Identifying transcription start sites and active enhancer elements using BruUV-seq

Sci Rep. 2015 Dec 11;5:17978. doi: 10.1038/srep17978.


BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5'-end of genes promoting the identification of transcription start sites (TSSs). Furthermore, transcripts associated with arrested RNA polymerases are protected from 3'-5' degradation and thus, unstable transcripts such as putative enhancer RNA (eRNA) are dramatically increased. Validation of BruUV-seq against GRO-cap that identifies capped run-on transcripts showed that most BruUV-seq peaks overlapped with GRO-cap signal over both TSSs and enhancer elements. Finally, BruUV-seq identified putative enhancer elements induced by tumor necrosis factor (TNF) treatment concomitant with expression of nearby TNF-induced genes. Taken together, BruUV-seq is a powerful new approach for identifying TSSs and active enhancer elements genome-wide in intact cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods
  • Databases, Nucleic Acid
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation / radiation effects*
  • Genome, Human
  • Genomics / methods
  • Humans
  • Molecular Sequence Annotation
  • Transcription Elongation, Genetic / radiation effects
  • Transcription Initiation Site*
  • Transcription, Genetic / radiation effects
  • Ultraviolet Rays*