Systematic mapping of 2’-O-methylation sites in rRNAs implicates new strategy for ribose methylation in Arabidopsis
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PROVIDER: PRJNA632477 | ENA |
REPOSITORIES: ENA
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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:Systematic mapping of 2’-O-methylation sites in rRNAs implicates new strategy for ribose methylation in Arabidopsis [20ME]
| PRJNA632481 | ENA
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 [FIB CLIP]
| PRJNA632480 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-12-31 | GSE150456 | 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:We used a whole-genome microarray based on the sequenced strain Lactobacillus sakei 23K to study ribose catabolism in three Lactobacillus sakei strains by screening for differentially expressed genes when grown on ribose compared to glucose
2010-12-01 | E-MEXP-2892 | biostudies-arrayexpress
Project description:Growth of B. breve UCC2003 on ribose leads to the transcriptional induction of the rbsACBDK gene cluster. Generation and phenotypic analysis of an rbsA insertion mutant established that the rbs gene cluster is essential for ribose utilization, and that its transcription is likely regulated by a LacI-type regulator encoded by rbsR, located immediately upstream of rbsA. Gel mobility shift assays using purified RbsRHis indicate that the promoter upstream of rbsABCDK is negatively controlled by RbsRHis binding to an 18-bp inverted repeat and that RbsRHis binding activity is modulated by D-ribose. The rbsK gene of the rbs operon of B. breve UCC2003 was shown to specify a ribokinase (EC 2.7.1.15), which specifically directs its phosphorylating activity towards D-ribose, converting this pentose sugar to ribose-5-phosphate. In order to investigate differences in global gene expression upon growth of B. breve UCC2003 on ribose, or a combination of ribose and glucose, as compared to glucose, DNA microarray experiments were performed. Total RNA was isolated from B. breve UCC2003 cultures grown on ribose, a combination of ribose and glucose, or glucose. All experiments were performed in duplicate. A dye swap was performed in one of the two biological replicates.
2010-05-19 | E-GEOD-17325 | biostudies-arrayexpress
Project description:Sequencing-based profiling of ribose methylations is a new approach that allows for experiments adrressing dynamic changes on a large scale. Here, we apply such a method to spliceosomal snRNAs present in human whole cell RNA. Analysis of solid tissue samples confirmed all previously known sites and demonstrated close to full methylation at almost all sites. Methylation changes were revealed in biological experimental settings, using T cell activation as an example, and in the T cell leukemia model, Jurkat cells. Such changes could impact the dynamics of snRNA interactions during the spliceosome cycle and affect mRNA splicing efficiency and splicing patterns.
2017-10-20 | GSE104947 | GEO
Project description:The major information-carrying macromolecules in the cell, DNA, RNA, and protein, carry an additional layer of information on top of their sequence in the form of modifications of residues. The modifications provide additional functional groups and impact the structure and function of the molecules. Cellular RNA molecules contain more than 100 different modifications and are found in all domains of life and in all major classes of RNA in eukaryotic organisms. Together these modifications constitute the epitranscriptome of which two-thirds are methylations with 2’-O methylation of the ribose moiety of the nucleotide as the most abundant. Many aspects of ribose methylation are underexplored because the existing methods for their detection are laborious and can only address a few modification sites at a time. Here, we introduce RiboMeth-Seq, a high-throughput sequencing based method and applies it to yeast ribosomal RNA. We detect all of the known as well as one new methylation site and provide evidence for hypomethylation at specific residues. Furthermore we demonstrate that many methylation events are interdependent and outline the timing of modifications during ribosome biogenesis. Our results demonstrate a novel and efficient approach to understanding of the role of modifications in ribosomal RNA folding and ribosome function. Recent evidence point to changes in ribose methylation patterns in cancer ribosomes and we anticipate that RiboMeth-Seq can be applied here as well as to other diseases in which ribosomes are affected, including the heritable ribosomopathies. Yeast RNA was degraded at denaturing conditions into small fragments, long enough to be mapped by sequence alignment to the reference genome (20-40 nucleotides). The fragments were ligated to RNA oligos using a tRNA ligase that was mutated to remove its kinase activity, reverse transcribed and the cDNA used as input for Ion semiconductor sequencing. The first and last nucleotides of the inserts were recorded using the full sequence for mapping and the read-ends plotted against the sequence. 2'-O-Methylated RNA positions are protected from cleavage, and read ends from such positions are therefore underrepresented compared to the surrounding positions.
2014-11-24 | E-GEOD-54655 | biostudies-arrayexpress