Determination of in vivo RNA kinetics using RATE-seq

被引：83

作者：

Neymotin, Benjamin ^{[1
]}

Athanasiadou, Rodoniki ^{[1
]}

Gresham, David ^{[1
]}

机构：

[1] NYU, Ctr Genom & Syst Biol, Dept Biol, New York, NY 10003 USA

来源：

RNA | 2014年 / 20卷 / 10期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

RATE-seq; RNA degradation; RNA synthesis; thiouracil; metabolic labeling; MESSENGER-RNA; STABILITY; TRANSCRIPTOME; QUANTIFICATION; SEQUENCES; CELLS; DECAY;

D O I：

10.1261/rna.045104.114

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1645 / 1652

页数：8