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| Status |
Public on Feb 01, 2018 |
| Title |
Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. These PAS termination events are enriched at the first few stable nucleosomes flanking CpG islands and suppressed by U1 snRNP. Thus, promoter-proximal Pol II pausing consists of two processes: TSS-proximal and +1 stable nucleosome pausing, with PAS termination coinciding with the latter. While pausing factors NELF/DSIF only function in the former step, flavopiridol-sensitive mechanism(s) and Myc modulate both steps. We propose that premature PAS termination near the nucleosome-associated pause site represents a common transcriptional elongation checkpoint regulated by U1 snRNP recognition, nucleosome stability, and Myc activity.
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| |
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| Overall design |
RNA sequencing (RNA-seq) in Exosc3 conditional KO mESCs
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| |
|
| Contributor(s) |
Chiu AC, Suzuki HI, Sharp PA |
| Citation(s) |
29398447 |
| Submission date |
Jun 27, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Hiroshi I. Suzuki |
| E-mail(s) |
hisuzuki-tky@umin.ac.jp
|
| Organization name |
Nagoya University
|
| Department |
DIvision of Molecular Oncology, Graduate School of Medicine
|
| Street address |
65 Tsurumai-cho, Showa-ku
|
| City |
Nagoya |
| ZIP/Postal code |
466-8550 |
| Country |
Japan |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (4)
|
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| This SubSeries is part of SuperSeries: |
| GSE100537 |
Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP |
|
| Relations |
| BioProject |
PRJNA392049 |
| SRA |
SRP110584 |
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