BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells

Methods. 2014 May 1;67(1):55-63. doi: 10.1016/j.ymeth.2013.07.014. Epub 2013 Jul 17.

Abstract

We recently developed a novel transcriptome analysis method, termed 5'-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis (BRIC-seq). BRIC-seq enables the determination of genome-wide RNA stability by chasing chronological decreases of BrU-labeled RNAs under physiologically undisturbed conditions. The RNA half-life of each transcript is calculated from the decreasing number of BrU-labeled RNA sequence tags measured by deep sequencing of BrU-labeled RNAs. Here, we describe a detailed protocol and provide tips for BRIC-seq, followed by computational analysis.

Keywords: Genome-wide technology; High-throughput sequencing; Massive sequencing analysis; RNA decay; RNA degradation; RNA stability.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bromouracil / analogs & derivatives
  • Chromosome Mapping
  • Gene Library
  • Gene Ontology
  • Genome
  • HEK293 Cells
  • Half-Life
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing
  • Humans
  • RNA Stability*
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA
  • Staining and Labeling
  • Uridine / analogs & derivatives
  • Uridine / chemistry

Substances

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