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Single-cell m6A profiling reveals mRNA methylation heterogeneity and unique cellular m6A signatures

ABSTRACT: Single-cell m6A profiling reveals mRNA methylation heterogeneity and unique cellular m6A signatures

PROVIDER: PRJNA750145 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15268500_1.fastq.gz	Fastqsanger.gz
	SRR15268500_2.fastq.gz	Fastqsanger.gz
	SRR15268600_1.fastq.gz	Fastqsanger.gz
	SRR15268600_2.fastq.gz	Fastqsanger.gz
	SRR15268700_1.fastq.gz	Fastqsanger.gz

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Single-cell m6A profiling reveals mRNA methylation heterogeneity and unique cellular m6A signatures

Project description:Single-cell m6A profiling reveals mRNA methylation heterogeneity and unique cellular m6A signatures

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Single-cell m6A profiling reveals mRNA methylation heterogeneity and unique cellular m6A signatures

Project description:We used DART-seq to map m6A methylation of RNA in single HEK293T cells. We also used DART-seq to map m6A from bulk RNA from HEK293T cells. Using the 10X Genomics and SMART-seq2 platforms, we sequenced a total of 19,533 experimental and control cells using the 10X Genomics platform, and 1,471 experimental and control cells using SMART-seq2. We then used a Bullseye, a computational pipeline developed within the lab, to identify m6A sites from the C-to-U mutations in bulk and single-cell datasets. We find that most m6A methylation is highly heterogenous from cell-to-cell. RNAs containing m6A methylation, are infrequently methylated, and that most individual sites are rarely methylated within the population. Additionally, we are able to identify differentially methylated RNAs in different cellular states from within a single population, and use m6A methylation information to perform clustering of single cells to find a source of novel cellular heterogeneity.

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Project description:m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, m6A differential patterns among organs have not been well characterized. The goal of the study is to comprehensively analyze m6A patterns of numerous types of RNAs, the relationship between transcript level and m6A methylation extent, and m6A differential patterns among organs in Arabidopsis. In total, 18 libraries were sequneced. For the 3 organs: leaf, flower and root, each organ has mRNA-Seq, m6A-Seq and Input sequenced. And each sequence has 2 replicats.

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2023-09-18 | PXD045434 |

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Structural basis of YTH domain as m6A reader

Project description:The N6-methyladenosine (m6A) is the most abundant internal modification in almost all eukaryotic messenger RNAs, and is dynamically regulated. Therefore, identification of m6A readers is especially important in determining the cellular function of m6A. YTHDF2 has recently been characterized as the first m6A reader that regulates the cytoplasmic stability of methylated RNA. Here we show that YTHDC1 is a nuclear m6A reader and report the crystal structure of the YTH domain of YTHDC1 bound to m6A-containing RNA. We further determined the structure of another YTH domain, YTHDF1, and found that the YTH domain utilizes a conserved aromatic cage to specifically recognize the methyl group of m6A. Our structural characterizations of the YTHDC1-m6A RNA complex also shed light on the molecular basis for the preferential binding of the GG(m6A)C sequence by YTHDC1 and confirm the YTH domain as a specific m6A RNA reader. PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) was applied to human YTHDC1 protein to identify its binding sites.

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