4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

Genome Biol. 2014 May 9;15(5):R69. doi: 10.1186/gb-2014-15-5-r69.


Although transcriptional elongation by RNA polymerase II is coupled with many RNA-related processes, genomewide elongation rates remain unknown. We describe a method, called 4sUDRB-seq, based on reversible inhibition of transcription elongation coupled with tagging newly transcribed RNA with 4-thiouridine and high throughput sequencing to measure simultaneously with high confidence genome-wide transcription elongation rates in cells. We find that most genes are transcribed at about 3.5 Kb/min, with elongation rates varying between 2 Kb/min and 6 Kb/min. 4sUDRB-seq can facilitate genomewide exploration of the involvement of specific elongation factors in transcription and the contribution of deregulated transcription elongation to various pathologies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Dichlororibofuranosylbenzimidazole / pharmacology*
  • Genome, Human
  • HeLa Cells
  • Humans
  • RNA Polymerase II / metabolism*
  • Sequence Analysis, RNA / methods
  • Thiouridine / metabolism*
  • Transcription Elongation, Genetic*


  • Thiouridine
  • Dichlororibofuranosylbenzimidazole
  • RNA Polymerase II

Associated data

  • GEO/GSE57116