Similar Datasets
Project description:The effect of NF90 on the abundance of miRNAs was measured using small RNA-seq.
2020-05-01 | GSE132335 | GEO
Project description:The effect of NF90 on transcript abundance was measured using RNA-seq.
2020-05-01 | GSE132332 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. MicroRNAs are predicted to regulate the expression of more than 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 dsRNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of 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, 25 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 ac quisition of NF90 association, as determined by RNA EMSA. NF90-bound and modulated pri-miRNAs are embedded in introns of host genes and expression of several is concomitantly modulated, including an oncogene implicated in metastasis of hepatocellular carcinoma, TIAM2. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.
2020-05-01 | GSE132341 | GEO
Project description:DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein that plays essential roles in development and immunity. It was found to act in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at transcriptional and/or post-transcriptional levels. However, its global effect on miRNA accumulation still is not known. To determine the global effect of DDL on the accumulation of miRNAs and siRNAs, we compared the small RNA profile in ddl-1 with that in WS (Wild-type, WT). Small RNA libraries prepared from inflorescences of ddl-1 and WS was subjected to Illumina deep sequencing analyses. The results show that many miRNAs and siRNAs were reduced in abundance in ddl relative to WS in two biological replicates
2018-03-01 | GSE104885 | GEO
Project description:In plants, DICER-LIKE1 is a critical enzyme in the biogenesis pathway of plant miRNAs. Zinc-finger nucleases were used to generate single and double-mutants of soybean DCL1 homologs. We created several small RNA libraries to investigate the effect on miRNA abundance in these various mutants. RNAseq transcript data was also generated in order to investigate targets of those impacted miRNAs.
2016-03-04 | GSE76036 | GEO
Project description:CDC5 is a conserved DNA-binding protein that is required for development and immunity. It promotes the accumulation of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which repress gene expression. In this project, we aim to determine its global effect of on the accumulation of miRNAs and siRNAs. We compared the small RNA profile in cdc5-1 with that in Col (Wild-type, WT). Small RNA libraries prepared from inflorescences of cdc5-1 and Col was subjected to Illumina deep sequencing analyses. The results show that many miRNAs and siRNAs were reduced in abundance in cdc5 relative to Col in two biological replicates.
2018-03-01 | GSE104677 | GEO
Project description:MAC5A and MAC3 are conserved proteins that are required for development and immunity. They promotes the accumulation of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which repress gene expression. In this project, we aim to determine the global effect of MAC3 and MAC5Aon the accumulation of miRNAs and siRNAs. We compared the small RNA profile in mac3a mac3b and mac5a with that in Col (Wild-type, WT). Small RNA libraries prepared from inflorescences of mac3a mac3b, mac5a and Col was subjected to Illumina deep sequencing analyses. The results show that many miRNAs and siRNAs were reduced in abundance in mac5a and mac3a mac3b relative to Col in two biological replicates.
2018-03-01 | GSE106110 | GEO
Project description:Our previous study has showed that complex of NF90 and nuclear factor 45 (NF45) (NF90-NF45) inhibits miRNA biogenesis through negative regulation of primary-miRNA processing step. On the other hand, miRNAs, the biogenesis of which is regulated by NF90-NF45 in hepatocellular carcinoma, are not clear. Thus, to identify the miRNAs, we performed a miRNA array using RNAs extracted from control Huh7 cells and the cells depleted of NF90. Comparison of miRNA expression profile in one non-targeting control siRNA (siNTC)- or two independent siNF90-treated Huh7 cells.
2015-03-31 | E-GEOD-67411 | biostudies-arrayexpress
Project description:Our previous study has showed that complex of NF90 and nuclear factor 45 (NF45) (NF90-NF45) inhibits miRNA biogenesis through negative regulation of primary-miRNA processing step. On the other hand, miRNAs, the biogenesis of which is regulated by NF90-NF45 in hepatocellular carcinoma, are not clear. Thus, to identify the miRNAs, we performed a miRNA array using RNAs extracted from control Huh7 cells and the cells depleted of NF90.
2015-03-31 | GSE67411 | GEO