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Series GSE57067 Query DataSets for GSE57067
Status Public on Mar 03, 2016
Title Role of Fun30 remodelers in retrotransposon regulation [MNase-Seq]
Organism Schizosaccharomyces pombe
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Retrotransposable elements are genomic parasites that are both key drivers of evolution and the ancestors of retroviruses. Although host cells have developed numerous mechanisms to keep these elements in check, there is also evidence from yeast to mammals that stressed cells sometimes activate transposition. Here we show that the fission yeast tf2 retrotransposons are regulated by alternative transcription start site (TSS) usage. Which TSS is used is determined by nucleosome positioning, which is in turn controlled by the Fun30 chromatin remodelers Fft2 and Fft3. By maintaining a high level of nucleosome occupancy at retrotransposon-flanking Long Terminal Repeat (LTR) elements, Fft2 and Fft3 promote the use of a downstream TSS and the production of RNA incapable of reverse transcription and retrotransposition. More generally, we show that Fft2 and Fft3 are involved in repressing the transcriptional response to stress, of which retrotransposon activation is a part. Finally, we show that in stressed cells retrotransposon TSS usage switches, allowing the production of full-length retrotransposon RNA. We propose that allowing retrotransposon transcription from a nonproductive TSS allows for the rapid activation of these elements in times of stress, while preventing their uncontrolled proliferation in the genome.
 
Overall design For MNase samples, duplicate mutant mononucleosome fractions were compared with duplicate WT mononucleosomes
 
Contributor(s) Persson J, Steglich B, Smialowska A, Ekwall K
Citation(s) 26902262
Submission date Apr 24, 2014
Last update date May 15, 2019
Contact name Babett Steglich
Organization name Universitätsklinikum Hamburg-Eppendorf
Street address Martinistrasse 52
City Hamburg
ZIP/Postal code 20246
Country Germany
 
Platforms (1)
GPL16192 Illumina MiSeq (Schizosaccharomyces pombe)
Samples (2)
GSM1374060 Wildtype mononucleosomes
GSM1374061 Fft2D fft3D mononucleosomes
This SubSeries is part of SuperSeries:
GSE57069 Role of Fun30 remodelers in retrotransposon regulation
Relations
SRA SRP041436
BioProject PRJNA245877

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE57067_Diff.wig.gz 8.1 Mb (ftp)(http) WIG
GSE57067_RAW.tar 13.7 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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