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Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster

ABSTRACT: Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster

PROVIDER: PRJNA1008074 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24782968_1.fastq.gz	Fastqsanger.gz
	SRR24782968_2.fastq.gz	Fastqsanger.gz
	SRR24782969_1.fastq.gz	Fastqsanger.gz
	SRR24782969_2.fastq.gz	Fastqsanger.gz
	SRR24782970_1.fastq.gz	Fastqsanger.gz

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Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster [Fib_KD_RiboMeth-seq]

Project description:The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). We built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing (TGIRT-seq).

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Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster [Fib_KD_RiboMeth-seq]

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Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster.

Project description:During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, methylation of the 2'-hydroxyl ribose moiety (Nm) is the most abundant modification of rRNAs. The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). These modifications impact interactions between rRNAs, tRNAs and mRNAs, and some are known to fine tune translation rates and efficiency. In this study, we built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing. We de novo identified 61 Nm sites, from which 55 are supported by both sequencing methods, we validated the expression of 106 C/D box snoRNAs and we predicted new or alternative rRNA Nm targets for 31 of them. Comparison of methylation level upon different stresses show only slight but specific variations, indicating that this modification is relatively stable in D. melanogaster. This study paves the way to investigate the impact of snoRNA-mediated 2'-O-methylation on translation and proteostasis in a whole organism.

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Project description:Small nucleolar RNAs (snoRNAs), a group of noncoding RNAs present amongst all eukaryotes, are known for their regulation of ribosome biogenesis and splicing. Despite their central cellular roles, current snoRNA annotations remain incomplete. Indeed, several eukaryote annotations contain few or no snoRNAs, and none distinguishes expressed snoRNAs from their pseudogenes—a recently characterized snoRNA subclass with distinct features and expression levels. To address this, we developed SnoBIRD, a BERT-based C/D box snoRNA predictor trained on snoRNAs spanning all eukaryote kingdoms. We show that SnoBIRD outperforms existing tools in a test set environment and is the only predictor capable of identifying snoRNA pseudogenes using biologically relevant signal. Applied on the fission yeast and human genomes, we demonstrate that only SnoBIRD scales well with genome size in terms of runtime, and we identify and experimentally validate several new SnoBIRD-predicted C/D box snoRNAs. By running SnoBIRD on multiple eukaryote genomes, we identify hundreds of novel C/D box snoRNA candidates and highlight SnoBIRD’s usefulness to determine the evolutionary paths of snoRNAs that share a common host locus but are distributed across different species. Overall, SnoBIRD represents a user‑friendly and efficient tool for reliably predicting C/D box snoRNAs and their pseudogenes across any eukaryote kingdom.

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