title: Measures of RNA metabolism rates: Toward a definition at the level of single bonds.
abstract: We give an overview of experimental and computational methods to estimate RNA metabolism rates genome-wide. We then advocate a local definition of RNA metabolism rate at the level of individual phosphodiester bonds. Rates of formation and disappearance of individual bonds are unambiguously defined, in contrast to rates of complete transcripts. We show that over previous approaches, the recently developed transient transcriptome sequencing (TT-seq) protocol allows for estimation of metabolism rates of individual bonds with least positional bias.
authors.affiliation: a Department of Informatics , Technical University of Munich, Garching bei München , Germany.
authors.forename: Leonhard
authors.initials: L
authors.lastname: Wachutka
authors.affiliation: a Department of Informatics , Technical University of Munich, Garching bei München , Germany.
authors.forename: Julien
authors.initials: J
authors.lastname: Gagneur
mesh_terms: D005091:Exons; D016678:Genome; D006801:Humans; D007700:Kinetics; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012326:RNA Splicing; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012313:RNA
keywords: RNA metabolism; RNA sequencing; kinetics; splicing; transcription