|
| Status |
Public on Jan 19, 2011 |
| Title |
Native elongating transcript sequencing (NET-seq) of wild type Saccharomyces cerevisiae and of DST1, RCO1, SET1, SET2, EAF3 deletion strains |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
We present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3’ ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that while promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo.
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| |
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| Overall design |
Examination of nascent transcripts in yeast and mutant strains
|
| |
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| Contributor(s) |
Churchman LS, Weissman JS |
| Citation(s) |
21248844 |
| |
| Submission date |
Nov 03, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
L. Stirling Stirling Churchman |
| Organization name |
University of California-San Francisco
|
| Street address |
1700 Fourth St. Byers Hall - Room 404
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL9377 |
Illumina Genome Analyzer II (Saccharomyces cerevisiae) |
|
| Samples (7)
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| Relations |
| SRA |
SRP004431 |
| BioProject |
PRJNA134499 |
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