TY - JOUR
T1 - In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation
AU - Zamorano, Absalom
AU - López-Camarillo, César
AU - Orozco, Esther
AU - Weber, Christian
AU - Guillen, Nancy
AU - Marchat, Laurence A.
N1 - Funding Information:
We thank Christiane Bouchier (Genopole at Pasteur Institute, France) for her help in automated cDNA sequencing. This work was supported by CONACyT, SIP-IPN, COFAA-IPN and UACM (Mexico).
PY - 2008/8
Y1 - 2008/8
N2 - 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.
AB - 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.
KW - Bioinformatics analysis
KW - Cis-regulatory elements
KW - Pre-mRNA 3′-end processing
KW - Protozoan parasite
UR - http://www.scopus.com/inward/record.url?scp=45849136307&partnerID=8YFLogxK
U2 - 10.1016/j.compbiolchem.2008.03.019
DO - 10.1016/j.compbiolchem.2008.03.019
M3 - Artículo
C2 - 18514032
SN - 1476-9271
VL - 32
SP - 256
EP - 263
JO - Computational Biology and Chemistry
JF - Computational Biology and Chemistry
IS - 4
ER -