title: circTAIL-seq, a targeted method for deep analysis of RNA 3' tails, reveals transcript-specific differences by multiple metrics.
abstract: Post-transcriptionally added RNA 3' nucleotide extensions, or tails, impose numerous regulatory effects on RNAs, including effects on RNA turnover and translation. However, efficient methods for in-depth tail profiling of a transcript of interest are still lacking, hindering available knowledge particularly of tail populations that are highly heterogeneous. Here, we developed a targeted approach, termed circTAIL-seq, to quantify both major and subtle differences of heterogeneous tail populations. As proof-of-principle, we show that circTAIL-seq quantifies the differences in tail qualities between two selected Trypanosoma brucei mitochondrial transcripts. The results demonstrate the power of the developed method in identification, discrimination, and quantification of different tail states that the population of one transcript can possess. We further show that circTAIL-seq can detect the tail characteristics for variants of transcripts that are not easily detectable by conventional approaches, such as degradation intermediates. Our findings are not only well supported by previous knowledge, but they also expand this knowledge and provide experimental evidence for previous hypotheses. In the future, this approach can be used to determine changes in tail qualities in response to environmental or internal stimuli, or upon silencing of genes of interest in mRNA-processing pathways. In summary, circTAIL-seq is an effective tool for comparing nonencoded RNA tails, especially when the tails are extremely variable or transcript of interest is low abundance.
authors.affiliation: Institute of Parasitology, McGill University, Québec H9X 3V9, Canada.
authors.forename: Vahid H
authors.initials: VH
authors.lastname: Gazestani
authors.affiliation: Department of Mathematics, University of Minnesota Duluth, Duluth, Minnesota 55812, USA.
authors.forename: Marshall
authors.initials: M
authors.lastname: Hampton
authors.affiliation: University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA.
authors.forename: Juan E
authors.initials: JE
authors.lastname: Abrahante
authors.affiliation: Institute of Parasitology, McGill University, Québec H9X 3V9, Canada.
authors.forename: Reza
authors.initials: R
authors.lastname: Salavati
authors.affiliation: Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota 55812, USA.
authors.forename: Sara L
authors.initials: SL
authors.lastname: Zimmer
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012333:RNA, Messenger / Q000235:genetics*; D016053:RNA, Protozoan / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014346:Trypanosoma brucei brucei / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012333:RNA, Messenger; D016053:RNA, Protozoan
keywords: Illumina; mitochondrion; polyadenylation; trypanosome; uridylation