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Targeted Manipulation of Cellular RNA m6A Methylation at the Single-Base Level

ABSTRACT: Targeted Manipulation of Cellular RNA m6A Methylation at the Single-Base Level

PROVIDER: PRJNA770674 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16301632_1.fastq.gz	Fastqsanger.gz
	SRR16301632_2.fastq.gz	Fastqsanger.gz
	SRR16301633_1.fastq.gz	Fastqsanger.gz
	SRR16301633_2.fastq.gz	Fastqsanger.gz
	SRR16301634_1.fastq.gz	Fastqsanger.gz

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Targeted Manipulation of Cellular RNA m6A Methylation at the Single-Base Level

Project description:We engineered m6A methyltransferase with dCas13-M14 to achieve site-specific editing of m6A. The resultant m6A editors can be programmed with a guide RNA, allowing functional comparison of single site methylation in different mRNA regions.

2024-10-12 | GSE185755 | GEO

Deciphering m6A dynamics at single-base level during planarian anterior-posterior (AP) axis specification [m6A]

Project description:Deciphering m6A dynamics at single-base level during planarian anterior-posterior (AP) axis specification [m6A]

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Deciphering m6A dynamics at single-base level during planarian anterior-posterior (AP) axis specification [m6A]

Project description:We accomplished the m6A landscapes at single-base resolution with multiple time-points during AP axis regeneration for planarian Dugesia japonica.

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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

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Deciphering m6A dynamics at single-base level during planarian anterior-posterior (AP) axis specification

Project description:Background: The establishment of the anterior-posterior (A-P) axis is a crucial step during tissue repair and regeneration. Despite the association reported recently of N6-methyladenosine (m6A) with regeneration, the mechanism underlying the regulation of m6A in A-P axis specification during regeneration remains unknown. Herein, we deciphered the m6A landscape at a single-base resolution at multiple time points during A-P axis regeneration and constructed the de novo transcriptome assembly of the Dugesia japonica planarian.

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Single base mapping of m6A by an antibody-independent method

Project description:N6-methyladenosine (m6A) is one of the most abundant mRNA modifications in eukaryotes, related to pivotal RNA metabolism processes. The most popular high-throughput m6A identification method relies on the commercial m6A antibody but suffers from poor reproducibility and limited resolution. Exact location of m6A site is of great vital for understanding the dynamics, functions and machinery of RNA methylation. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease–Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic single base m6A map generated by m6A-REF-seq displayed a typical distribution pattern with enrichment adjacent to stop codon. Ligase-based and qPCR validation methods were used to confirm the individual m6A sites and quantify the methylation level, reinforcing the high accuracy of m6A-REF-seq. We applied m6A-REF-seq on five tissues from three mammals, showing that m6A sites were conserved and tend to gather together among species. (m6A-REF-seq had been named as Aim-seq.)

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m6A-Label-seq directly reports m6A methylome at base resolution

Project description:Here we report a metabolic labeling method to map mRNA N6-methyladenosine (m6A) modification transcriptome-wide at base resolution, termed m6A-label-seq. The cells were fed with Se-allyl-L-selenohomocysteine, an analog of methoine, which serves as the precursor of methylation enzyme cofactor, so that cellular RNAs were continuously deposited with N6-allyladenosine (a6A) at supposed m6A sites. We enriched a6A-containing mRNAs and sequenced their a6A sites which are identical to m6A sites, based on iodination-induced misincorporation during reverse transcription.

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m6A-Label-seq directly reports m6A methylome at base resolution

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Deciphering m6A dynamics at single-base level during planarian anterior-posterior (AP) axis specification [mRNA]

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| PRJNA893586 | ENA