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| Status |
Public on Oct 22, 2019 |
| Title |
R-loops promote antisense transcription across the mammalian genome |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
We report the correlation we found between R-loops and antisense trasncription initiation. Our in vitro data suggests that RNA pol II can initiate transcription off the displaced single stranded DNA from within the R-loop. Therefore we generated Chromatin associated RNA-seq with and without over-expressing RNaseH1 and RDIP-seq (the directional RNA-seq of the RNA moeity from within the S9.6 pull down R-loop) as well as RR-ChIP-seq (the directional RNA-seq of the RNA moeity from within the catalytically dead RNaseH1-GFP GFP pull down R-loop) and confirm the correlation in vivo. We also aligned our findings with ChrCAP-seq (which is is a library enriched for RNA polymerase II capped RNA using chromatin associated RNA as the initial source) and found that capped antisense RNA were sensitive to RNase H1 overexpression.
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| Overall design |
Examination of chromatin associated RNA of HeLa cells and capped RNA with and without over-expressing RNAseH1. Directional R-loop occupancy was conducted by 1) sequencing the RNA moeity of the R-loop fragments which were immunoprecipitated by mouse monoclonal S9.6 antibody and by 2) sequencing the RNA moeity of the RNA:DNA hybrids caught in a catalytically dead RNaseH1-GFP.
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| Contributor(s) |
Tan-Wong SM, Dhir S, Proudfoot NJ |
| Citation(s) |
31679819 |
| Submission date |
Oct 04, 2016 |
| Last update date |
Aug 27, 2020 |
| Contact name |
Nicholas Proudfoot |
| E-mail(s) |
nicholas.proudfoot@path.ox.ac.uk
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| Organization name |
Sir William Dunn School of Pathology, University of Oxford
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| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3RE |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA345371 |
| SRA |
SRP090821 |
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