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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.

SUBMITTER: Fuchs G

PROVIDER: S-EPMC4072947 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Fuchs Gilad G Voichek Yoav Y Benjamin Sima S Gilad Shlomit S Amit Ido I Oren Moshe M

Genome biology 20140509 5

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, w ...[more]

PMID: 24887486

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