2005
DOI: 10.1261/rna.2107305
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Abstract: Polyadenylation is an essential step for the maturation of almost all cellular mRNAs in eukaryotes. In human cells, most poly(A) sites are flanked by the upstream AAUAAA hexamer or a close variant, and downstream U/GU-rich elements. In yeast and plants, additional cis elements have been found to be located upstream of the poly(A) site, including UGUA, UAUA, and U-rich elements. In this study, we have developed a computer program named PROBE (Polyadenylation-Related Oligonucleotide Bidimensional Enrichment) to … Show more

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Cited by 217 publications
(319 citation statements)
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“…S4B). This result is consistent with our earlier observation that multiple UGUA elements are often observed within poly(A) site upstream sequences (37). Thus the structure of the CFI m 25 homodimer suggests a mechanism for the coordinate recognition of eight nucleotides: a set of two UGUA elements separated by a variable number of bases.…”
Section: Resultssupporting
confidence: 92%
See 1 more Smart Citation
“…S4B). This result is consistent with our earlier observation that multiple UGUA elements are often observed within poly(A) site upstream sequences (37). Thus the structure of the CFI m 25 homodimer suggests a mechanism for the coordinate recognition of eight nucleotides: a set of two UGUA elements separated by a variable number of bases.…”
Section: Resultssupporting
confidence: 92%
“…We speculate that the array of recognition mechanisms that we observe provides strong selective pressure to maintain not only the integrity of the protein fold and the identity of key amino acids but also the specific RNA sequence required for binding. Indeed, the UGUA sequence has been found to be a component of the poly(A) signals of a wide range of organisms, from Chlamydomonas to humans (37,38).…”
Section: Resultsmentioning
confidence: 99%
“…According to Retelska et al (2006), 46.73% polyadenylation events are dependent on the AAUAAA canonical polyadenylation signal (PAS) but 37.08% of them also occur in the presence of infrequently used PAS including GAUAAA (1.64%). As we found a conserved 'GATAAA' motif in mammals (Figure 1f and Supplementary Figure S1) as well as TGTA, TATA, G-rich and C-rich polyadenylation regulatory elements in intron2 (Gilmartin 2005;Hu et al, 2005;Lee et al, 2008) we performed 3 0 RACE PCR on polyA-mRNA from DLD1 cells, which confirmed the existence of SOX9 mRNA ended by a polyA tract located 409-bp downstream of the exon2 border (Figure 1f and Supplementary Figure S1). …”
Section: Sox9 Mrna Variants Are Expressed In Colon Cancer Cellssupporting
confidence: 55%
“…1A), does not have a consensus sequence, but often consists of a U-rich element (UUUU) [2] or similar sequences (UGUA, UAUA) [54]. The efficiency of cleavage and polyadenylation is enhanced by the presence of this auxiliary element, as it promotes the binding of other polyadenylation factors to the cleavage site [55][56][57][58].…”
Section: The Downstream Element (Dse)-mentioning
confidence: 99%