Basic Information
| Dataset | GSE120574 |
|---|---|
| Status | 2019-03-06 |
| Species | Homo sapiens |
| Source | NCBI GEO |
| Subcellular Localization | Nucleoplasm |
| PMID | 30840897 |
| Title | The immediate impact of exoribonucleolysis on nuclear RNA processing, turnover and transcriptional control revealed by rapid depletion of DIS3, EXOSC10 or XRN2 from human cells |
| Citation | Davidson L, Francis L, Cordiner RA, Eaton JD et al. Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control. Cell Rep 2019 Mar 5;26(10):2779-2791.e5. |
| Experimental Design | Nuclear RNA-seq was performed on an auxin-inducible degron (AID) tagged cell lines in treated with or without auxin inducing rapid depletion of EXOSC10 or DIS3 protein. HCT116 cells also ectopically express TIR1 from a sleeping beauty transposon integrated cassette. AID incorporated proteins contain in-frame insertion of AID tag, P2A cleavage site, antibiotic resistance marker and SV40 polyA site. Two repair templates expressing different antibiotic resistance markers (neomycin and hygromycin) were used to ensure biallelic intersion of the repair cassette using CRISPR/Cas9. We also performed individual nucleotide cross-linking and immunoprecipitation (iCLIP) on a catalytic mutant of EXOSC10 (D313N), in order to complement a previous iCLIP experiment using EXOSC10 WT. We reasoned that by using a catalytic mutant of EXOSC10 we would be able to stabilize interactions between the exoribonuclease and it global RNA substrates. In the process we identified 30nt footprints of iCLIP density downstream of pre-rRNAs and pre-snoRNAs exclusively seen in EXOSC10 CAT CLIP profiles. |
Sample Information
| BioProject | Sample Name | Localization | Treatment | Genotype | Source | Label |
|---|---|---|---|---|---|---|
| PRJNA493621 | GSM3403542 | Nucleoplasmic RNA | Control: auxin untreated Nuclear RNA | EXOSC10-AID | HCT116 cells | Nuclear RNA-seq EXOSC10-AID Minus auxin rep 1 |
| PRJNA493621 | GSM3403543 | Nucleoplasmic RNA | auxin treated Nuclear RNA | EXOSC10-AID | HCT116 cells | Nuclear RNA-seq EXOSC10-AID Plus auxin rep 1 |
| PRJNA493621 | GSM3403544 | Nucleoplasmic RNA | Control: auxin untreated Nuclear RNA | EXOSC10-AID | HCT116 cells | Nuclear RNA-seq EXOSC10-AID Minus auxin rep 2 |
| PRJNA493621 | GSM3403545 | Nucleoplasmic RNA | auxin treated Nuclear RNA | EXOSC10-AID | HCT116 cells | Nuclear RNA-seq EXOSC10-AID Plus auxin rep 2 |
| PRJNA493621 | GSM3403546 | Nucleoplasmic RNA | Control: auxin untreated Nuclear RNA | DIS3-AID | HCT116 cells | Nuclear RNA-seq DIS3-AID Minus auxin rep 1 |
| PRJNA493621 | GSM3403547 | Nucleoplasmic RNA | auxin treated Nuclear RNA | DIS3-AID | HCT116 cells | Nuclear RNA-seq DIS3-AID Plus auxin rep 1 |
| PRJNA493621 | GSM3403548 | Nucleoplasmic RNA | Control: auxin untreated Nuclear RNA | DIS3-AID | HCT116 cells | Nuclear RNA-seq DIS3-AID Minus auxin rep 2 |
| PRJNA493621 | GSM3403549 | Nucleoplasmic RNA | auxin treated Nuclear RNA | DIS3-AID | HCT116 cells | Nuclear RNA-seq DIS3-AID Plus auxin rep 2 |
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