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Series GSE122423 Query DataSets for GSE122423
Status Public on Dec 31, 2021
Title The DNA polymerase subunit Pol32 and RNase H1 are required for stress granule formation through R-loop regulation
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Strong cellular stress causes wide-spread perturbations in the transcriptome and in several types of DNA/RNA interactions, and through incompletely understood pathways to formation of cytoplasmic stress granules (SGs). We have investigated the relationships between strong transcriptional induction, RNA:DNA hybrid stretches (R-loops), and SG formation under severe hyperosmotic and glucose stress. Several mutations affecting DNA processing proteins, including the DNA polymerase subunit Pol32, confer SG formation defects. Severe stress increased R loop levels globally. We found that facilitating removal of R-loops by RNase H overexpression, with activity towards RNA:DNA hybrids, accelerated and enhanced transcriptional induction of stress-activated genes. Thus, overexpression of RNase H1, but not RNase H2, reduced R-loops globally around the 1 h mark. Remarkably, it also reduced SG formation. We performed a genome-wide analysis of the induction or repression kinetics of gene expression under severe stress conditions. RNase H1 overexpression reduced R-loops locally in highly transcribed stress-affected genes, as expected. Notably, it also increased expression of several stress-induced genes. Conversely, in cells where R-loops are not efficiently resolved, transcriptional induction of the same genes under stress was muted and occurred with a delay. Thus, in pol32∆ mutants, where SG accumulation is delayed, R-loop levels are elevated, and induction of stress genes suppressed. The pol32∆ mutants are also refractory to the effects of RNase H1 overexpression on stress gene induction, R-loop resolution, and SG formation, indicating that Pol32 may act downstream of Rnh1 in the regulation of these three processes. These findings demonstrate an unexpected link between R-loops and formation of SGs. Together, these observations indicate that under stress, strong transcriptional induction of specific genes or genomic regions causes R-loop accumulation, which then requires RNase H1 activity for resolution. If unresolved, the accumulated R-loops impede continued stress-induced transcription, and delay or prevent SG formation.
 
Overall design Samples were collected every 30 min after onset of 1.5 M KCl stress, up to 2 h. Samples were collected from two independent replicate experiment time series Total number of samples = 10. Control samples were collected at the 0 h time point.
 
Contributor(s) Kim H, Sunnerhagen P
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Submission date Nov 12, 2018
Last update date Dec 31, 2021
Contact name Per Sunnerhagen
E-mail(s) per.sunnerhagen@cmb.gu.se
Phone +46317863830
Organization name University of Gothenburg
Department Chemistry and Molecular Biology
Street address Box 462
City Gothenburg
ZIP/Postal code 40530
Country Sweden
 
Platforms (1)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (10)
GSM3466373 a 0
GSM3466374 a 05
GSM3466375 a 1
Relations
BioProject PRJNA505169
SRA SRP168403

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Supplementary file Size Download File type/resource
GSE122423_Expression_data_Kim_et_al.csv.gz 6.6 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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