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Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes
Published on: April 12, 2015
NF90 modulates processing of a subset of human pri-miRNAs
Giuseppa Grasso1, Takuma Higuchi2, Victor Mac1
1UMR9002 CNRS-UM, Institut de Génétique Humaine-Université de Montpellier, Gene Regulation lab, Montpellier 34396, France.
Abstract:
MicroRNAs (miRNAs) are predicted to regulate the expression of >60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The double stranded RNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of primary miRNAs (pri-miRNAs). Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 22 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to acquisition of NF90 association, as determined by RNA electrophoretic mobility shift assay (EMSA). NF90-bound and downregulated pri-miRNAs are embedded in introns of host genes and expression of several host genes is concomitantly reduced. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.
Insights
The double-stranded RNA-binding protein NF90 regulates microRNA (miRNA) biogenesis by binding to specific pri-miRNAs. Loss of NF90 increases mature miRNA production from these targets, impacting gene expression.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- MicroRNAs (miRNAs) are crucial regulators of gene expression, implicated in numerous biological processes and cancer.
- Dysregulation of miRNA biogenesis is a key feature of cancer, necessitating further research into regulatory mechanisms.
- The double-stranded RNA-binding protein NF90 was previously known to compete with Microprocessor for a few primary miRNAs (pri-miRNAs).
Purpose of the Study:
- To investigate the broader role of NF90 in pri-miRNA biogenesis.
- To identify pri-miRNAs regulated by NF90 and understand the mechanism of regulation.
Main Methods:
- Genome-wide approaches to identify NF90-bound pri-miRNAs.
- RNA electrophoretic mobility shift assay (EMSA) to assess NF90 binding to pri-miRNAs with varying stability.
- Analysis of mature miRNA abundance following NF90 depletion.
- Investigation of the genomic location and host gene expression of NF90-targeted pri-miRNAs.
Main Results:
- NF90 associates with the stem region of 38 pri-miRNAs, largely independent of Microprocessor.
- Loss of NF90 leads to increased mature miRNA production from 22 of these bound pri-miRNAs.
- NF90 preferentially binds to highly stable pri-miRNAs.
- NF90-bound pri-miRNAs are often intronic, and their host gene expression is reduced.
Conclusions:
- NF90 plays a significant, widespread role in regulating pri-miRNA biogenesis.
- NF90 controls the processing of a subset of highly stable, intronic pri-miRNAs.
- NF90-mediated regulation of intronic miRNAs may impact host gene expression.
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