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TAS-seq: Subcellular RNA secondary structure profiling by signal peptide-assisted adenosine deamination

ABSTRACT: TAS-seq: Subcellular RNA secondary structure profiling by signal peptide-assisted adenosine deamination

PROVIDER: PRJNA1047552 | ENA |

REPOSITORIES: ENA

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TAS-seq: Subcellular RNA secondary structure profiling by signal peptide-assisted adenosine deamination

Project description:RNA structure critically facilitates RNA function and regulation across a range of biological processes. Recent developments have led to a diversity of structure profiling technologies. Nonetheless, these methods are challenged to profile RNA structure at the resolution of the subcellular compartment. Here, we present TadA-8e-assisted subcellular RNA secondary structure sequencing (TAS-seq), a deaminase-assisted sequencing technology that probes adenosine in single-strand RNA, especially the loop of hairpin structure, and labels it with A-to-G base substitution. By anchoring TadA-8e to nuclear or cytoplasm with signal peptides, TAS-seq profiled the secondary RNA structure of transcriptome localized in these two subcellular compartments respectively. Together, our data revealed that while the majority of the RNA structures remain stable, certain RNAs are subject to conformational change as transit from the nucleus to the cytoplasm, revealing the structural regulation of RNA.

2025-01-01 | GSE249148 | GEO

Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [probes_assay]

Project description:We report evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology for quantitative, base-resolution profiling of m6A. eTAM-seq functions by global adenosine deamination, enabling detection of m6A as persistent A. We demonstrate adenosine-to-inosine (I) conversion rates up to 99% using a hyperactive TadA variant. With eTAM-seq, we profile and quantify m6A in the whole transcriptomes of HeLa cells and mouse embryonic stem cells (mESCs), with simultaneous deconvolution of the transcriptome and epitranscriptome. Further, we showcase deep sequencing-free, site-specific m6A quantification with as few as 10 cells, an input demand that is at least 4 orders of magnitude lower than existing methods. Collectively, eTAM-seq enables sensitive detection and faithful quantification of m6A with limited RNA input, representing a novel solution to deciphering the epitranscriptome.

2022-10-24 | GSE201062 | GEO

Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [site_specific_quantification]

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Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [eTAM-seq]

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Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination

Project description:Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination

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Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [site_specific_quantification]

Project description:Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [site_specific_quantification]

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Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [probes_assay]

Project description:Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [probes_assay]

| PRJNA828168 | ENA

Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [eTAM-seq]

Project description:Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [eTAM-seq]

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Small Molecule-Catalyzed Deamination: Applications in Transcriptome-Wide Profiling of N6-Methyladenosine in RNA (Maize)

Project description:We present a novel N-nitrosation strategy for deamination capable of tolerating DNA/RNA biological macromolecules under mild conditions. A cooperative catalysis combining a carbonyl organocatalyst with a Lewis acid catalyst facilitates the formation of a C-nitro intermediate from a primary amine, which, upon rearrangement into N-nitrosamine, leads to selective deamination of unsubstituted canonical DNA/RNA bases under mild conditions. We employed this new approach to deamination of adenine into hypoxanthine, read as guanine by reverse transcriptases or DNA polymerases, while N6-methyladenosine (m6A) sites resist deamination and remain identified as adenine. We therefore report a chemically mild, low-input detection method for adenosine methylation sequencing at base resolution, named Chemical cooperative catalysis-Assisted for m6A sequencing (CAM-seq).

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Small Molecule-Catalyzed Deamination: Applications in Transcriptome-Wide Profiling of N6-Methyladenosine in RNA (human)

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