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

Gilad Fuchs1*, Yoav Voichek2, Sima Benjamin3, Shlomit Gilad3, Ido Amit4 and Moshe Oren1*

Author Affiliations

1 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel

2 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel

3 The Israel National Center for Personalized Medicine (INCPM), Weizmann Institute of Science, Rehovot 76100, Israel

4 Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel

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Genome Biology 2014, 15:R69  doi:10.1186/gb-2014-15-5-r69

Published: 16 May 2014

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.