title: Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.
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.
authors.affiliation: Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie cellulaire et infection, F-75015 Paris, France, INSERM U786, F-75015 Paris, France. chung-chau.hon@pasteur.fr
authors.forename: Chung-Chau
authors.initials: CC
authors.lastname: Hon
authors.forename: Christian
authors.initials: C
authors.lastname: Weber
authors.forename: Odile
authors.initials: O
authors.lastname: Sismeiro
authors.forename: Caroline
authors.initials: C
authors.lastname: Proux
authors.forename: Mikael
authors.initials: M
authors.lastname: Koutero
authors.forename: Marc
authors.initials: M
authors.lastname: Deloger
authors.forename: Sarbashis
authors.initials: S
authors.lastname: Das
authors.forename: Mridula
authors.initials: M
authors.lastname: Agrahari
authors.forename: Marie-Agnes
authors.initials: MA
authors.lastname: Dillies
authors.forename: Bernd
authors.initials: B
authors.lastname: Jagla
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Coppee
authors.forename: Alok
authors.initials: A
authors.lastname: Bhattacharya
authors.forename: Nancy
authors.initials: N
authors.lastname: Guillen
mesh_terms: D017398:Alternative Splicing; D004748:Entamoeba histolytica / Q000235:genetics* / Q000378:metabolism; D005091:Exons; D007438:Introns; D008957:Models, Genetic; D059372:Nucleotide Motifs; D011061:Poly A / Q000032:analysis; D026723:Polyadenylation; D059368:RNA Isoforms / Q000032:analysis; D012333:RNA, Messenger / Q000737:chemistry; D013269:Stochastic Processes
chemical_list: D059368:RNA Isoforms; D012333:RNA, Messenger; D011061:Poly A