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

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-thiou...

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Bibliographic Details
Published in:Genome biology 2014-05, Vol.15 (5), p.R69-R69, Article R69
Main Authors: Fuchs, Gilad, Voichek, Yoav, Benjamin, Sima, Gilad, Shlomit, Amit, Ido, Oren, Moshe
Format: Article
Language:English
Subjects:
Dichlororibofuranosylbenzimidazole - pharmacology
Genome, Human
HeLa Cells
Humans
Method
RNA Polymerase II - metabolism
Sequence Analysis, RNA - methods
Thiouridine - metabolism
Transcription Elongation, Genetic
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Summary: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.
ISSN:1474-760X
1465-6906
1474-760X
1465-6914
DOI:10.1186/gb-2014-15-5-r69