Determination of in vivo RNA kinetics using RATE-seq

Benjamin Neymotin, Rodoniki Athanasiadou, David Gresham

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1645-1652
Number of pages8
JournalRNA
Volume20
Issue number10
DOIs
StatePublished - Oct 1 2014

Keywords

  • Metabolic labeling
  • RATE-seq
  • RNA degradation
  • RNA synthesis
  • Thiouracil

ASJC Scopus subject areas

  • Molecular Biology

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