title: 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells.
abstract: 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.
authors.forename: Gilad
authors.initials: G
authors.lastname: Fuchs
authors.forename: Yoav
authors.initials: Y
authors.lastname: Voichek
authors.forename: Sima
authors.initials: S
authors.lastname: Benjamin
authors.forename: Shlomit
authors.initials: S
authors.lastname: Gilad
authors.forename: Ido
authors.initials: I
authors.lastname: Amit
authors.forename: Moshe
authors.initials: M
authors.lastname: Oren
mesh_terms: D004004:Dichlororibofuranosylbenzimidazole / Q000494:pharmacology*; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D012319:RNA Polymerase II / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D013891:Thiouridine / Q000378:metabolism*; D061805:Transcription Elongation, Genetic
chemical_list: D013891:Thiouridine; D004004:Dichlororibofuranosylbenzimidazole; D012319:RNA Polymerase II