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PMID: 24887486 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

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

Genome biology ·Vol. 15 ·No. 5 ·2014-05-09 ·Pages R69

Fuchs G, Voichek Y, Benjamin S, Gilad S, Amit I, Oren M

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.

MeSH Terms
Dichlororibofuranosylbenzimidazole/pharmacology Genome, Human HeLa Cells Humans RNA Polymerase II/metabolism Sequence Analysis, RNA/methods Thiouridine/metabolism Transcription Elongation, Genetic
Chemicals
Thiouridine Dichlororibofuranosylbenzimidazole RNA Polymerase II
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Fuchs Gilad
Voichek Yoav
Benjamin Sima
Gilad Shlomit
Amit Ido
Oren Moshe
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2014-15-5-r69
Published
2014-05-09
Epub
2014-00-09
Pages
R69
Language
English
Region
England
NLM ID
100960660
PMCID
PMC4072947
Subset
IM
Databases
GEO
GSE57116
External Links
PubMed source DOI: 10.1186/gb-2014-15-5-r69 PMC Full Text View journal details
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