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A bifunctional snoRNA with separable activities in guiding rRNA 2’-O-methylation and scaffolding gametogenesis effectors

ABSTRACT: Bifunctional snoRNA snr107 in gametogenesis S.pombe

PROVIDER: PRJEB79915 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13655600.fastq.gz	Fastqsanger.gz
	ERR13655601.fastq.gz	Fastqsanger.gz
	ERR13655602.fastq.gz	Fastqsanger.gz
	ERR13655603.fastq.gz	Fastqsanger.gz
	ERR13655604.fastq.gz	Fastqsanger.gz

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A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (meiosis RNA-Seq)

Project description:Small nucleolar RNAs (snoRNAs) are non-coding transcripts that guide chemical modifications of RNA substrates and contribute to gene expression at the epigenetic and post-transcriptional levels. However, the extent of their regulatory potential and the underlying molecular mechanisms remain poorly understood. Here, we identify a previously unannotated intronic C/D-box snoRNA, termed snR107, hosted in the fission yeast long non-coding RNA (lncRNA) mamRNA and carrying two independent cellular functions. On one hand, snR107 guides site-specific 25S rRNA 2’-O-methylation and promotes pre-rRNA processing/60S subunit biogenesis. On the other hand, snR107 associates with the gametogenic RNA-binding proteins Mmi1 and Mei2, mediating their reciprocal inhibition and restricting meiotic gene expression during sexual differentiation. Both functions require distinct cis-motifs within snR107, including a conserved 2’-O-methylation guiding sequence. Together, our results position snR107 as a dual regulator of rRNA modification and gametogenesis effectors, expanding our vision on the non-canonical functions exerted by snoRNAs in cell fate decisions.

2025-03-17 | GSE276244 | GEO

A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (direct RNA-Seq)

2025-03-17 | GSE276242 | GEO

A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (total and polyA RNA-Seq)

2025-03-17 | GSE276243 | GEO

A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (meiosis RNA-Seq)

Project description:A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (meiosis RNA-Seq)

| PRJNA1156082 | ENA

A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (direct RNA-Seq)

Project description:A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (direct RNA-Seq)

| PRJNA1156085 | ENA

A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (total and polyA RNA-Seq)

Project description:A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (total and polyA RNA-Seq)

| PRJNA1156084 | ENA

Gene expression comparison between WT, U17 snoRNA knockdown and U17 overexpression NIH-3T3 cells to identify target mRNAs regulated by U17 snoRNA

Project description:Comparison of mRNA transcriptome after differential expression of U17 snoRNA. We hypothesiaed that if U17 snoRNA regulates cholesterol homeostasis by modulating the expression of target mRNAs, genes that are differentially expressed by the loss-of-function or gain-of-function of U17 snoRNA would be candidate U17 targets. Results revealed negative regulation of target genes by U17 snoRNA, in which increasing dosage of U17 snoRNA from U17 knockdown to WT to U17 overexpression lead to decreases in target levels. Total RNA were isolated by TRIzol reagent (Invitrogen) from WT, U17 snoRNA KD (ShSnhg3 stable clone), and U17 snoRNA OE (pMDβglobinU17b stable clone) cells grown in LPDS media for 24 hours.

2015-04-04 | E-GEOD-67569 | biostudies-arrayexpress

SnoRNA-facilitated protein secretion revealed by transcriptome-wide snoRNA target identification

Project description:Small nucleolar RNAs (snoRNA) are non-coding RNAs known for guiding RNA modifications including 2ʹ-O-methylation (Nm) and pseudouridine (Ψ). While snoRNAs may also interact with other RNAs such as mRNA, the full repertoire of RNAs targeted by snoRNA remains elusive due to the lack of effective technologies that identify snoRNA targets transcriptome-wide. Here we develop a chemical crosslinking-based approach that comprehensively detects cellular RNA targets of snoRNAs, yielding thousands of previously unrecognized snoRNA-mRNA interactions in human cells and mouse brain tissues. Many interactions occur outside of snoRNA-guided rRNA modification sites, hinting at non-canonical functions beyond RNA modification. We find that one of these snoRNAs, SNORA73, targets mRNAs that encode secretory proteins and membrane proteins. SNORA73 also interacts with 7SL RNA, part of the signal recognition particle (SRP) required for protein secretion. The mRNA-SNORA73-7SL RNA interactions enhance the association of the SNORA73-target mRNAs with SRP, thereby facilitating secretion of the encoded proteins.

2024-11-21 | GSE261702 | GEO

Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

Project description:Background: Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. Results: We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. 59% of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs. Conclusions: Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

2021-05-13 | GSE157846 | GEO

Atypical U3 snoRNA Suppresses the Process of Pterygia through Modulating 18S Ribosomal RNA Synthesis

Project description:Ribosome biosynthesis plays a crucial role in regulating protein translation and is essential for cell growth and development in physiological progress. The progression and recurrence of Pterygia mainly occur due to the abnormal proliferation and migration of stromal Pterygia fibroblasts. Small nucleolar RNA U3 (U3 snoRNA), harboring the atypical C/D boxes, is involved in 18S ribosomal RNA (18S rRNA) synthesis; however, the mechanism of U3 snoRNA in Pterygia remains unclear. Methods: Primary HCFs and HPFs were separated and cultured from fresh conjunctival grafts and Pterygia tissues. The PLKO.1 lentiviral system and CRISPR/Cas9 recombinant construct were, respectively, used to overexpress and silence U3 snoRNA in HPF and HCF cells for further specific phenotypes analysis. RNA-seq and TMT-labeled quantitative protein mass spectrometry were utilized to evaluate the effect of U3 snoRNA on mRNA transcripts and protein synthesis. Results: Reduced U3 snoRNA in Pterygia promotes HCF or HPF cells' proliferation, migration, and cell cycle but has no significant effect on apoptosis. U3 snoRNA modulates 18S rRNA synthesis through shearing precursor ribosomal RNA 47S rRNA at the 5′ external transcribed spacer (5′ ETS). Moreover, the altered U3 snoRNA causes mRNA and protein differential expression in HCF or HPF cells. Conclusion: The atypical U3 snoRNA regulates the translation of specific proteins to exert a suppressive function in Pterygia through modulating the 18S RNA synthesis. Here, we uncover a novel insight into U3 snoRNA biology in the development of Pterygia.

2022-05-20 | PXD030801 | Pride

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