Similarities and differences of polyadenylation signals in human and fly.
BACKGROUND
Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich region upstream of the cleavage site containing a motif with consensus AAUAAA, followed by a U or UG rich region downstream of the cleavage site.


RESULTS
We studied these signals using exhaustive databases of cleavage sites obtained from aligning raw expressed sequence tags (EST) sequences to genomic sequences in Homo sapiens and Drosophila melanogaster. These data show that the polyadenylation signal is highly conserved in human and fly. In addition, de novo motif searches generated a refined description of the U-rich downstream sequence (DSE) element, which shows more divergence between the two species. These refined motifs are applied, within a Hidden Markov Model (HMM) framework, to predict mRNA cleavage sites.


CONCLUSIONS
We demonstrate that the DSE is a specific motif in both human and Drosophila. These findings shed light on the sequence correlates of a highly conserved biological process, and improve in silico prediction of 3' mRNA cleavage and polyadenylation sites.
Retelska
Dorota
D
Swiss Institute of Bioinformatics, Batiment Genopode, UNIL, 1015 Lausanne, Switzerland. dorota@binf.ku.dk
Iseli
Christian
C
Bucher
Philipp
P
Jongeneel
C Victor
CV
Naef
Felix
F
D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D004331:Drosophila melanogaster / Q000235:genetics*; D020224:Expressed Sequence Tags; D006801:Humans; D008957:Models, Genetic; D011061:Poly A / Q000235:genetics*; D026723:Polyadenylation / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000235:genetics
D020413:3' Untranslated Regions; D012333:RNA, Messenger; D011061:Poly A