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

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

PROVIDER: PRJNA1008077 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25736553_1.fastq.gz	Fastqsanger.gz
	SRR25736553_2.fastq.gz	Fastqsanger.gz
	SRR25736554_1.fastq.gz	Fastqsanger.gz
	SRR25736554_2.fastq.gz	Fastqsanger.gz
	SRR25736555_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_TGIRT-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 [Tissues_TGIRT-seq]

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

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

| PRJNA1008074 | ENA

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

Project description: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 [Fib_KD_TGIRT-seq]

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

| PRJNA978096 | ENA

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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Next generation sequencing identifies discrete classes of box C/D snoRNAs featuring different ends and RNA binding protein dependency

Project description:The paired-end next-generation sequencing of all small RNAs of less than 200 nucleotides in length from four different human cell lines (SKOV3ip1, MCF-7, BJ-Tielf, INOF) allowed us to determine the exact sequence(s) and variations of human box C/D snoRNAs (small nucleolar RNAs), revealing processing patterns of this class of molecules. Two distinct groups of box C/D snoRNAs were identified based on the position of their ends with respect to their characteristic boxes and the terminal base pairing potential. Short box C/D snoRNAs start sharply 4 or 5 nucleotides upstream of their box C and end 2 or 3 nucleotides downstream of their box D. In contrast, long box C/D snoRNAs start 5 or 6 nucleotides upstream of their box C and end 4 or 5 nucleotides downstream of their box D, increasing the likelihood of formation of a k-turn between their boxes C and D. Sequencing of SKOV3ip1 cells following the depletions of NOP58, a core box C/D snoRNA-binding protein and of RBFOX2, a splicing factor, shows that the short box C/D snoRNA forms are significantly more affected by the depletion of RBFOX2 while the long snoRNA forms, which display more canonical box C/D snoRNA features, are significantly more affected by the depletion of NOP58. Together the data suggest that box C/D snoRNAs are divided into at least two groups of RNA with distinct maturation and functional preferences. Small RNAs (<200 nucleotides) were isolated from different human cell lines that were either untreated or depleted of NOP58 or RBFOX2 using specific siRNAs. The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.

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SnoBIRD: A tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes

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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Orphan box C/D snoRNAs guide rRNA base acetylations in yeast

Project description:Box C/D snoRNAs snR4 and snR45, whose role was unknown, guide 18S rRNA acetylations by Kre33 in yeast. UV-crosslinking (CRAC) was used to determine binding sites of Kre33 on RNA.

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