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Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (Nm-mut-seq)

ABSTRACT: Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (Nm-mut-seq)

PROVIDER: PRJNA1251609 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33170676.fastq.gz	Fastqsanger.gz
	SRR33170677.fastq.gz	Fastqsanger.gz
	SRR33170678.fastq.gz	Fastqsanger.gz
	SRR33170679.fastq.gz	Fastqsanger.gz
	SRR33170680.fastq.gz	Fastqsanger.gz

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Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (Nm-mut-seq)

Project description:2′-O-methylation (Nm) is an abundant RNA modification exists on different mammalian RNA species. However, potential Nm recognition by proteins has not been extensively explored. Here, we employed RNA affinity purification followed by mass spectrometry to identify Nm-binding proteins. The candidates exhibit enriched binding at known Nm sites. Interestingly, some candidates display nuclear localization and functions. We focused on the splicing factor FUBP1. Electrophoretic mobility shift assay (EMSA) validated preference of FUBP1 to Nm-modified RNA. As FUBP1 predominantly binds intronic regions, we profiled Nm sites in chromatin-associated RNA (caRNA) and found Nm enrichment within introns. Depletion of Nm led to increased exon skipping, suggesting Nm-dependent splicing regulation. The caRNA Nm sites overlap with FUBP1 binding sites, and Nm depletion reduced FUBP1 occupancy on modified regions. Furthermore, FUBP1 depletion induced exon skipping in Nm-modified genes, supporting its role in mediating Nm-dependent splicing regulation. Overall, our findings identify FUBP1 as an Nm-binding protein and uncover previously unrecognized nuclear functions for RNA Nm modification.

2025-04-20 | GSE294792 | GEO

Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (CLIP-seq and PAR-CLIP)

2025-04-20 | GSE294793 | GEO

Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (RNA-seq and RIP-seq)

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FUBP1 is a core splicing factor that facilitates 3' splice site recognition and splicing of long introns [RNA-Seq]

Project description:Splicing is a central process in metazoans and greatly expands their proteome by alternative splicing of pre-mRNA transcripts. An essential regulatory step during early spliceosome assembly is the recognition of cis-regulatory RNA motifs in pre-mRNAs. Here, we identified the RNA binding protein FUBP1 as a novel core splicing factor with a ubiquitous footprint on pre-mRNAs. FUBP1 binds to a previously unknown cis-regulatory motif upstream of the branch point of human introns. We show that FUBP1 binds and stabilises known 3' splice site components such as the essential splicing factor U2AF2. FUBP1 mutant cell lines and patient data indicate that FUBP1 is particularly relevant for efficient splicing of exons flanked by long introns. In addition to its role at the 3’ splice site, FUBP1 shows multiple interactions with U1 snRNP- associated proteins. This demonstrates an important role for FUBP1 in splice site bridging in the context of long introns.

2023-07-27 | GSE220180 | GEO

FUBP1 is a core splicing factor that facilitates 3' splice site recognition and splicing of long introns [In vivo iCLIP]

2023-07-27 | GSE220184 | GEO

FUBP1 is a core splicing factor that facilitates 3' splice site recognition and splicing of long introns [In vitro iCLIP]

2023-07-27 | GSE220183 | GEO

Nm-Mut-seq: The base-resolution quantitative method for mapping transcriptome-wide 2’-O-methylations

Project description:2’-O-methylation (Nm) is a prevalent post-transcriptional RNA modification present in many cellular RNAs and plays a critical role in modulating both the physical properties and regulation of eukaryotic RNAs. Studies of Nm modifications in RNA have long been hampered by a lack of effective mapping methods. Previously reported approaches can work well for detecting Nm modifications on abundant RNAs, but face challenges when applied to low-abundant RNAs, such as mRNA, lack stoichiometric information, and are challenged by issues of RNA sample degradation due to chemical treatment. Here, we present Nm-Mut-seq, a mutation signature-based Nm mapping method, which uses a custom reverse transcriptase (RT) that installs mutations at Am, Cm, and Gm-modified sites (Um is undetectable by this method). Our work provides a much-needed approach to detect Nm at base resolution in low abundant RNAs and to estimate the stoichiometry of each modified site transcriptome-wide.

2023-06-01 | GSE174518 | GEO

Identification of FUBP1 as a long tail driver and widespread regulator of tumor suppressor and oncogene alternative splicing

Project description:Comprehensive sequencing approaches have allowed for the identification of the most frequent contributors to cancer, known as drivers. They have also revealed a class of mutations in understudied, infrequently altered genes, referred to as “long tail” (LT) drivers. A key challenge has been to find clinically relevant LT drivers and understand how they cooperate to drive disease. Here, we identified Far Upstream Binding Protein 1 (FUBP1) as a LT driver using an in vivo CRISPR screen. FUBP1 cooperates with other tumor suppressor genes to transform mammary epithelial cells by disrupting cellular differentiation and tissue architecture. Mechanistically, FUBP1 participates in regulating m6A RNA methylation, and its loss leads to global changes in RNA splicing and widespread expression of aberrant driver isoforms. These findings suggest that somatic alteration of a single gene involved in RNA splicing and m6A methylation can produce the necessary panoply of contributors for neoplastic transformation.

2019-09-12 | GSE122416 | GEO

Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (RNA-seq and RIP-seq)

Project description:Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (RNA-seq and RIP-seq)

| PRJNA1251608 | ENA

Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (CLIP-seq and PAR-CLIP)

Project description:Nuclear 2′-O-methylation regulates RNA splicing through its binding protein FUBP1 (CLIP-seq and PAR-CLIP)

| PRJNA1251610 | ENA