Open Access Open Badges Research article

Similarities and differences of polyadenylation signals in human and fly

Dorota Retelska123, Christian Iseli13, Philipp Bucher12, C Victor Jongeneel13 and Felix Naef12*

Author Affiliations

1 Swiss Institute of Bioinformatics, Batiment Genopode, UNIL, 1015 Lausanne, Switzerland

2 Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne (EPFL), AAB-021, CH-1015 Lausanne, Switzerland

3 Ludwig Institute for Cancer Research, Batiment Genopode, UNIL, 1015 Lausanne, Switzerland

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BMC Genomics 2006, 7:176  doi:10.1186/1471-2164-7-176

Published: 12 July 2006



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.


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.


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.