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| 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
Other
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.
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| 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.
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| 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 |
| E-mail(s) |
andrzejd@ibb.waw.pl
|
| 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 |
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| Platforms (2) |
| GPL18460 |
Illumina HiSeq 1500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA270769 |
| SRA |
SRP051331 |
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