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The two-step purification method ViREn identifies a single NSUN6- mediated 5-methylcytosine modification promoting dengue virus RNA genome turnover

ABSTRACT: NSUN6- mediated 5-methylcytosine (m5C) in Dengue virus RNA

PROVIDER: PRJEB88116 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR14821732.fastq.gz	Fastqsanger.gz
	ERR14821733.fastq.gz	Fastqsanger.gz
	ERR14821734.fastq.gz	Fastqsanger.gz
	ERR14821735.fastq.gz	Fastqsanger.gz
	ERR14821736.fastq.gz	Fastqsanger.gz

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Sequence- and structure-specific cytosine-5 methylation in mRNAs by NSUN6

Project description:Methylation is the most common internal modification in mRNA. While the highly abundant N6-methyladonsine (m6A) modification affects most aspects of mRNA function, the precise functions of the rarer 5-methylcytosine (m5C) remains largely unknown. Here, we map m5C in the human transcriptome using methylation-dependent individual-nucleotide resolution cross-linking and immunoprecipitation (miCLIP) combined with RNA bisulfite sequencing. We identify NSUN6 as a methyltransferase with strong substrate specificity towards mRNA. NSUN6 primarily targeted three prime untranslated regions (3’UTR) at the consensus sequence motif CTCCA. Knockout and rescue experiments revealed that only mRNA methylation sites containing the consensus motif depended on the presence of NSUN6. Furthermore, ribosome profiling demonstrated that NSUN6-specific consensus motifs marked translation termination. However, even though NSUN6-methylated mRNAs were reduced in NSUN6 knockout cells, NSUN6 was dispensable for mouse embryonic development. Thus, our study identifies NSUN6 as methyltransferase targeting mRNA in a sequence- and structure-specific manner.

2020-11-20 | GSE140997 | GEO

A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m5C modification

Project description:mRNA modifications are vital in regulating cellular processes. Beyond N6-methyladenosine (m6A), most other internal mRNA modifications lack dedicated catalytic machinery and are typically introduced by tRNA-modifying enzymes. The distribution and stoichiometry of these modifications on mRNAs remain debated and require further validation. Furthermore, their precise function remains controversial due to the challenges of excluding the intricate combinational effects of tRNA modifications. Here, we biochemically validate that NSUN6, a tRNA structure-dependent methyltransferase, independently catalyzes 5-methylcytidine (m5C) formation with robust activity on mRNA by recognizing the CUCCA motif in a certain stem-loop structure. NSUN6 employs different strategies to recognize tRNA and mRNA substrates. By introducing mutations, we further separate its catalytic capabilities toward mRNA and tRNA revealing that NSUN6 promotes breast cancer cell migration depending on mRNA m5C modification. Mechanistically, a cohort of mRNAs involved in cell migration carries high levels of NSUN6-mediated site-specific m5C modification, thus being stabilized by the preferential binding of m5C readers YBX1 and YBX3. Moreover, introducing a single-site high-level m5C can significantly increase the stability of therapeutic mRNAs in cells. Our findings underscore the pivotal role of m5C-modified mRNAs in promoting breast cancer metastasis and their potential for therapeutic applications.

2025-05-05 | GSE280051 | GEO

A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m5C modification to promote breast cancer metastasis

2025-05-05 | GSE279973 | GEO

Effects of NSUN6 deficiency by systematic transcriptomes and m5C profiles in mice across tissue [RNA-Seq]

Project description:we constructed Nsun6-KO mouse, and observed that the wight and appearance of KO mice didn’t show abnormality. Through Bisulfite sequencing (BS-seq) in wild-type (WT) as well as KO mice and mRNA-seq, we identified high confident Nsun6-dependent m5C sites and performed the transcriptome analysis across five tissues.

2022-06-16 | GSE200952 | GEO

Effects of NSUN6 deficiency by systematic transcriptomes and m5C profiles in mice across tissue [BS-Seq]

2022-06-16 | GSE200951 | GEO

Malignant transformed cells of bladder epithelium: control CdC12-V2 vs NSUN6-knockout Malignant transformed cells of bladder epithelium

Project description:m5C-specific methylated small RNA immunoprecipitation microarray analysis in CdC12-V2 vs NSUN6-knockout Malignant transformed cells of bladder epithelium

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Programmable RNA 5-methylcytosine (m5C) modification of cellular RNAs using dCasRx conjugated methyltransferase and demethylase

Project description:5-methylcytosine, an abundant RNA modification, plays a crucial role in regulating RNA fate and gene expression. While recent progress has been made in understanding the biological roles of m5C, the inability to introduce m5C at specific sites within transcripts has hindered efforts to elucidate direct links between specific m5C and phenotypic outcomes. Here we developed a CRISPR-Cas13d-based tool, named reengineered m5C modification systems (termed ‘RCMS’), for targeted m5C methylation and demethylation in specific transcripts. The RCMS editors consist of a nuclear-localised dCasRx conjugated to either to a methyltransferase, NSUN2/NSUN6 or a demethylase, the catalytic domain of mouse Tet2 (Tet2 CD), enabling the manipulation of methylation events at precise m5C sites. We demonstrate that the RCMS editors can direct site-specific m5C incorporation and demethylation. Furthermore, we confirm their effectiveness in modulating m5C levels within tRNAs and their ability to induce changes in transcript abundance and cell proliferation through m5C-mediated mechanisms. These findings collectively establish RCMS editors as a focused epitranscriptome engineering tool, facilitating the identification of individual m5C alterations and their consequential effects.

2025-01-19 | GSE253659 | GEO

Epitranscriptomic maps of 5-methylcytosine reveal substrate diversity of NSUN methyltransferases and links to mRNA translation and turnover

Project description:Multiple epitranscriptomic maps of the RNA modification 5-methylcytosine (m5C) have been prepared, often diverging markedly from each other in terms of site abundance and identity. Differences in detection methods, data depth and analysis pipelines, but also biological factors underly much of this disparity. To address this, we re-analysed available datasets from five human cell lines and seven tissues, generated by the prevailing bisulfite RNA sequencing method, with a coherent m5C site calling pipeline. We used the resulting union list of 6,393 m5C sites called across the broader transcriptome to study site distribution, enzymology, interaction with RNA-binding proteins and molecular function. We confirmed prior observations such as predominance of m5C sites within mRNA exons, enrichment around start codons, and that the tRNA:m5C methyltransferases (MTases) NSUN2 and 6 are the main m5C ‘writers’ for mRNAs. Each NSUN enzyme recognises mRNA features that strongly resemble their respective canonical substrates. Assessing proximity between mRNA m5C sites and footprints of RNA-binding proteins reconfirmed the mRNA export factor ALYREF as an m5C ‘reader’ and identified new candidates for functional interactions, including the RNA helicases DDX3X, involved in mRNA translation, and UPF1, an mRNA decay factor. Experiments in HeLa cells lacking NSUN2 showed that this affected both, steady-state level and UPF1-binding to target mRNAs. Our studies emphasise the emerging diversity of both, m5C writers and readers, affecting mRNA function.

2024-07-04 | GSE252369 | GEO

NSUN2-mediated 5-methylcytosine enhances purine metabolism through ALYREF in retinoblastoma

Project description:5-methylcytosine (m5C) RNA modification installed by methyltransferase NSUN2 regulates gene expression and cell fate. Retinoblastoma (RB) is the most common primary intraocular tumor in children. However, the functional role of m5C modification in retinoblastoma remains unclear. Here, we show that 5-methylcytosine significantly promotes the progression of retinoblastoma. Retinoblastoma samples showed increased m5C levels, indicating a poor prognosis. Changes in global m5C modification were highly associated with tumor progression in vitro and in vivo. Mechanistically, NSUN2 stabilized the methylated PFAS mRNA, a tumor promoter in retinoblastoma. Our work uncovers a critical function for m5C methylation in retinoblastoma and provides additional insight into the understanding of m5C modification.

2022-10-07 | GSE214685 | GEO

5-methylcytosine modification and the ALYREF reader protein promote retrovirus replication

Project description:The 5-methylcytosine (m5C) modification is present at appreciable amounts in the mammalian transcriptome, but its precise location and function is still poorly understood. Here, we identify high m5C levels and map their locations in a model retrovirus, the murine leukemia virus, and show that the ALYREF m5C reader protein regulates viral replication. Our results reveal a single-nucleotide m5C profile in a virus and its function in a eukaryotic mRNA.

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