Ontology highlight
ABSTRACT:
PROVIDER: PRJNA482875 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7594410_1.fastq.gz | Fastqsanger.gz | |||
| SRR7594410_2.fastq.gz | Fastqsanger.gz | |||
| SRR7594411_1.fastq.gz | Fastqsanger.gz | |||
| SRR7594411_2.fastq.gz | Fastqsanger.gz | |||
| SRR7594402.fastq.gz | Fastqsanger.gz |
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Project description:Ribonuclease (RNase) MRP is a conserved RNA-based enzyme that is essential for maturation of ribosomal RNA (rRNA) in eukaryotes. However, the composition and RNA substrate specificity of this multisubunit ribonucleoprotein complex in higher eukaryotes remain a mystery. Here, we identify NEPRO and C18ORF21 as constitutive subunits of metazoan RNase MRP. Both proteins are specific to RNase MRP and are the only ones distinguishing this enzyme from the closely related RNase P, which selectively cleaves transfer RNA-like substrates. We find that NEPRO and C18ORF21 each form a complex with all other subunits of RNase MRP, stabilize its catalytic RNA, and are required for rRNA maturation and cell proliferation. We harness our discovery to identify a full suite of in vivo RNA targets of each enzyme, including positions of potential cleavage sites at nucleotide resolution. These findings resolve the general composition of metazoan RNase MRP, illuminate its RNA binding specificity, and provide valuable assets for functional exploration of this essential eukaryotic enzyme.
2025-08-05 | GSE290995 | GEO
Project description:Mechanistic studies have revealed ribonuclease (RNase) MRP, a conserved RNA-based enzyme, is crucial for the maturation of ribosomal RNA in eukaryotes. However, the composition and RNA substrate specificity of this multisubunit ribonucleoprotein complex in higher eukaryotes remain unknown. Here, we identify NEPRO and C18ORF21 as constitutive subunits of metazoan RNase MRP. Both proteins are specific to RNase MRP and are the only ones distinguishing this enzyme from the closely related RNase P, which selectively cleaves transfer RNA-like substrates. We find that NEPRO and C18ORF21 each form a complex with all other subunits of RNase MRP, stabilize its catalytic RNA, and are required for rRNA maturation and cell proliferation. We harness our discovery to identify a full suite of in vivo RNA targets of each enzyme, including positions of potential cleavage sites at nucleotide resolution. In Summary, this project shows the general composition of metazoan RNase MRP, illuminate its RNA binding specificity, and provide valuable assets for functional exploration of this essential eukaryotic enzyme.
2025-09-15 | PXD061658 | Pride
Project description:RNase MRP and RNase P are evolutionarily related complexes that facilitate rRNA and tRNA biogenesis, respectively. The two enzymes share nearly all protein subunits and have evolutionarily related catalytic RNAs. Notably, RNase P includes a unique subunit, RPP21, whereas no RNase MRP-specific proteins have been found in humans, limiting molecular analyses of RNase MRP function. Here, we identify the RNase MRP-specific proteins, C18orf21/RMP24 and NEPRO/RMP64. C18orf21/RMP24 and RPP21 display significant structural homology, but we identify specific regions that drive interactions with their respective complexes. By targeting these RNase MRP-specific subunits, our functional analysis reveals that RNase MRP is essential rRNA processing and preferentially required for 40S ribosome biogenesis. Finally, we determine that disease-associated mutations in RMP64 impair its association with RNase MRP subunits. Together, our findings elucidate the molecular determinants of RNase MRP function and underscore its critical role in ribosome biogenesis and disease.
2025-10-23 | PXD065571 | Pride
Project description:RNase P and RNase MRP are evolutionarily-related ribonucleoprotein complexes that share common protein subunits, but carry out distinct site-specific endonuclease activities. Here, we identify two RNase MRP-specific proteins C18orf21 (RMP24) and Nepro (RMP64). C18orf21 contains a structurally similar N-terminal domain to Rpp21, but has a distinct subcellular localization and RNA-binding specificity, allowing C18orf21 to uniquely associate with RNase MRP. We ectopically express C18orf21 (RNase MRP specific), Nepro (RNase MRP specific), Rpp21 (RNase P specific), and Rpp14 (shared subunit), with a C-terminal GFP and performed RIP-seq to identify bound RNAs. Our data provide a model to understand C18orf21 physical interactions along with its role in ribosomal RNA processing. In addition to this, we knock out C18orf21, Rpp21, and Rpp14 and analyze their transcriptome. We additionally analyze rRNA intermediates in knockout cells.
2025-08-11 | GSE279079 | GEO
Project description:To identify mRNA substrates for the human RNase MRP complex, we examined the effects of siRNA-mediated depletion of RNase MRP (and RNase P) on the transcriptome of HEp-2 cells. The expression of two RNase MRP protein components, hPop1 and Rpp40, was knocked-down and after 48 hours mRNA was isolated from these cells as well as from cells transfected with an siRNA targeting the GFP mRNA (siEGFP), which was used as a control. The expression levels of mRNAs were analyzed on a genome-wide scale using 21K microarrays.
2011-04-01 | E-TABM-981 | biostudies-arrayexpress
Project description:Identification of RNAs containing TOP3B cleavage complexes
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Project description:The N6-methyladenosine (m6A) is the most abundant internal modification in almost all eukaryotic messenger RNAs, and is dynamically regulated. Therefore, identification of m6A readers is especially important in determining the cellular function of m6A. YTHDF2 has recently been characterized as the first m6A reader that regulates the cytoplasmic stability of methylated RNA. Here we show that YTHDC1 is a nuclear m6A reader and report the crystal structure of the YTH domain of YTHDC1 bound to m6A-containing RNA. We further determined the structure of another YTH domain, YTHDF1, and found that the YTH domain utilizes a conserved aromatic cage to specifically recognize the methyl group of m6A. Our structural characterizations of the YTHDC1-m6A RNA complex also shed light on the molecular basis for the preferential binding of the GG(m6A)C sequence by YTHDC1 and confirm the YTH domain as a specific m6A RNA reader. PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) was applied to human YTHDC1 protein to identify its binding sites.
2014-09-18 | E-GEOD-58352 | biostudies-arrayexpress
Project description:Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability and discordant abundance among co-transcribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity towards the cggR-gapA operon, an event that differentiates the expression of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified that is also required for this cleavage in vivo, raising the possibility that it is an accessory factor acting to regulate RNase Y. However, whether the Y-complex is broadly required for RNase Y activity is unknown. Here we used end-enrichment RNA sequencing (Rend-seq) to globally identify operon mRNAs that undergo maturation post-transcriptionally by RNase Y and the Y-complex. We found that the Y-complex is required for the majority of RNase Y-mediated mRNA maturation events and affects riboswitch abundance in B. subtilis. In contrast, noncoding RNA maturation by RNase Y often do not require the Y-complex. Furthermore, deletion of RNase Y has more pleiotropic effects on the transcriptome and cell growth than deletions of the Y-complex. We propose that the Y-complex is a specificity factor for RNase Y, with evidence that its role is broadly distributed across low-GC Firmicutes.
2018-05-12 | GSE108295 | GEO
Project description:Abstract: Ribonuclease E (RNase E) has a key role in mRNA degradation and the processing of catalytic and structural RNAs in E. coli. We report the discovery of an evolutionarily conserved 17.4 kDa protein, here named RraA (regulator of ribonuclease activity A) that binds to RNase E and inhibits RNase E endonucleolytic cleavages without altering cleavage site specificity or interacting detectably with substrate RNAs. Overexpression of RraA circumvents the effects of an autoregulatory mechanism that normally maintains the RNase E cellular level within a narrow range, resulting in the genome-wide accumulation of RNase E-targeted transcripts. While not required for RraA action, the C-terminal RNase E region that serves as a scaffold for formation of a multiprotein degradosome complex modulates the inhibition of RNase E catalytic activity by RraA. Our results reveal a possible mechanism for the dynamic regulation of RNA decay and processing by inhibitory RNase binding proteins. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4383 | GEO
Project description:The RNase III enzyme, DICER, is instrumental in the production of small RNAs, including miRNAs and siRNAs, by cleaving their precursors, such as pre-miRNAs, shRNAs, and long duplex RNAs. Utilizing High-throughput (HT) cleavage assays, our study delves into the cleavage activity of DICER. We challenge the widely accepted 2-nt loop counting rule in the previous study, revealing a divergent mechanism, the bipartite base pairing rule. This rule directs DICER's cleavage sites via the RNase III domain. Moreover, we demystify the recognition mechanism of the previously identified YCR motif. Building on this understanding, a secondary YCR motif that also influences DICER's cleavage sites has been discovered. We also address a long-debated issue concerning DICER's cleavage sites on long stem RNAs, such as pre-siRNAs or long shRNAs/pre-miRNAs. Our study shows that the dsRBD plays a crucial role in determining the cleavage sites of DICER in long-stem RNAs. In sum, our research provides a comprehensive understanding of several fundamental DICER mechanisms, challenging the long-standing model of the loop counting rule. This newfound knowledge reshapes our understanding of DICER's mechanisms, providing a robust foundation for future studies investigating the vast number of DICER mutations linked to various diseases.
2024-06-01 | GSE252433 | GEO