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| Status |
Public on Nov 28, 2019 |
| Title |
Effects of CRISPR/Cas9-mediated deletion of Safb1 and Safb2 genes on the mature miRNA transcriptome |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are 20-25 nucleotides (nt) RNAs that are predicted to post-transcriptionally silence expression of >60% of all protein coding genes in mammals. As such, they form an additional layer of gene regulation that controls most if not all biological processes. MiRNAs are generated from primary transcripts containing single or multiple clustered stem-loop structures that are thought to be recognized and cleaved by the DGCR8/DROSHA Microprocessor complex as independent entities. Contrasting this view, we find that the primary miR-15a stem-loop within the bicistronic miR-15a-16-1 cluster is a poor Microprocessor substrate and is consequently not processed on its own, but that the presence of the neighboring primary miR-16-1 stem-loop on the same transcript can compensate for this deficiency in cis. Using a CRISPR/Cas9 screen, we identify SAFB2 (scaffold attachment factor B2) as an essential co-factor in this miR-16-1-assisted primary miR-15 cleavage. Small RNA sequencing further revealed that deletion of Safb1 and 2 genes reduces not only miR-15a levels, but also affects other clustered miRNAs, among them miR-15b, miR-181b and miR-92a. We therefore postulate a model in which SAFB2 enables processing of suboptimal substrates in a subset of clustered pri-miRNA transcripts.
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| Overall design |
Comparison of control CRISPR/Cas9 cells and Safb1/Safb2 CRISPR/Cas9 cells (independent knockout clones per group; 2 different cell lines)
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| Contributor(s) |
Herzog S |
| Citation missing |
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| Submission date |
Nov 27, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Sebastian Herzog |
| E-mail(s) |
Sebastian.Herzog@i-med.ac.at
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| Organization name |
Medical University of Innsbruck, Biocenter
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| Department |
Institute of Developmental Immunology
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| Street address |
Innrain 80-82
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| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
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| Platforms (1) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA592072 |
| SRA |
SRP233482 |
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