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Nucleic Acids Research, 2000, Vol. 28, No. 4 1000-1010
© 2000 Oxford University Press

Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals

Jacques van Helden*, Marcel.lí del Olmo1,2 and José E. Pérez-Ortín1

Unité de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles, CP 160/16, 50 avenue F.D. Roosevelt, B-1050 Bruxelles, Belgium, 1Departamento de Bioquímica y Biología Molecular, Universitat de València, C/ Dr Moliner 50, E-46100 Burjassot, Spain and 2Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Polígono La Coma s/n, E-46100, Burjassot, Spain

The study of a few genes has permitted the identification of three elements that constitute a yeast polyadenyl­ation signal: the efficiency element (EE), the positioning element and the actual site for cleavage and poly­adenyl­ation. In this paper we perform an analysis of oligonucleotide composition on the sequences located downstream of the stop codon of all yeast genes. Several oligonucleotide families appear over-represented with a high significance (referred to herein as ‘words’). The family with the highest over-representation includes the oligonucleotides shown experimentally to play a role as EEs. The word with the highest score is TATATA, followed, among others, by a series of single-nucleotide variants (TATGTA, TACATA, TAAATA . . .) and one-letter shifts (ATATAT). A position analysis reveals that those words have a high preference to be in 3' flanks of yeast genes and there they have a very uneven distribution, with a marked peak around 35 bp after the stop codon. Of the predicted ORFs, 85% show one or more of those sequences. Similar results were obtained using a data set of EST sequences. Other clusters of over-represented words are also detected, namely T- and A-rich signals. Using these results and previously known data we propose a general model for the 3' trailers of yeast mRNAs.

* To whom correspondence should be addressed. Tel: +32 2 650 20 13; Fax: +32 2 648 89 54; Email: jvanheld@ucmb.ulb.ac.be


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