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Series GSE64332 Query DataSets for GSE64332
Status Public on Aug 20, 2015
Title Human DIS3 shapes the RNA polymerase II transcriptome degrading variety of unwanted transcripts.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Human DIS3 is a nuclear, catalytic subunit of the exosome complex containing exonucleolytic and endonucleolytic active domains. To identify DIS3 targets genome-wide we conducted comprehensive transcriptomic analysis of HEK293 cells producing mutated DIS3 versions and Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) experiments. Pervasive transcription products like Promoter Upstream Transcripts (PROMPTs) accumulated robustly in catalytic DIS3 mutants, representing ~8% of PAR-CLIP reads. Importantly, RNAs originating from unannotated genomic regions increased ~2.5 times in double DIS3 mutants, covering ~70% of genome and allowing for discovery of thousands of novel transcripts. The first intron of many pre-mRNAs accumulated in DIS3 mutants indicating a widespread premature RNA polymerase II termination. The short form of NEAT1 lincRNA was overexpressed in DIS3 mutants, leading to increased number of paraspeckles. Moreover, there was a global deregulation of mRNAs in DIS3 double mutant. Finally, snoRNA precursors accumulated, which correlated with a strong PAR-CLIP signal indicating that DIS3 but not RRP6 is a main snoRNA processing enzyme. In aggregate, we demonstrate that DIS3 is a major nucleoplasmic activity responsible for shaping the human transcriptome.
Overall design RNA-seq experiments were performed in triplicates for DIS3 wild type (control), DIS3 PIN, DIS3 RNB domain mutants and DIS3 PIN RNB double mutant. RNA-seq samples from DIS3 wild type and DIS3 double mutant were additionally sequenced in deeper resolution, also in triplicates. DIS3 PAR-CLIP experiment was performed in duplicate. Pol II ChIP-seq experiment in WT and DIS3 PIN RNB double-mutants cells was performed in triplicates.
Contributor(s) Szczepińska T, Kalisiak K, Tomecki R, Labno A, Borowski LS, Kulinski TM, Adamska D, Dziembowski A
Citation(s) 26294688
Submission date Dec 18, 2014
Last update date May 15, 2019
Contact name Andrzej Dziembowski
Phone +48 22 5922033
Organization name Institute of Biochemistry and Biophysics Polish Academy of Sciences
Lab Laboratory of RNA Biology and Functional Genomics
Street address Pawinskiego 5A
City Warszawa
ZIP/Postal code 02-106
Country Poland
Platforms (2)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (17)
GSM1568709 hDIS3_WT_RNA-seq
GSM1568710 hDIS3_PIN_mut_RNA-seq
GSM1568711 hDIS3_RNB_mut_RNA-seq
BioProject PRJNA270769
SRA SRP051331

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Supplementary file Size Download File type/resource
GSE64332_PolII_ChIPseq.tsv.gz 4.7 Mb (ftp)(http) TSV
GSE64332_RAW.tar 76.4 Mb (http)(custom) TAR (of BEDGRAPH, TSV)
GSE64332_merged.gtf.gz 38.4 Mb (ftp)(http) GTF
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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