Bromouridine Pulse-chase Sequencing

BruChase-Seq uses bromouridine tagging to map and quantify the relative stability of nascent RNA transcripts (Paulsen et al., 2013). RNAPII synthesizes RNA in the presence of Br-UTP. Untagged uridine is added to chase out bromouridine from RNAs with high turnover. Long-lived RNA transcripts will remain tagged. The tagged RNA transcripts are immunoseparated from total RNA using magnetic beads coated with anti-BrdU antibodies. The captured RNA transcripts are eluted and fragmented before synthesis of cDNA strands via RT and PCR amplification. The resultant cDNA strands are prepared for sequencing using an Illumina TruSeq RNA Library Prep Kit.


  • Determines RNA stability through pulse-chase with bromouridine
  • Predicts nonsense and frameshift mutations (Paulsen et al., 2013)
  • Detects transcription anywhere on the genome
  • No prior knowledge of transcription sites is needed


  • Limited to cell cultures and other artificial systems, due to the requirement for incubation in the presence of labeled nucleotides


Illumina Library prep and Array Kit Selector


Andrade-Lima L., Veloso A. and Ljungman M. Transcription Blockage Leads to New Beginnings. Biomolecules. 2015;5:1600


Lefkofsky H. B., Veloso A. and Ljungman M. Transcriptional and post-transcriptional regulation of nucleotide excision repair genes in human cells. Mutat Res. 2015;776:9-15

Kocab A. J., Veloso A., Paulsen M. T., Ljungman M. and Duckett C. S. Effects of physiological and synthetic IAP antagonism on c-IAP-dependent signaling. Oncogene. 2015;