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Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq(illumina)]

ABSTRACT: Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq(illumina)]

PROVIDER: PRJNA1000935 | ENA |

REPOSITORIES: ENA

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Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq(illumina)]

Project description:The distribution of m6A across various RNA isoforms and its heterogeneity within single cells are still not well understood. Here, we develop m6A-isoSC-seq, which employs both Oxford Nanopore long-read and Illumina short-read sequencing on the same 10x Genomics single-cell cDNA library with APOBEC1-YTH induced C-to-U mutations near m6A sites. Through m6A-isoSC-seq on a pooled sample of three cell line origins, we unveil a profound degree of m6A heterogeneity at both the isoform and single-cell levels. Through comparisons across single cells, we identify widespread specific m6A methylation on certain RNA isoforms, usually those mis-processed RNA isoforms. Compared to the coding isoforms of the same genes, the expression of highly methylated misprocessed RNA isoforms is more sensitive to METTL3 depletion. These mis-processed RNAs tend to have excessive m6A sites in coding regions, which are targets of CDS-m6A decay (CMD). This study offers undocumented insights into the role of m6A on RNA surveillance.

2025-04-24 | GSE239764 | GEO

Isoform characterization of m6A in single cells identifies its role in RNA surveillance

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Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq(nanopore)]

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Isoform characterization of m6A in single cells identifies its role in RNA surveillance [eDART-Seq]

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Isoform characterization of m6A in single cells identifies its role in RNA surveillance [Direct RNA-seq]

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m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome

Project description:N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (âm6A levelsâ), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3â untranslated regions (3â-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates

2016-06-24 | E-GEOD-66086 | biostudies-arrayexpress

Isoform characterization of m6A in single cells identifies its role in RNA surveillance

Project description:Isoform characterization of m6A in single cells identifies its role in RNA surveillance

| PRJNA1000928 | ENA

Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq(nanopore)]

Project description:Isoform characterization of m6A in single cells identifies its role in RNA surveillance [m6A-isoSC-seq(nanopore)]

| PRJNA1000932 | ENA

Isoform characterization of m6A in single cells identifies its role in RNA surveillance [eDART-Seq]

Project description:Isoform characterization of m6A in single cells identifies its role in RNA surveillance [eDART-Seq]

| PRJNA1000933 | ENA

Isoform characterization of m6A in single cells identifies its role in RNA surveillance [Direct RNA-seq]

Project description:Isoform characterization of m6A in single cells identifies its role in RNA surveillance [Direct RNA-seq]