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Series GSE141098 Query DataSets for GSE141098
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
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.
Overall design Comparison of control CRISPR/Cas9 cells and Safb1/Safb2 CRISPR/Cas9 cells (independent knockout clones per group; 2 different cell lines)
Contributor(s) Herzog S
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Submission date Nov 27, 2019
Last update date Dec 01, 2019
Contact name Sebastian Herzog
Organization name Medical University of Innsbruck, Biocenter
Department Institute of Developmental Immunology
Street address Innrain 80-82
City Innsbruck
ZIP/Postal code 6020
Country Austria
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (12)
GSM4194965 Ramos_control_clone_1
GSM4194966 Ramos_control_clone_2
GSM4194967 Ramos_control_clone_3
BioProject PRJNA592072
SRA SRP233482

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE141098_293T_edgeR_output.txt.gz 34.7 Kb (ftp)(http) TXT
GSE141098_Ramos_edgeR_output.txt.gz 42.4 Kb (ftp)(http) TXT
GSE141098_total_reads_293T_all_samples.txt.gz 14.2 Kb (ftp)(http) TXT
GSE141098_total_reads_Ramos_all_samples.txt.gz 16.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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