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Effect of DGCR8 knockout and heterozygosity pri-miRNA processing in PA-1 cells

ABSTRACT: In this dataset we extract and sequence chromatin-associated RNA to study the effect of DGCR8 knockout and heterozygosity on pri-miRNA processing

ORGANISM(S): Homo sapiens

PROVIDER: GSE197469 | GEO | 2025/02/14

REPOSITORIES: GEO

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Effect of DGCR8 knockout and heterozygosity pri-miRNA processing in PA-1 cells

Project description:Effect of DGCR8 knockout and heterozygosity pri-miRNA processing in PA-1 cells

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Effect of DGCR8 heterozygosity on steady state RNA levels in embryonic teratocarcinoma PA-1 cells

Project description:In this dataset we use total RNA-seq to study the effect of DGCR8 heterozygosity on steady state RNA levels

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Effect of DGCR8 heterozygosity on steady state miRNA levels in embryonic teratocarcinoma PA-1 cells

Project description:In this dataset we use small RNA-seq to study the effect of DGCR8 heterozygosity on steady state miRNA levels

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The DGCR8-UGU interaction in microRNA biogenesis

Project description:Human Microprocessor is a trimeric complex composed of the RNase III enzyme, DROSHA, and a dimer of DGCR8 (its cofactor). Microprocessor initiates the biogenesis of microRNA by processing primary microRNAs (pri-miRNAs), during which, its cleavage efficiency and accuracy are enhanced because DGCR8 interacts with the apical UGU motif of pri-miRNAs. However, the mechanism of DGCR8-UGU interaction and influence of this interaction on the expression of cellular miRNA are still elusive. In this study, we demonstrated that the Rhed domain (i.e., the RNA-binding heme domain, amino acids 285-478) of DGCR8 is sufficient to recognize and interact with UGU. In addition, we identified three amino acid residues in Rhed (amino acids 361-363), which are critical for the UGU interaction, and we showed that these residues are essential for the Microprocessor complex to accurately and efficiently process pri-miRNAs in vitro. Furthermore, we found that within the DGCR8 dimer, the UGU-binding site from just one monomer is capable of discriminating between UGU- and non-UGU-containing pri-miRNAs. Finally, we showed that these amino acids are more important for the expression of UGU miRNAs than non-UGU miRNAs in human cells. This study improves our understanding of the substrate-recognizing mechanism of DGCR8, and implicates the roles of this recognition in differentiating miRNA expression in human cells.

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Effect of DGCR8 heterozygosity on steady state RNA levels in embryonic teratocarcinoma PA-1 cells

Project description:Effect of DGCR8 heterozygosity on steady state RNA levels in embryonic teratocarcinoma PA-1 cells

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Effect of DGCR8 heterozygosity on steady state miRNA levels in embryonic teratocarcinoma PA-1 cells

Project description:Effect of DGCR8 heterozygosity on steady state miRNA levels in embryonic teratocarcinoma PA-1 cells

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DGCR8-dependent efficient pri-miRNA processing of human pri-miR-9-2.

Project description:Microprocessor complex, including DiGeorge syndrome critical region gene 8 (DGCR8) and DROSHA, recognizes and cleaves primary transcripts of microRNAs (pri-miRNAs) in the maturation of canonical miRNAs. The study of DGCR8 haploinsufficiency reveals that the efficiency of this activity varies for different miRNA species. It is thought that this variation might be associated with the risk of schizophrenia with 22q11 deletion syndrome caused by disruption of the DGCR8 gene. However, the underlying mechanism for varying action of DGCR8 with each miRNA remains largely unknown. Here, we used in vivo monitoring to measure the efficiency of DGCR8-dependent microprocessor activity in cultured cells. We confirmed that this system recapitulates the microprocessor activity of endogenous pri-miRNA with expression of a ratiometric fluorescence reporter. Using this system, we detected mir-9-2 as one of the most efficient targets. We also identified a novel DGCR8-responsive RNA element, which is highly conserved among mammalian species and could be regulated at epi-transcriptome (RNA modification) level. This unique feature between DGCR8 and pri-miR-9-2 processing may suggest a link to the risk of schizophrenia.

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Targeted determination of pri-miRNA processing

Project description:Targeted sequencing at Microprocessor cleavage sites in pri-miRNAs to determine processing efficiency of several pri-miRNAs in vivo in one experiment

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Targeted determination of pri-miRNA processing

Project description:Targeted sequencing at Microprocessor cleavage sites in pri-miRNAs to determine processing efficiency of several pri-miRNAs in vivo in one experiment

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Genome wide identification of targets of the drosha-pasha/DGCR8 complex

Project description:Drosha is a type III RNAse, which plays a critical role in miRNA biogenesis. Drosha and its double-stranded RNA-binding partner protein Pasha/DGCR8 likely recognize and cleave miRNA precursor RNAs or pri-miRNA hairpins co-transcriptionally. To identify RNAs processed by Drosha, we used tiling microarrays to examine transcripts after depletion of drosha mRNA with dsRNA in Drosophila Schneider S2 cells. This strategy identified 137 Drosha-regulated RNAs, including 11 putative pri-miRNAs comprising 15 annotated miRNAs. Most of the identified pri-miRNAs seem extremely large, >10 kilobases as revealed by both the Drosha knock down strategy and by RNA PolII chromatin IP followed by Drosophila tiling microarrays. Surprisingly, more than a hundred additional RNAs not annotated as miRNAs are under Drosha control and are likely to be direct targets of Drosha action. This is because many of them encode annotated genes, and unlike bona fide pri-miRNAs, they are not affected by depletion of the miRNA processing factor, dicer-1. Moreover, application of the evofold analysis software indicates that at least 25 of the Drosha-regulated RNAs contain evolutionarily conserved hairpins similar to those recognized by the Drosha-Pasha/DGCR8 complex in pri-miRNAs. One of these hairpins is located in the 5′ UTR of both pasha and mammalian DGCR8. These observations suggest that a negative feedback loop acting on pasha mRNA may regulate the miRNA-biogenesis pathway: i.e., excess Drosha cleaves pasha/DGCR8 primary transcripts and leads to a reduction in pasha/DGCR8 mRNA levels and Pasha/DGCR8 synthesis. Keywords: time course, ChIP-chip

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