5'-Bromouridine IP Chase (BRIC)-Seq to Determine RNA Half-Lives

Methods Mol Biol. 2018:1720:1-13. doi: 10.1007/978-1-4939-7540-2_1.

Abstract

Analysis of RNA stability at genome-wide level is an advanced method in RNA biology that examines the half-life of each transcript. In particular, a pulse-labeling method using uridine analogs enables the determination of half-life of each transcript under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromouridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

Keywords: 5′-Bromouridine; BRIC-seq; Deep sequencing; RNA degradation; RNA half-life.

MeSH terms

  • Animals
  • Bromouracil / analogs & derivatives
  • Cell Line
  • Half-Life
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Immunoprecipitation / methods*
  • RNA Stability*
  • RNA, Messenger / chemistry*
  • RNA, Messenger / immunology
  • Sequence Analysis, RNA / methods*
  • Staining and Labeling / methods
  • Time Factors
  • Transcriptome
  • Uridine / analogs & derivatives
  • Uridine / chemistry

Substances

  • RNA, Messenger
  • Bromouracil
  • 5-bromouridine
  • Uridine