title: Similarities and differences of polyadenylation signals in human and fly.
abstract: 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.
authors.affiliation: Swiss Institute of Bioinformatics, Batiment Genopode, UNIL, 1015 Lausanne, Switzerland. dorota@binf.ku.dk
authors.forename: Dorota
authors.initials: D
authors.lastname: Retelska
authors.forename: Christian
authors.initials: C
authors.lastname: Iseli
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
authors.forename: C Victor
authors.initials: CV
authors.lastname: Jongeneel
authors.forename: Felix
authors.initials: F
authors.lastname: Naef
mesh_terms: 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
chemical_list: D020413:3' Untranslated Regions; D012333:RNA, Messenger; D011061:Poly A