|
Status |
Public on Jun 01, 2018 |
Title |
Improved mapping and characterization of R-loop forming loci in fission yeast. |
Organism |
Schizosaccharomyces pombe |
Experiment type |
Expression profiling by high throughput sequencing Other Non-coding RNA profiling by high throughput sequencing
|
Summary |
R-loops both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loop forming loci in the fission yeast, we used the S9.6-based DRIPc-seq approach to obtain improved strand-specific maps of R-loop forming loci at near nucleotide resolution. We show that the weak affinity of the S9.6 antibody for double-stranded RNA (dsRNA) is sufficient to confound the mapping of genuine R-loops by this approach. dsRNA elimination allowed the identification of two distinct classes of R-loops that differ by their sensitivity to endogenous RNase H activity. Both classes associate with common chromatin features, which are similar to those associated with R-loop formation in human. We used RNA-seq to identify transcripts whose steady-state levels were affected by genome-wide manipulation of R-loop levels. gdh2 is such a transcript and we show that extra RNase H1 stimulates the cis-acting transcription interference between an upstream non-coding RNA and gdh2. Surprisingly, we found that most transcripts whose levels were altered by in vivo manipulation of R-loop levels did not form R-loops. Conversely, the abundance of only few R-loop forming transcripts was impacted by genome-wide variation of R-loop levels. We conclude that prolonged manipulation of R-loop levels imparts indirect effects on the transcriptome that could complicate the use of this strategy to understand R-loop functions.
|
|
|
Overall design |
DNA-RNA immunoprecipitation strand-specific (DRIPc-seq) were performed on Schizosaccaromyces pombe cells from different genotypes (Wild-type, RNaseH1 overexpressed, RRP6 KO, RNaseH1+2 KO). Genomic DNA was treated with either RNaseA, RNaseA+H, RNaseA+III prior DRIPc-seq. Total RNA-seq was performed on Schizosaccaromyces pombe cells treated with several conditions (Wild-type, RNaseH1 overexpression, RNaseH1+2 KO). Small RNA-seq was performed on Schizosaccaromyces pombe Wild-type cells.
|
|
|
Contributor(s) |
Hartono SR, Malapert A, Legros P, Bernard P, Chedin F, Vanoosthuyse V |
Citation missing |
Has this study been published? Please login to update or notify GEO. |
Submission date |
Jul 10, 2017 |
Last update date |
Jul 25, 2021 |
Contact name |
Frederic Chedin |
E-mail(s) |
flchedin@ucdavis.edu
|
Organization name |
UC Davis
|
Department |
MCB
|
Lab |
Chedin
|
Street address |
1 Shields Avenue
|
City |
Davis |
State/province |
CA |
ZIP/Postal code |
95616 |
Country |
USA |
|
|
Platforms (2) |
GPL17225 |
Illumina HiSeq 2500 (Schizosaccharomyces pombe) |
GPL23689 |
NextSeq 550 (Schizosaccharomyces pombe) |
|
Samples (29)
|
|
Relations |
BioProject |
PRJNA393690 |
SRA |
SRP111464 |