Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading
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PROVIDER: PRJNA640818 | ENA |
REPOSITORIES: ENA
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Project description:Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading[RNA-seq]
| PRJNA640822 | ENA
Project description:Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading [sRNA-seq]
| PRJNA640823 | ENA
Project description:MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing.
2022-02-26 | GSE152910 | GEO
Project description:MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing.
2022-02-26 | GSE152909 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-02-26 | GSE152911 | GEO
Project description:Circular RNAs (circRNAs) are natural outputs of eukaryotic transcription and RNA processing and have emerged as critical regulators in physiology and human diseases. Although a series of cis-elements and trans-factors are reported to globally regulate circRNA biogenesis, most of these regulations are unconserved or at most mammalian conserved. Here, using a genome-wide CRISPR knockout screen, we have identified an evolutionarily conserved polyadenosine RNA-binding protein ZC3H14 to regulate circRNA biogenesis in eukaryotes. Mechanistically, ZC3H14 associates with spliceosome to bind to 3' and 5' exon-intron boundaries of circularized exons, and forms a dimer to promote circRNA biogenesis. ZC3H14 knockout mice exhibit disrupted spermatogenesis and reduced testicular circRNA levels. Additionally, human ZC3H14 is associated with male infertility. Our findings reveal a conserved requirement for ZC3H14/Nab2 in the modulation of eukaryotic backsplicing and link ZC3H14 along with circRNAs to mammalian testicular disorders.
2024-02-10 | GSE254916 | GEO
Project description:Plant microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, AGO1 also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5’-3’ RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5’-3’ exonuclease genes XRN2 and XRN3, we found that a large number of 21-nt risiRNAs were generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlated with pre-rRNA processing defects in these mutants. We also show that these risiRNAs were loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation.
2019-10-08 | GSE133411 | GEO
Project description:Plant microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, AGO1 also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5’-3’ RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). In mutants of FRY1 and the nuclear 5’-3’ exonuclease genes XRN2 and XRN3, we found that a large number of 21-nt risiRNAs were generated through an endogenous siRNA biogenesis pathway. The production of risiRNAs correlated with pre-rRNA processing defects in these mutants. We also show that these risiRNAs were loaded into AGO1, causing reduced loading of miRNAs. This study reveals a previously unknown link between rRNA processing and miRNA accumulation.
2019-10-08 | GSE126482 | GEO
Project description:Drosophila Argonaute-1 and Argonaute-2 differ in function and small RNA content. AGO2 binds to siRNAs, whereas AGO1 is almost exclusively occupied by microRNAs. microRNA duplexes are intrinsically asymmetric, with one strand, the miR strand, preferentially entering AGO1 to recognize and regulate the expression of target mRNAs. The other strand, miR*, has been viewed as a by-product of microRNA biogenesis. Here, we show that miR*s are often loaded as functional species into AGO2. This indicates that each microRNA precursor can potentially produce two mature small RNA strands that are differentially sorted within the RNAi pathway. miR* biogenesis depends upon the canonical microRNA pathway, but loading into AGO2 is mediated by factors traditionally dedicated to siRNAs. By inferring and validating hierarchical rules that predict differential AGO loading, we find that intrinsic determinants, including structural and thermodynamic properties of the processed duplex, regulate the fate of each RNA strand within the RNAi pathway. These were independently processed and sequenced using the Illumina GAII platform. In total, five libraries were analyzed.
2009-11-15 | E-GEOD-17734 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are processed from longer precursors with fold-back structures. While animal MIRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach (SPARE) to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the evolutionary conserved miRNAs present in Arabidopsis thaliana. We found that plant MIRNAs are processed by four mechanisms, depending on the sequential direction of the processing machinery and the number of cuts required to release the miRNA. Classification of the precursors according to their processing mechanism revealed specific structural determinants for each group. We found that the complexity of the miRNA processing pathways occurs in both ancient and evolutionary young sequences, and that members of the same family can be processed in different ways. We observed that different structural determinants compete for the processing machinery and that alternative miRNAs can be generated from a single precursor. The results provide a mechanistic explanation for the structural diversity of MIRNA precursors in plants and new insights towards the understanding of the biogenesis of small RNAs. Approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of conserved and young miRNAs present in Arabidopsis thaliana. MiRNA processing intermediates profiles of Wild type and Fiery mutants Arabidopsis plants were analyzed, using Illumina GAIIx.
2013-06-12 | E-GEOD-46429 | biostudies-arrayexpress