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Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [mouse frontal cortex]

ABSTRACT: Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [mouse frontal cortex]

PROVIDER: PRJNA872028 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR21161032_1.fastq.gz	Fastqsanger.gz
	SRR21161033_1.fastq.gz	Fastqsanger.gz
	SRR21161034_1.fastq.gz	Fastqsanger.gz
	SRR21161035_1.fastq.gz	Fastqsanger.gz

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Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution

Project description:Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution

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Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [mouse frontal cortex]

Project description:The expanding field of epitranscriptomics might rival the epigenome in the diversity of biological processes impacted. However, the identification of multiple modification types in individual RNA molecules remains challenging. We present CHEUI, a new method that detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual transcript molecules in a single condition as well as differential methylation between two conditions, using nanopore signals. CHEUI processes observed and expected signals with convolutional neural networks to achieve high single-molecule accuracy and outperform other methods in detecting m6A and m5C sites and quantifying their stoichiometry. Moreover, CHEUI’s unique capability to identify different modifications in the same signal data reveals a non-random co-occurrence of m6A and m5C in transcripts in human cell lines and during mouse embryonic brain development. CHEUI unlocks the capability of studying links between multiple RNA modifications and phenotypes, enabling the discovery of new epitranscriptome functions. Furthermore, CHEUI's training and testing protocols are adaptable to other modifications, making it a versatile RNA technology.

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Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [HeLa cells]

Project description:Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [HeLa cells]

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Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution [HeLa cells]

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NSUN1-m5C is linked to TDP-43 neurotoxicity

Project description:In amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), the nuclear RNA-binding protein TDP-43 mislocalises to the cytoplasm and forms insoluble aggregates, but the mechanisms controlling this remain unclear. We define a native TDP-43 interactome in human SH-SY5Y cells and identify proteins linked to the 5-methylcytosine (m5C) RNA modification as highly enriched. Using a Drosophila model of TDP-43 pathology, we show that aberrant activity of m5C-RNA methyltransferases Nsun1 drives TDP-43-induced m5C-RNA hypermethylation, while Nsun1 downregulation alleviates TDP-43–induced degeneration, lifespan deficits, and cytoplasmic accumulation. In human cells, TDP-43 selectively interacts with NSUN1 isoform 3 independently of RNA. Furthermore, NSUN1 is nucleolar and TDP-43 is largely nucleoplasmic, yet they interact in both compartments, suggesting functional roles beyond their predominant localisations. In ALS/FTD post-mortem frontal cortex, NSUN1 isoform 3 persists, while the shorter isoform is reduced, suggesting that a pool of NSUN1 capable of contributing to pathological TDP-43 interactions remains in disease. These findings suggest that TDP-43 neurotoxicity is coupled to NSUN1 activation and m5C-RNA methylation, revealing a potential therapeutic axis in ALS/FTD.

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Simultaneous identification of m6A and m5C reveals coordinated RNA modification at single-molecule resolution

Project description:This SuperSeries is composed of the SubSeries listed below.

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Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications

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Project description:Here we report m5C-TAC-seq, a base-resolution sequencing method to directly detect m5C sites without affecting unmodified C. In m5C-seq, we combined TET-mediated oxidation of RNA m5C to f5C with the selective chemical labeling reaction of f5C, enabling both pre-enrichment of m5C-containing RNA and a m5C-to-T transition in reverse transcription. m5C-seq identifies 2,500 sites in the transcriptome of HeLa and 768 sites in the transcriptome-wide of HEK293T. In addition, taking advantage of barcoding and pooling strategy, m5C-seq detected differential m5C sites upon specific methyltransferases depletion in mESCs and dynamically regulated m5C sites under cell fate transition. Moreover, we also detected 215 sites in chromatin-associated RNAs, demonstrating that portion of m5C sites can be co-transcriptionally catalyzed and the existence of m5C methylations in repeat RNAs.

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