Similar Datasets
Project description:2’-O-methylation (2’-O-me) is one of the most abundant covalent modifications in ribosomal RNAs (rRNAs) vital for the functionality of the ribosome, in particular, translational regulation. Aberrant 2’-O-me causes developmental defects in animals and is associated with human cancer. However, a lack of systematic delineation of 2’-O-me sites significantly impedes our understanding of 2’-O-me in plants. Here we report the global profiling of 2’-O-me in Arabidopsis rRNAs, leading to the identification of 221 2’-O-me sites, including 137 novel ones compared to the Arabidopsis database that documents predicted rRNA 2-O-me sites. We show that 65% of yeast and 53% of human 2’-O-me sites are conserved in Arabidopsis. We discover not only 2’-O-me guided by box C/D snoRNAs, but also unprecedentedly a prevalent snoRNA-independent mechanism in Arabidopsis: 48% of the 2’-O-me sites are devoid of snoRNAs, including some conserved sites where snoRNAs are indispensable in human and yeast. Through HITS-CLIP (high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation), we show that Fibrillarin (FIB1) and FIB2 predominantly associate with box C/D snoRNAs in vivo and uncover previously unknown snoRNAs. By generating and analyzing mutants in the FIB genes, we demonstrate that they are responsible for the ribose methylation at many rRNA sites regardless of their snoRNA-dependent or independent nature. We report, for the first time, extensive 2’-O-me of chloroplast rRNAs and, intriguingly, the dependence of FIB1/2 at some sites. Our studies reveal the landscape of 2’-O-me in nuclear and chloroplast rRNAs and provide novel insights into the deposition of rRNA 2’-O-me.
2024-12-31 | GSE150455 | GEO
Project description:2’-O-methylation (2’-O-me) is one of the most abundant covalent modifications in ribosomal RNAs (rRNAs) vital for the functionality of the ribosome, in particular, translational regulation. Aberrant 2’-O-me causes developmental defects in animals and is associated with human cancer. However, a lack of systematic delineation of 2’-O-me sites significantly impedes our understanding of 2’-O-me in plants. Here we report the global profiling of 2’-O-me in Arabidopsis rRNAs, leading to the identification of 221 2’-O-me sites, including 137 novel ones compared to the Arabidopsis database that documents predicted rRNA 2-O-me sites. We show that 65% of yeast and 53% of human 2’-O-me sites are conserved in Arabidopsis. We discover not only 2’-O-me guided by box C/D snoRNAs, but also unprecedentedly a prevalent snoRNA-independent mechanism in Arabidopsis: 48% of the 2’-O-me sites are devoid of snoRNAs, including some conserved sites where snoRNAs are indispensable in human and yeast. Through HITS-CLIP (high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation), we show that Fibrillarin (FIB1) and FIB2 predominantly associate with box C/D snoRNAs in vivo and uncover previously unknown snoRNAs. By generating and analyzing mutants in the FIB genes, we demonstrate that they are responsible for the ribose methylation at many rRNA sites regardless of their snoRNA-dependent or independent nature. We report, for the first time, extensive 2’-O-me of chloroplast rRNAs and, intriguingly, the dependence of FIB1/2 at some sites. Our studies reveal the landscape of 2’-O-me in nuclear and chloroplast rRNAs and provide novel insights into the deposition of rRNA 2’-O-me.
2024-12-31 | GSE150454 | GEO
Project description:Systematic mapping of 2’-O-methylation sites in rRNAs implicates new strategy for ribose methylation in Arabidopsis
| PRJNA632477 | ENA
Project description:Systematic mapping of 2’-O-methylation sites in rRNAs implicates new strategy for ribose methylation in Arabidopsis [20ME]
| PRJNA632481 | ENA
Project description:Systematic mapping of 2’-O-methylation sites in rRNAs implicates new strategy for ribose methylation in Arabidopsis [FIB CLIP]
| PRJNA632480 | ENA
Project description:Eukaryotic rRNAs and snRNAs are decorated with abundant 2'-O-methylated nucleotides (Nm) that are predominantly synthesized by box C/D snoRNA-guided enzymes. In the model plant Arabidopsis thaliana, C/D snoRNAs have been well categorized, but there is a lack of systematic mapping of Nm. Here, we applied RiboMeth-seq to profile Nm in cytoplasmic, chloroplast and mitochondrial rRNAs and snRNAs. We identified 111 Nm in cytoplasmic rRNAs and 19 Nm in snRNAs and assigned guide for majority of the detected sites using an updated snoRNA list. At least four sites are directed by guides with multiple specificities as shown in yeast. We found that C/D snoRNAs frequently form extra pairs with nearby sequences of methylation sites, potentially facilitating the substrate binding. Chloroplast and mitochondrial rRNAs contain five almost identical methylation sites, including two novel sites mediating ribosomal subunit joining. Deletion of FIB1 or FIB2 gene reduced the accumulation of C/D snoRNA and rRNA methylation with FIB1 playing a bigger role in methylation. Our data reveal the comprehensive 2'-O-methylation maps for Arabidopsis rRNAs and snRNAs and would facilitate study of their function and biosynthesis.
| S-EPMC8053127 | biostudies-literature
Project description:Ribosomal RNA modifications are important in optimizing ribosome function. Sugar 2'-O-methylation performed by fibrillarin-associated box C/D antisense guide snoRNAs impacts all steps of translation, playing a role in disease etiology (cancer). As it renders adjacent phosphodiester bonds resistant to alkaline treatment, 2'-O-methylation can be monitored qualitatively and quantitatively by applying next-generation sequencing to fragments of randomly cleaved RNA. We remapped all sites of 2'-O-methylation in human rRNAs in two isogenic diploid cell lines, one producing and one not producing the antitumor protein p53. We identified sites naturally modified only partially (confirming the existence in cells of compositionally distinct ribosomes with potentially specialized functions) and sites whose 2'-O-methylation is sensitive to p53. We mapped sites particularly vulnerable to a reduced level of the methyltransferase fibrillarin. The remarkable fact that these are largely sites of natural hypomodification provides initial insights into the mechanism of partial RNA modification. Sites where methylation appeared vulnerable lie peripherally on the 3-D structure of the ribosomal subunits, whereas the numerous modifications present at the core of the subunits, where the functional centers lie, appeared robustly made. We suggest that vulnerable sites of 2'-O-methylation are highly likely to undergo specific regulation during normal and pathological processes.
| S-EPMC5597630 | biostudies-literature
Project description:Targeting the genome with sequence-specific synthetic molecules is a major goal at the interface of chemistry, biology, and personalized medicine. Pyrrole/imidazole-based polyamides can be rationally designed to target specific DNA sequences with exquisite precision in?vitro; yet, the biological outcomes are often difficult to interpret using current models of binding energetics. To directly identify the binding sites of polyamides across the genome, we designed, synthesized, and tested polyamide derivatives that enabled covalent crosslinking and localization of polyamide-DNA interaction sites in live human cells. Bioinformatic analysis of the data reveals that clustered binding sites, spanning a broad range of affinities, best predict occupancy in cells. In contrast to the prevailing paradigm of targeting single high-affinity sites, our results point to a new design principle to deploy polyamides and perhaps other synthetic molecules to effectively target desired genomic sites in?vivo.
| S-EPMC4160732 | biostudies-literature
Project description:PARylation [poly(ADP-ribosyl)ation] is involved in the maintenance of genomic methylation patterns through its control of Dnmt1 [DNA (cytosine-5)-methyltransferase 1] activity. Our previous findings indicated that Ctcf (CCCTC-binding factor) may be an important player in key events whereby PARylation controls the unmethylated status of some CpG-rich regions. Ctcf is able to activate Parp1 [poly(ADP-ribose) polymerase 1], which ADP-ribosylates itself and, in turn, inhibits DNA methylation via non-covalent interaction between its ADP-ribose polymers and Dnmt1. By such a mechanism, Ctcf may preserve the epigenetic pattern at promoters of important housekeeping genes. The results of the present study showed Dnmt1 as a new protein partner of Ctcf. Moreover, we show that Ctcf forms a complex with Dnmt1 and PARylated Parp1 at specific Ctcf target sequences and that PARylation is responsible for the maintenance of the unmethylated status of some Ctcf-bound CpGs. We suggest a mechanism by which Parp1, tethered and activated at specific DNA target sites by Ctcf, preserves their methylation-free status.
| S-EPMC3258657 | biostudies-literature
Project description:Methylation of ribose sugars at the 2'-OH group is one of the major chemical modifications in rRNA, and is catalyzed by snoRNA directed C/D box snoRNPs. Previous biochemical and computational analyses of the C/D box snoRNAs have identified and mapped a large number of 2'-OH ribose methylations in rRNAs. In the present study, we systematically analyzed ribose methylations of 18S rRNA in Saccharomyces cerevisiae, using mung bean nuclease protection assay and RP-HPLC. Unexpectedly, we identified a hitherto unknown ribose methylation at position G562 in the helix 18 of 5' central domain of yeast 18S rRNA. Furthermore, we identified snR40 as being responsible to guide snoRNP complex to catalyze G562 ribose methylation, which makes it only second snoRNA known so far to target three ribose methylation sites: Gm562, Gm1271 in 18S rRNA, and Um898 in 25S rRNA. Our sequence and mutational analysis of snR40 revealed that snR40 uses the same D' box and methylation guide sequence for both Gm562 and Gm1271 methylation. With the identification of Gm562 and its corresponding snoRNA, complete set of ribose methylations of 18S rRNA and their corresponding snoRNAs have finally been established opening great prospects to understand the physiological function of these modifications.
| S-EPMC4344503 | biostudies-literature