SLIRP mediated rRNA 2'-O-methylation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA548975 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9305721.fastq.gz | Fastqsanger.gz | |||
| SRR9305722.fastq.gz | Fastqsanger.gz | |||
| SRR9305723.fastq.gz | Fastqsanger.gz | |||
| SRR9305724.fastq.gz | Fastqsanger.gz | |||
| SRR9305725.fastq.gz | Fastqsanger.gz |
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Project description:We determined the methylation landscape on rRNA of Leishmania major.
2025-07-06 | PXD053706 | JPOST Repository
Project description:SLIRP is a versatile protein that can interact with stem-loop structure in RNA and with G quadruplex DNA. By using a quantitative proteomic experiment, we found that SLIRP interacts with the majority of the human helicase proteome. We found that these interactions facilitate 2'-O-methylation of rRNA and promote protein translation. Hence, we uncovered a novel function of SLIRP protein and offered novel mechanistic insights into its function as a RNA chaperone and into the regulation of 2'-O-methylation of rRNA.
2019-06-24 | GSE132789 | GEO
Project description:Ribosomal RNAs (rRNAs) are main effectors of mRNA decoding, peptide-bond formation and ribosome dynamics during translation. Ribose 2'-O-methylation is the most abundant rRNA chemical modification, and display a complex pattern in rRNA. We globally challenged rRNA 2'-O-Me by inhibiting the rRNA methyl-transferase fibrillarin (FBL) in human cells. Since FBL participates in rRNA processing, we wonder if FBL knockdown could alter the assembly of ribosomes.
2018-04-09 | PXD007244 | Pride
Project description:Regulation of RNA helicase activity, often accomplished by protein cofactors, is essential to ensure target specify within the complex cellular environment. The largest family of RNA helicase cofactors are the G-patch proteins, but the cognate RNA helicases and cellular functions of numerous human G-patch proteins remain elusive. Here, we discover that GPATCH4 is a stimulatory cofactor of DHX15 that interacts with the helicase in the nucleolus via residues in its G-patch domain. We reveal that GPATCH4 associates with pre-ribosomal particles, and crosslinks to the transcribed ribosomal DNA locus and precursor ribosomal RNAs as well as binding to small nucleolar- and small Cajal body-associated- RNAs that guide rRNA and snRNA modifications. Global analysis of rRNA and snRNA 2’-O-methylation revealed that lack of GPATCH4 impairs methylation at various sites. We further demonstrated that the regulation of 2’-O-methylation by GPATCH4 is both dependent on, and independent of, its interaction with DHX15. Intriguingly, the ATPase activity of DHX15 is necessary for efficient methylation of DHX15-dependent sites, suggesting a function of DHX15 in regulating snoRNA-guided 2’-O-methylation of rRNA that requires activation by GPATCH4. Overall, our findings extend knowledge on RNA helicase regulation by G-patch proteins and also provide important new insights into the mechanisms regulating installation of rRNA and snRNA modifications, which are essential for ribosome function and pre-mRNA splicing.
2025-08-15 | PXD043301 | Pride
Project description:RNA helicases play important roles in diverse aspects of RNA metabolism through their functions in remodelling ribonucleoprotein complexes (RNPs), such as pre-ribosomes. Here, we show that the DEAD box helicase Dbp3 is required for efficient processing of the U18 and U24 intron-encoded snoRNAs and 2'-O-methylation of various sites within the 25S ribosomal RNA (rRNA) sequence. Furthermore, numerous box C/D snoRNPs accumulate on pre-ribosomes in the absence of Dbp3. Many snoRNAs guiding Dbp3-dependent rRNA modifications have overlapping pre-rRNA basepairing sites and therefore form mutually exclusive interactions with pre-ribosomes. Analysis of the distribution of these snoRNAs between pre-ribosome-associated and 'free' pools demonstrated that many are almost exclusively associated with pre-ribosomal complexes. Our data suggest that retention of such snoRNPs on pre-ribosomes when Dbp3 is lacking may impede rRNA 2'-O-methylation by reducing the recycling efficiency of snoRNPs and by inhibiting snoRNP access to proximal target sites. The observation of substoichiometric rRNA modification at adjacent sites suggests that the snoRNPs guiding such modifications likely interact stochastically rather than hierarchically with their pre-rRNA target sites. Together, our data provide new insights into the dynamics of snoRNPs on pre-ribosomal complexes and the remodelling events occurring during the early stages of ribosome assembly.
2021-03-18 | GSE155720 | GEO
Project description:Fibrillarin (FBL) is a dual function nucleolar protein which catalyses 2´-O methylation of pre-rRNA and methylation of histone H2A at glutamine 104 (H2AQ104me). The mechanisms that regulate FBL activity are unexplored. Here we show that FBL is acetylated at several lysine residues by the acetyltransferase CBP and deacetylated by SIRT7. While reversible acetylation does not impact FBL-mediated pre-rRNA methylation, hyperacetylation impairs the interaction of FBL with histone H2A and chromatin, thereby compromsing H2AQ104 methylation (H2AQ104me) and rDNA transcription. SIRT7-dependent deacetylation of FBL ensures H2AQ104me and high levels of rRNA synthesis during interphase. At the onset of mitosis, nucleolar disassembly is accompanied by hyperacetylation of FBL, loss of H2AQ104me and repression of Pol I transcription. H2AQ104me and transcriptional activity are restored by overexpression of an acetylation-deficient but not by an acetylation-mimicking FBL mutant. The results reveal that SIRT7-dependent deacetylation impacts nucleolar activity by a FBL-driven circuitry that mediates cell cycle-dependent fluctuation of rDNA transcription.
2018-12-12 | GSE115360 | GEO
Project description:N6-methyladenosine (m6A) plays critical roles in a wide range of physiological and pathological processes, and m6A methyltransferases are still being discovered for different RNA species in mammals. Here report a new m6A methyltransferase ZCCHC4 that methylates ribosomal RNA (rRNA) and interacts with messenger RNA (mRNA), ZCCHC4 has methylation activity on rRNA with a preference for AAC consensus sequence. ZCCHC4 can affect global translation through m6A methylation, mostly on 28S rRNA.
2018-09-25 | GSE102336 | GEO
Project description:In this study we profiled the complete repertoire of 2'-O-methylation sites present in the rRNA and a subset of small RNAs of Leishmania major rRNA using RibOxi-seq.
2024-05-01 | GSE186878 | GEO
Project description:Since REIIBP contains a complete SET domain and is associated with pre-rRNA processing factors in the nucleolus, we ask if REIIBP may methylate pre-rRNA processing factors in the nucleolus.To investigate this, we conducted LC-MS/MS analysis to identify potential protein substrates for methylation.
2025-10-06 | PXD062856 | Pride
Project description:The interplay between multiple transcription factors precisely regulates eukaryotic transcription. Here, we report that the protein methyltransferases, MLL2 and PRMT1, interact directly and act collectively to regulate gene expression. PRMT1 binds to the N-terminal region of MLL2, considered an intrinsically disordered region, and methylates multiple arginine residues within its RGG/RG motifs. Notably, overexpression of PRMT1 decreased poly-ubiquitylation of MLL2, whereas mutations on methylation sites in MLL2 increased MLL2 poly-ubiquitylation, suggesting that PRMT1-mediated methylation stabilizes MLL2. MLL2 and PRMT1 cooperatively stimulated the expression of a chromosomal reporter gene in a PRMT1-mediated, MLL2-methylation–dependent manner. RNA-seq analysis found that MLL2 and PRMT1 jointly regulate the expression of genes involved in cell membrane and extracellular matrix functions, and depletion of either resulted in impaired cell migration and invasion. Our study provides evidence that PRMT1-mediated MLL2 methylation regulates MLL2 protein stability and the expression of their target genes.
2024-10-21 | PXD055018 | JPOST Repository