In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation.
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.
Zamorano
Absalom
A
ENMH-IPN, Programa Institucional de Biomedicina Molecular, Guillermo Massieu Heguera #239, Ticoman, CP 07320, México, D.F., Mexico.
López-Camarillo
César
C
Orozco
Esther
E
Weber
Christian
C
Guillen
Nancy
N
Marchat
Laurence A
LA
D000818:Animals; D019295:Computational Biology; D016208:Databases, Factual; D004748:Entamoeba histolytica / Q000235:genetics*; D020224:Expressed Sequence Tags; D016678:Genome / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D011061:Poly A / Q000235:genetics / Q000378:metabolism; D026723:Polyadenylation / Q000235:genetics*; D011237:Predictive Value of Tests; D026721:RNA 3' End Processing / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D016053:RNA, Protozoan / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D012322:RNA Precursors; D012333:RNA, Messenger; D016053:RNA, Protozoan; D011061:Poly A