6533b7cffe1ef96bd1259074
RESEARCH PRODUCT
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
Jacques Van HeldenJosé E. Pérez-ortínMarcel·lí Del Olmosubject
Expressed Sequence TagsGeneticsExpressed sequence tagBase SequencePolyadenylation[SDV]Life Sciences [q-bio]Saccharomyces cerevisiaeSaccharomyces cerevisiaeBiologybiology.organism_classificationSaccharomycesArticleYeastStop codonSaccharomycesGeneticsCluster Analysis[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]Genome FungalORFSPoly AGeneComputingMilieux_MISCELLANEOUSdescription
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.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2000-01-01 |