|
| Status |
Public on Jun 15, 2012 |
| Title |
RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Recent genome-wide chromatin immunoprecipitation coupled high throughput
sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed
RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this
study we have further investigated genome-wide binding of Pol II downstream of the 3'
end of the annotated genes (EAGs) by ChIP-seq in human cells. At almost all
expressed genes we observed Pol II occupancy downstream of the EAGs suggesting
that Pol II pausing 3' from the transcription units is a rather common phenomenon.
Downstream of EAGs Pol II transcripts can also be detected by global run-on and
sequencing, suggesting the presence of functionally active Pol II. Based on Pol II
occupancy downstream of EAGs we could distinguish distinct clusters of Pol II pause
patterns. On core histone genes, coding for non-polyadenylated transcripts, Pol II
occupancy is quickly dropping after the EAG. In contrast, on genes, whose transcripts
undergo polyA tail addition [poly(A)+], Pol II occupancy downstream of the EAGs can
be detected up to 4-6 kb. Inhibition of polyadenylation significantly increased Pol II
occupancy downstream of EAGs at poly(A)+ genes, but not at the EAGs of core
histone genes. The differential genome-wide Pol II occupancy profiles 3' of the EAGs
have also been confirmed in mouse embryonic stem (mES) cells, indicating that Pol II
pauses genome-wide downstream of the EAGs in mammalian cells. Moreover, in mES
cells the sharp drop of Pol II signal at the EAG of core histone genes seems to be
independent of the phosphorylation status of the C-terminal domain of the large
subunit of Pol II. Thus, our study uncovers a potential link between different mRNA 3'
end processing mechanisms and consequent Pol II transcription termination
processes.
|
| |
|
| Overall design |
Examination of RNA Polymerase II in MCF-7 cell line
|
| |
|
| Contributor(s) |
Krishanpal A, Akos G, Laszlo T |
| Citation(s) |
22701709 |
| |
| Submission date |
Nov 29, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Anamika Krishanpal |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)
|
| Street address |
1 rue Laurent Fries / BP 10142
|
| City |
Strasbourg |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
|
| Samples (2) |
|
| Relations |
| SRA |
SRP009461 |
| BioProject |
PRJNA150577 |
