Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica

Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie cellulaire et infection, F-75015 Paris, France, INSERM U786, F-75015 Paris, France, Institut Pasteur, Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, F-75015 Paris, France, Jawaharlal Nehru University, School of Life Sciences, New Delhi 110067, India, and Jawaharlal Nehru University, School of Computational and Integrative Sciences, New Delhi 110067, India.
Nucleic Acids Research (Impact Factor: 9.11). 12/2012; 41(3). DOI: 10.1093/nar/gks1271
Source: PubMed


Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alternative usage of splicing and polyadenylation sites in Entamoeba histolytica using RNA-Seq. First, we identified a large number of rarely spliced alternative junctions and then showed that the occurrence of these alternative splicing events is correlated with splicing site sequence, occurrence of constitutive splicing events and messenger RNA abundance. Our results implied the majority of these alternative splicing events are likely to be stochastic error of splicing machineries, and we estimated the corresponding error rates. Second, we observed extensive microheterogeneity of polyadenylation cleavage sites, and the extent of such microheterogeneity is correlated with the occurrence of constitutive cleavage events, suggesting most of such microheterogeneity is likely to be stochastic. Overall, we only observed a small fraction of alternative splicing and polyadenylation isoforms that are unlikely to be solely stochastic, implying the functional relevance of alternative splicing and polyadenylation in E. histolytica is limited. Lastly, we revised the gene models and annotated their 3'UTR in AmoebaDB, providing valuable resources to the community.

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    • "All splicing junctions identified by HMMSplicer [37] were clustered as mentioned in a previous study [52]. A junction cluster is considered to be ‘antisense’ when its representative junction is located within the coding region of a gene on the opposite strand. "
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    • "The two E. histolytica LMW-PTP proteins (Gen- Bank: XP 656359, coded by GenBank: XM 651267, and GenBank: XP 653357, coded by GenBank: XM 648265), are identical except for a single conservative residue change at position 85 in the protein sequence: XP 656359 has an alanine and XP 653357 a valine. Both genes are expressed in cultured trophozoites, clinical isolates, and cysts [17] [18]. XM 651267, the gene encoding XP 656359, was cloned and expressed for this study, as was its Cys to Ser substrate-trapping mutant form. "
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