@inbook{7b87d54db7f1485e83d026583169340b,
title = "Determining mRNA decay rates using RNA approach to equilibrium sequencing (RATE-seq)",
abstract = "RATE-seq is a 4-thiouracil (4-tU)-based method that enables the in vivo measurement of transcriptome-wide RNA degradation rates. 4-tU is an analog of uracil that is rapidly incorporated into newly synthesized RNA and facilitates the conjugation of a biotinylated molecule containing a reactive thiol group. The biotinylated RNA can then be fractionated from the unlabeled RNA with streptavidin magnetic beads. By adding 4-tU to a culture of cells growing in steady-state conditions, fractionating the labeled population of RNA at multiple time points following 4-tU addition, and quantifying the abundance of newly transcribed RNAs using RNAseq, it is possible to estimate the degradation rates of all transcripts in a single experiment. The analysis of the RATE-seq data entails normalization of RNAseq libraries to thiolated RNA spike-ins and nonlinear model fitting to estimate the degradation rate constant for each RNA species.",
keywords = "4-thiouracil, Metabolic labeling, RNA degradation, RNA stability, RNA turnover",
author = "Farah Abdul-Rahman and David Gresham",
note = "Publisher Copyright: {\textcopyright} 2018, Springer Science+Business Media LLC.",
year = "2018",
doi = "10.1007/978-1-4939-7540-2_2",
language = "English (US)",
isbn = "9781493975402",
volume = "1720",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "15--24",
booktitle = "Methods in Molecular Biology",
}