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Poly(A)-specific ribonuclease sculpts the 3′ ends of microRNAs

ABSTRACT: Poly(A)-specific ribonuclease sculpts the 3′ ends of microRNAs

PROVIDER: PRJNA497399 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8074870.fastq.gz	Fastqsanger.gz
	SRR8074871.fastq.gz	Fastqsanger.gz
	SRR8074872.fastq.gz	Fastqsanger.gz
	SRR8074873.fastq.gz	Fastqsanger.gz
	SRR8074874.fastq.gz	Fastqsanger.gz

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poly(A) specific ribonuclease (PARN)-dependent trimming of H ACA box RNAs

Project description:Microarray comprising probe sets for miRNAs and other small RNAs was used to determine which and how many small RNAs are potential substrates of poly(A) specific ribonuclease (PARN) in U2OS cells . Hybridization probes were generated by oligo(dT) priming.

2012-02-17 | E-MEXP-3344 | biostudies-arrayexpress

Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs.

Project description:The 3' ends of metazoan microRNAs (miRNAs) are initially defined by the RNase III enzymes during maturation, but subsequently experience extensive modifications by several enzymatic activities. For example, terminal nucleotidyltransferases (TENTs) elongate miRNAs by adding one or a few nucleotides to their 3' ends, which occasionally leads to differential regulation of miRNA stability or function. However, the catalytic entities that shorten miRNAs and the molecular consequences of such shortening are less well understood, especially in vertebrates. Here, we report that poly(A)-specific ribonuclease (PARN) sculpts the 3' ends of miRNAs in human cells. By generating PARN knockout cells and characterizing their miRNAome, we demonstrate that PARN digests the 3' extensions of miRNAs that are derived from the genome or attached by TENTs, thereby effectively reducing the length of miRNAs. Surprisingly, PARN-mediated shortening has little impact on miRNA stability, suggesting that this process likely operates to finalize miRNA maturation, rather than to initiate miRNA decay. PARN-mediated shortening is pervasive across most miRNAs and appears to be a conserved mechanism contributing to the 3' end formation of vertebrate miRNAs. Our findings add miRNAs to the expanding list of noncoding RNAs whose 3' end formation depends on PARN.

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Investigation of transcript 3' ends in Campylobacter jejuni wildtype and ribonuclease mutants

Project description:Termination site sequencing (term-seq) (Dar et al., 2016) was used to map transcript 3' ends and potential processing sites in Campylobacter jejuni NCTC11168 wildtype and ribonuclease deletion strains.

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Poly(A)-specific ribonuclease sculpts the 3′ ends of microRNAs

Project description:The role of 3ʹ-5ʹ exonuclease, PARN, in the 3ʹ end miRNA transcriptome in human cells

2019-02-27 | GSE121466 | GEO

Investigation of transcript 3' ends in Campylobacter jejuni wildtype and ribonuclease mutants

Project description:Investigation of transcript 3' ends in Campylobacter jejuni wildtype and ribonuclease mutants

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Poly(A)-specific ribonuclease (PARN) mediates 3' end maturation of the telomerase RNA component

Project description:Mutations in the poly(A) ribonuclease (PARN) gene cause telomere diseases including familial idiopathic pulmonary fibrosis (IPF) and dyskeratosis congenita (DC)1,2, but how PARN deficiency impacts telomere maintenance is unclear. Here, using somatic cells and induced pluripotent stem (iPS) cells from DC patients with PARN mutations, we show that PARN is required for the 3′ end maturation of the telomerase RNA component (TERC). Patient cells as well as immortalized cells in which PARN is disrupted show decreased levels of TERC. Deep sequencing of TERC RNA 3′ termini reveals that PARN is required for removal of posttranscriptionally acquired oligo(A) tails that target nuclear RNAs for degradation. Diminished TERC levels and the increased oligo(A) forms of TERC are normalized by restoring PARN, which is limiting for TERC maturation in cells. Our results reveal a novel role for PARN in the biogenesis of TERC, and provide a mechanism linking PARN mutations to telomere diseases. mRNA sequencing of fibroblasts, induced pluripotent stem cells, and 293 cell line.

2015-09-08 | E-GEOD-71709 | biostudies-arrayexpress

Specific Parallel Analysis of RNA Ends

Project description:Specific Parallel Analysis of RNA Ends

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Poly(A)-specific ribonuclease (PARN) mediates 3' end maturation of the telomerase RNA component

2015-09-08 | GSE71709 | GEO

Mapping of internal monophosphate 5’ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains

Project description:The narrow-specificity endoribonuclease RNase III and the 5’ exonuclease RNase J1 have been recently found to be not essential in the Gram-positive model organism, Bacillus subtilis. In this study, we performed a global analysis of internal 5’ ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5’ monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions were direct targets of RNase III. A set of regular RNA-seq experiments were performed to investigate RNA profiles in these strains and used to account for the changes in RNA abundance indirectly caused by the loss of RNase III in PARE. The PARE analysis also revealed an accumulation of 3’-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. In addition, an endonuclease cleavage just two nucleotides downstream of the 16S rRNA 3’ end was discovered with PARE analysis. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic vs. endonucleolytic nature of 16S rRNA maturation

2016-01-27 | GSE77217 | GEO

Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs.

Project description:MicroRNAs (miRNAs) are typically generated as ~22-nucleotide double-stranded RNAs via the processing of precursor hairpins by the ribonuclease III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form an RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, occurs independently of Dicer and instead requires cleavage of the 3' arm of the pre-miR-451 precursor hairpin by Ago2. The 3' end of the Ago2-cleaved pre-miR-451 intermediate is then trimmed to the mature length by an unknown nuclease. Here, using a classical chromatographic approach, we identified poly(A)-specific ribonuclease (PARN) as the enzyme responsible for the 3'-5' exonucleolytic trimming of Ago2-cleaved pre-miR-451. Surprisingly, our data show that trimming of Ago2-cleaved precursor miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than the mature length. Our findings define the maturation step in the miRNA biogenesis pathway that depends on Ago2-mediated cleavage.

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