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Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [MeRIP-seq, RNA-seq, Ribo-seq]

ABSTRACT: Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [MeRIP-seq, RNA-seq, Ribo-seq]

PROVIDER: PRJNA1033620 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26590535_1.fastq.gz	Fastqsanger.gz
	SRR26590535_2.fastq.gz	Fastqsanger.gz
	SRR26590536_1.fastq.gz	Fastqsanger.gz
	SRR26590536_2.fastq.gz	Fastqsanger.gz
	SRR26590537_1.fastq.gz	Fastqsanger.gz

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Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [MeRIP-seq, RNA-seq, Ribo-seq]

Project description:Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study found that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetrically distribution along mature transcripts. In Amphidinium carterae, we identified 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many involved in regulating carbon and nitrogen metabolism. With enrichment within 3'UTR, dinoflagellate mRNA m1A exhibits negative correlation with translation efficiency. Notably, nitrogen depletion led to a significant decrease in mRNA m1A. Furthermore, our analysis revealed that distinctive patterns of m1A modification influence the expression of metabolism-related genes through translation control. Thus, this study provides a comprehensive map of m1A in dinoflagellate mRNA, highlighting its crucial role as a post-transcriptional regulatory layer and enhancing the understanding of mRNA m1A modification.

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Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [m1A-seq-TGIRT]

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Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation

Project description:Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation

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Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [Nanopore]

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Reversible and Dynamic m1A Methylation in the Human Transcriptome

Project description:N1-methyladenosine (m1A) is an abundant post-transcriptional RNA modification, yet little is known about its prevalence, topology and dynamics in mRNA. Here, we show that m1A is abundant in human mRNA, with an m1A/A ratio of ~0.02%. We develop m1A-ID-Seq, based on m1A immunoprecipitation and the inherent property of m1A to stall reverse transcription, for the transcriptome-wide m1A analysis. m1A-ID-Seq identifies 901 m1A peaks (from 583 genes) in mRNA and ncRNA, and reveals a prominent feature of enrichment in the 5â-untranslated region of mRNA transcripts, distinct from that of N6-methyladenosine, the most abundant internal mammalian mRNA modification. m1A in mRNA is also reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, m1A responds dynamically to stimuli and hundreds of stress-induced m1A sites are identified. Collectively, our approaches allow comprehensive analysis of m1A methylation and provide an important tool for functional studies of potential epigenetic regulation via the reversible and dynamic m1A methylation. Identification of m1A sites in human embryonic kidney cells. Comparisons of m1A profiles of wild type HEK293T with ALKBH3 knock out cell line reveals the ALKBH3 specific sites. Stress inducible m1A sites are also identified by comparing the profiles of untreated cells with stress treated cells.

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Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation

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Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation

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

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