title: Determination of in vivo RNA kinetics using RATE-seq.
abstract: The abundance of a transcript is determined by its rate of synthesis and its rate of degradation; however, global methods for quantifying RNA abundance cannot distinguish variation in these two processes. Here, we introduce RNA approach to equilibrium sequencing (RATE-seq), which uses in vivo metabolic labeling of RNA and approach to equilibrium kinetics, to determine absolute RNA degradation and synthesis rates. RATE-seq does not disturb cellular physiology, uses straightforward normalization with exogenous spike-ins, and can be readily adapted for studies in most organisms. We demonstrate the use of RATE-seq to estimate genome-wide kinetic parameters for coding and noncoding transcripts in Saccharomyces cerevisiae.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Neymotin
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA.
authors.forename: Rodoniki
authors.initials: R
authors.lastname: Athanasiadou
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA dgresham@nyu.edu.
authors.forename: David
authors.initials: D
authors.lastname: Gresham
mesh_terms: D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D007700:Kinetics; D012326:RNA Splicing / Q000235:genetics; D020871:RNA Stability / Q000235:genetics*; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism*
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins
keywords: RATE-seq; RNA degradation; RNA synthesis; metabolic labeling; thiouracil