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

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

PROVIDER: PRJNA497375 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8074430.fastq.gz	Fastqsanger.gz
	SRR8074431.fastq.gz	Fastqsanger.gz
	SRR8074432.fastq.gz	Fastqsanger.gz
	SRR8074433.fastq.gz	Fastqsanger.gz
	SRR8074425.fastq.gz	Fastqsanger.gz

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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

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]

2019-02-08 | GSE121450 | GEO

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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N4-acetylcytidine modifies primary microRNAs for processing in cancer cells

Project description:N4-acetylcytidine modifies primary microRNAs for processing in cancer cells

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Angel2 phosphatase activity is required for non-canonical mitochondrial RNA processing in metazoa

Project description:Canonical RNA processing in mammalian mitochondria necessitates that tRNAs are recognised by nucleases to release flanking transcripts. However, not all mitochondrial transcripts are punctuated by tRNAs, and the mechanism and factors involved in their processing has remained unsolved. Here, we demonstrate that phosphatase activity of the carbon catabolite repressor 4 domain containing family member ANGEL2 is required for the hydrolysis of 3′ phosphates, resulting from non-canonical processing. Interaction studies in Drosophila further identify that members of the FAST kinase domain containing protein family are involved in the formation of these 3′ phosphates. Our results therefore resolve the mechanism of RNA processing in metazoan mitochondria, by defining the outstanding non-canonical processing mechanism.

2022-09-04 | GSE189750 | GEO

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

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

2019-02-08 | GSE121456 | GEO

N4-acetylcytidine modifies primary microRNAs for processing in cancer cells

Project description:N4 acetylcytidine (ac4C) modification mainly occurs on tRNA, rRNA, and mRNA, playing an important role in the expression of genetic information. However, it is still unclear whether microRNAs have undergone ac4C modification and their potential physiological and pathological functions. In this study, we identified that NAT10/THUMPD1 acetylates primary microRNAs (pri-miRNAs) with ac4C modification. Knockdown of NAT10 suppresses and augments the expression levels of mature miRNAs and pri-miRNAs, respectively. Molecular mechanism studies found that pri-miRNA ac4C promotes the processing of pri-miRNA into precursor miRNA (pre-miRNA) by enhancing the interaction of pri-miRNA and DGCR8, thereby increasing the biogenesis of mature miRNA. Knockdown of NAT10 attenuates the oncogenic characters of lung cancer cells by regulating miRNA production in cancers. Moreover, NAT10 is highly expressed in various clinical cancers and negatively correlated with poor prognosis. Thus, our results reveal that NAT10 plays a crucial role in cancer initiation and progression by modulating pri-miRNA ac4C to affect miRNA production, which would provide an attractive therapeutic strategy for cancers.

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Project description:Many ncRNAs serve as regulatory molecules in various physiological pathways. Distinct from protein-coding RNA expression, ncRNA expression is regulated solely by transcription and RNA processing/stability. Transcriptional regulation in ncRNA genes is thus important to be understood and is yet to be known completely. Previously, we identified that a subset of mammalian ncRNA genes is transcriptionally regulated by RNA Pol II promoter-proximal pausing and in a tissue-specific manner. In this study, human stimulus-inducible ncRNA genes were monitored to assess the function of P-TEFb, a master Pol II pausing regulator for protein-coding genes, in ncRNA transcription. Our findings indicate that the expression of many ncRNA genes is regulated by P-TEFb. Interestingly, a biphasic characteristic of P-TEFb inhibition in serum responsive ncRNA genes was observed: S2 phospho-Pol II was largely increased in the TSS (–300 to +300) whereas overall, it was decreased in the gene body (> +350) upon chemical inhibition of P-TEFb. In addition, the three representative ncRNAs, MALAT1, NEAT1, and XIST, were further analyzed for determining P-TEFb association. Taken together, we propose the transcriptional activation of many human ncRNAs utilizing pausing and releasing Pol II and the regulatory mechanism of transcriptional elongation of these genes requiring the function of P-TEFb.

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Angel2 phosphatase activity is required for non-canonical mitochondrial RNA processing in metazoa

Project description:Angel2 phosphatase activity is required for non-canonical mitochondrial RNA processing in metazoa

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