ArticleNucleic acids research2013
Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Entamoeba histolytica clones presenting transient virulent phenotypes: subsequent fate of forcibly induced virulent clones by hamster's liver abscess model.Gut pathogens · 2026Article
- Multi-omics profiling and bile-acid exposure assays implicate a gut microbiome-parasite axis linked to persistent Entamoeba histolytica carriage.Gut pathogens · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Article
- Exploring virulence and stress response inMicrobiology spectrum · 2025Article
- Role of EhLINE1_ORF1p outside retrotransposition: Downregulation causes growth defects inJournal of biosciences · 2025Article
- Unraveling the interaction between a glycolytic regulator protein EhPpdk and an anaphase promoting complex protein EhApc10: yeast two hybrid screening, in vitro binding assays and molecular simulation study.The protein journal · 2024Article
- Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists.Genome research · 2024Article
- Comparative genomics and interactomics of polyadenylation factors for the prediction of new parasite targets: Entamoeba histolytica as a working model.Bioscience reports · 2023Article
- In Silico Identification and Characterization of circRNAs as Potential Virulence-Related miRNA/siRNA Sponges fromNon-coding RNA · 2022Article
- Gene expression of axenically-isolated clinical Entamoeba histolytica strains and its impact on disease severity of amebiasis.PLoS pathogens · 2022Article
- The Role of Acetate Kinase in the Human ParasiteParasitologia (Basel, Switzerland) · 2022Article
- Precise gene models using long-read sequencing reveal a unique poly(A) signal inRNA (New York, N.Y.) · 2022Article
- RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs inMicroorganisms · 2022Article
- The non-LTR retrotransposons of Entamoeba histolytica: genomic organization and biology.Molecular genetics and genomics : MGG · 2022Review
- Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth.PLoS pathogens · 2021Article
- Unraveling the relevance of the polyadenylation factor EhCFIm25 in Entamoeba histolytica through proteomic analysis.FEBS open bio · 2021Article
- Two StAR-related lipid transfer proteins play specific roles in endocytosis, exocytosis, and motility in the parasitic protist Entamoeba histolytica.PLoS pathogens · 2021Article
- Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets.Methods in enzymology · 2021Article
- Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica.Scientific reports · 2020Article
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Authors and funding
13 authors.
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Abstract
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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