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

Genome-wide analysis of long noncoding RNA turnover.

Author information

1
Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.

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.

PMID:
25555590
DOI:
10.1007/978-1-4939-2253-6_19
[Indexed for MEDLINE]

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