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The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE121456 | GEO | 2019/02/08

REPOSITORIES: GEO

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The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [ncRNA-Seq]

Project description:Protein phosphatase 4 (PP4) is a highly conserved serine/threonine protein phosphatase in yeast, plants, and animals. The composition and functions of the plant PP4 are poorly understood. Here, we uncovered previously unsuspected complexity of Arabidopsis PP4 and identified the composition of one form of PP4 containing the regulatory subunit PP4R3A. We showed that PP4R3A, together with one of two redundant catalytic subunit genes PPX1 and PPX2, promotes the biogenesis of microRNAs. PP4R3A is a chromatin-associated protein, interacts with RNA polymerase II (Pol II), and recruits Pol II to the promoters of MIR genes to promote their transcription. PP4R3A probably also promotes the cotranscriptional processing of miRNA precursors as it recruits the microprocessor component HYPONASTIC LEAVES1 (HYL1) to MIR genes and nuclear dicing bodies. Moreover, we showed that hundreds of introns exhibit splicing defects in pp4r3a mutants. Together, this study revealed a role of Arabidopsis PP4 in transcription and nuclear RNA metabolism.

2019-02-08 | GSE121453 | GEO

The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [RNA-Seq]

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The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis

Project description:The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis

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The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [RNA-Seq]

Project description:The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [RNA-Seq]

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The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [ncRNA-Seq]

Project description:The Protein Phosphatase 4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis [ncRNA-Seq]

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Coupled RNA processing and transcription of intergenic primary microRNAs.

Project description:The first step in microRNA (miRNA) biogenesis occurs in the nucleus and is mediated by the Microprocessor complex containing the RNase III-like enzyme Drosha and its cofactor DGCR8. Here we show that the 5'-->3' exonuclease Xrn2 associates with independently transcribed miRNAs and, in combination with Drosha processing, attenuates transcription in downstream regions. We suggest that, after Drosha cleavage, a torpedo-like mechanism acts on nascent long precursor miRNAs, whereby Xrn2 exonuclease degrades the RNA polymerase II-associated transcripts inducing its release from the template. While involved in primary transcript termination, this attenuation effect does not restrict clustered miRNA expression, which, in the majority of cases, is separated by short spacers. We also show that transcripts originating from a miRNA promoter are retained on the chromatin template and are more efficiently processed than those produced from mRNA or snRNA Pol II-dependent promoters. These data imply that coupling between transcription and processing promotes efficient expression of independently transcribed miRNAs.

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STV1, a ribosomal protein, binds primary microRNA transcripts to promote their interaction with the processing complex in Arabidopsis.

Project description:MicroRNAs (miRNAs) are key regulators of gene expression. They are processed from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by DNA-dependent polymerase II (Pol II). miRNA levels are precisely controlled to maintain various biological processes. Here, we report that SHORT VALVE 1 (STV1), a conserved ribosomal protein, acts in miRNA biogenesis in Arabidopsis A portion of STV1 localizes in the nucleus and binds pri-miRNAs. Using pri-miR172b as a reporter, we show that STV1 binds the stem-loop flanked by a short 5' arm within pri-miRNAs. Lack of STV1 reduces the association of pri-miRNAs with their processing complex. These data suggest that STV1 promotes miRNA biogenesis through facilitating the recruitment of pri-miRNAs to their processing complex. Furthermore, we show that STV1 indirectly involves in the occupancy of Pol II at the promoters of miRNA coding genes (MIR) and influences MIR promoter activities. Based on these results, we propose that STV1 refines the accumulation of miRNAs through its combined effects on pri-miRNA processing and transcription. This study uncovers an extraribosomal function of STV1.

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N6-methyladenosine marks primary microRNAs for processing.

Project description:The first step in the biogenesis of microRNAs is the processing of primary microRNAs (pri-miRNAs) by the microprocessor complex, composed of the RNA-binding protein DGCR8 and the type III RNase DROSHA. This initial event requires recognition of the junction between the stem and the flanking single-stranded RNA of the pri-miRNA hairpin by DGCR8 followed by recruitment of DROSHA, which cleaves the RNA duplex to yield the pre-miRNA product. While the mechanisms underlying pri-miRNA processing have been determined, the mechanism by which DGCR8 recognizes and binds pri-miRNAs, as opposed to other secondary structures present in transcripts, is not understood. Here we find in mammalian cells that methyltransferase-like 3 (METTL3) methylates pri-miRNAs, marking them for recognition and processing by DGCR8. Consistent with this, METTL3 depletion reduced the binding of DGCR8 to pri-miRNAs and resulted in the global reduction of mature miRNAs and concomitant accumulation of unprocessed pri-miRNAs. In vitro processing reactions confirmed the sufficiency of the N(6)-methyladenosine (m(6)A) mark in promoting pri-miRNA processing. Finally, gain-of-function experiments revealed that METTL3 is sufficient to enhance miRNA maturation in a global and non-cell-type-specific manner. Our findings reveal that the m(6)A mark acts as a key post-transcriptional modification that promotes the initiation of miRNA biogenesis.

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The PAF1 complex promotes 3‘ processing of pervasive transcripts

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-03-15 | GSE162843 | GEO

RNA binding protein DDX1 promotes subset of primary miRNA processing

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