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Title: Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA.

Authors: Paulsen, Michelle T; Veloso, Artur; Prasad, Jayendra; Bedi, Karan; Ljungman, Emily A; Magnuson, Brian; Wilson, Thomas E; Ljungman, Mats

Published In Methods, (2014 May 01)

Abstract: Gene expression studies commonly examine total cellular RNA, which only provides information about its steady-state pool of RNA. It remains unclear whether differences in the steady-state reflects variable rates of transcription or RNA degradation. To specifically monitor RNA synthesis and degradation genome-wide, we developed Bru-Seq and BruChase-Seq. These assays are based on metabolic pulse-chase labeling of RNA using bromouridine (Bru). In Bru-Seq, recently labeled RNAs are sequenced to reveal spans of nascent transcription in the genome. In BruChase-Seq, cells are chased in uridine for different periods of time following Bru-labeling, allowing for the isolation of RNA populations of specific ages. Here we describe these methodologies in detail and highlight their usefulness in assessing RNA synthesis and stability as well as splicing kinetics with examples of specific genes from different human cell lines.

PubMed ID: 23973811 Exiting the NIEHS site

MeSH Terms: Animals; Codon, Nonsense; DNA, Complementary/genetics; Frameshift Mutation; Genome, Human; HeLa Cells; High-Throughput Nucleotide Sequencing; Humans; Hyaluronan Receptors/genetics; Hyaluronan Receptors/metabolism; K562 Cells; Kinetics; Molecular Sequence Annotation; RNA Splicing; RNA Stability; RNA, Messenger/biosynthesis*; RNA, Messenger/chemistry; RNA, Messenger/genetics; RNA, Messenger/isolation & purification; Retinoblastoma Protein/genetics; Retinoblastoma Protein/metabolism; Sequence Analysis, RNA; Staining and Labeling; Tumor Suppressor Protein p53/genetics; Tumor Suppressor Protein p53/metabolism; Uridine/analogs & derivatives*; Uridine/chemistry

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