Genome-wide analysis of long noncoding RNA turnover

Methods Mol Biol. 2015;1262:305-20. doi: 10.1007/978-1-4939-2253-6_19.

Abstract

Genome-wide analysis for determining RNA turnover is an advanced method in RNA biology that examines the specific half-life of nuclear noncoding RNA (ncRNA). In particular, a pulse-labeling method using uridine analogs enables the determination of RNA stability under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromo-uridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing. The method is called BrU immunoprecipitation chase assay (BRIC) or BRIC through deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq.

MeSH terms

  • Animals
  • Bromodeoxyuridine / chemistry
  • Cell Line
  • Computational Biology / methods
  • Genome
  • HEK293 Cells
  • Half-Life
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Mammals / genetics*
  • RNA Stability
  • RNA, Long Noncoding / chemistry*
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / isolation & purification
  • Sequence Analysis, RNA

Substances

  • RNA, Long Noncoding
  • Bromodeoxyuridine