of cyto-plasmic translation more than50–55 nucleotides upstreamof the 39-most exon–exon junc-tion causes mRNA decay: acomponent of the translation-termination complex couldinteract with a ‘mark’ pos-itioned at the 39-most exon–exon junction; alternatively,the cytoplasmic translation-elongation complex might failto interact with such amark5,6,8,9. We envision asso-ciation between the mark andmRNA being a consequenceof nuclear pre-mRNA splicing.

Transcripts for T-cell re-ceptor b, in which nonsensecodons less than 50 nucleo-tides upstream of the 39-mostintron reduce mRNA abun-dance7, certain selenoproteinRNAs in which the UGA seleno-cysteine codon does not me-diate a reduction in mRNAabundance when recognized

as nonsense11,12, and transcripts thatreinitiate translation downstream of apremature termination codon in order toescape decay8 are exceptions to the rulefor termination-codon position.

Testing the rule for termination-codonposition

The normal termination codon of mostintron-containing genes resides within thelast exon13, which is consistent with therule for termination-codon position. How-ever, we imagined that a particularly re-vealing test of the rule would be an analy-sis of genes that possess one or more39-untranslated exons. Therefore, we undertook an exhaustive survey of genesof this type from a variety of organisms,including fungi, plants, insects and ver-tebrates. Only 7% of the 1500 genes

A rule for termination-codon position

within intron-containing genes:

when nonsense affects RNA abundance

TIBS 23 – JUNE 1998

199

surveyed were found to have one ormore 39-untranslated exons. Remarkably,in 98% of these genes, the normal termi-nation codon resides ,50 base pairs upstream of the 39-most intron (Fig. 1).Note that, in the case of genes havingtwo 39-untranslated exons, this mea-surement is made after discounting theintervening intron, which would be re-moved from the mRNA product beforenonsense-codon recognition (see Fig.1b). Two genes are exceptions to the rulefor termination-codon position: they en-code a chicken homeodomain proteinand human HLA 6.09. Notably, the ma-jority (80%) of mRNA that derives fromthe homeodomain gene retains the 39-most intron14, indicating that the intronis not always recognized as such; there-fore, at least in theory, product mRNA isnot always subject to nonsense-medi-ated decay. The human HLA 6.09 genediffers from conventional HLA genes inthat it is expressed only in certain celltypes and harbors an open readingframe that terminates within the third-to-last exon rather than the last exon.Genes that are predicted by the rule fortermination-codon position to producemRNA that is normally subject to non-sense-mediated decay could presum-ably require a post-transcriptional de-crease in the levels of their productRNAs, in order to preclude the gener-ation of deleteriously high amounts ofencoded protein.

Significance of the rule for termination-codon position

The rule for termination-codon pos-ition has broad implications given that, inprinciple, any intron located more than50–55 nucleotides downstream of a ter-mination codon could mediate a reduc-tion in mRNA abundance. For example,the rule predicts that insertion of an in-tron more than 50–55 nucleotides down-stream of a normal termination codonshould elicit a reduction in mRNA abun-dance. In fact, this has been shown for theb-globin gene, and mutation of the nor-mal b-globin termination codon so thattranslation terminates only 44 nucleo-tides upstream of the inserted introneliminates the reduction15. By analogy,expression vectors for cDNAs that derivefrom intron-containing genes should notcontain an intron more than 50–55 basepairs downstream of the cDNA open read-ing frame, if the aim is to achieve a maxi-mal level of cDNA expression. Therefore,users should be wary of the multitude ofcDNA expression vectors that employ theSV40 intron–polyadenylation cassette16,17.

Vectors such as these, whichare now commercially avail-able (e.g. pCDM8 and itsderivatives from Invitrogen),are widely used, despite con-taining polylinkers that arelocated a minimum of 82base pairs upstream of theSV40 intron.

The rule for termination-codon position will also beuseful in organizing genomesequence information intoexons, introns and coding re-gions. Additionally, the rulecan be used to predict theseverity of particular diseases,such as b-thalassemia18, thattake on a dominant negativephenotype when they arecaused by the failure of premature termination codonsto mediate decreases inmRNA abundance. A diseasethat has the potential to manifest a dominant negativephenotype could be charac-terized by the presence ofpremature termination codonslocated near or downstreamof the 39-most intron in agene that encodes a compo-nent of a multisubunit com-plex. A truncated protein pos-sessing sufficient stabilityand structure to assembleinto such a complex could re-sult in the latter’s functionalinactivation.

AcknowledgementsThis work was supported

by Public Health Service research grantsfrom the NIH to L. E. M. (grant numbersDK33933 and GM52822). We thankTamás Henics for drawing the cartoon.

References1 Maquat, L. E. (1995) RNA 1, 453–4652 Ruiz-Echevarria, M. J. and Peltz, S. W. (1996)

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9 Zhang, J. et al. RNA (in press)10 Moriarty, P. M. et al. Mol. Cell. Biol. (in press)11 Lei, X. G. et al. (1995) J. Nutr. 125, 1438–144612 Bermano, G. et al. (1996) FEBS Lett. 387,

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2031–2037

ESZTER NAGY AND LYNNE E. MAQUAT

Dept of Human Genetics, Roswell Park CancerInstitute, Elm and Carlton Streets, Buffalo, NY 14263, USA.

FRONTLINES

D

Stop

(a) Single 3′-untranslated exon

Mammals

Organism Number of genes

D < 50 bp D > 50 bp

70 (46) 0Birds 5 1Fish 1 0Insects 14 0Nematodes 1 0Fungi 1 0Plants 1 0

D′

IStop

(b) Two 3′-untranslated exons

Mammals

Organism Number of genes

D′ < 50 bp D′ > 50 bp

5 (3) 1

Figure 1Genes characterized by 39-untranslated exons. (a) Genescharacterized by a single 39-untranslated exon. D repre-sents the distance between the normal terminationcodon (Stop) and the 39-most intron within each gene.(b) Genes characterized by two 39-untranslated exons.D9 represents the distance between the normal termi-nation codon (Stop) and the 39-most intron, discountingthe intervening intron (I) within each gene. Numbers inparentheses indicate the number of genes obtained aftercross-species duplicates are eliminated. bp, base pairs.A more detailed version of this figure can be found athttp://rpci.med.buffalo.edu/scientific.report/maquat1.html

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