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© Research
Publication : Computational biology and chemistry

In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Computational biology and chemistry - 12 Apr 2008

Zamorano A, López-Camarillo C, Orozco E, Weber C, Guillen N, Marchat LA

Link to Pubmed [PMID] – 18514032

Comput Biol Chem 2008 Aug;32(4):256-63

In most eukaryotic cells, the poly(A) tail at the 3′-end of messenger RNA (mRNA) is essential for nuclear export, translatability, stability and transcription termination. Poly(A) tail formation involves multi-protein complexes that interact with specific sequences in 3′-untranslated region (3′-UTR) of precursor mRNA (pre-mRNA). Here we have performed a computational analysis of a large EST and genomic sequences collection from Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, to identify conserved elements that could be involved in pre-mRNA polyadenylation. Results evidenced the presence of an AU-rich domain corresponding to the consensus UA(A/U)UU polyadenylation signal or variants, the cleavage and polyadenylation site that is generally denoted by U residue and flanked by two U-rich tracts, and a novel A-rich element. This predicted array was validated through the analysis of genomic sequences and predicted mRNA folding of genes with known polyadenylation site. The molecular organization of pre-mRNA 3′-UTR cis-regulatory elements appears to be roughly conserved through evolutionary scale, whereas the polyadenylation signal seems to be species-specific in protozoan parasites and the novel A-rich element is unique for the primitive eukaryote E. histolytica. To our knowledge, this paper is the first work about the identification of potential pre-mRNA 3′-UTR cis-regulatory sequences through in silico analysis of large sets of cDNA and genomic sequences in a protozoan parasite.

http://www.ncbi.nlm.nih.gov/pubmed/18514032