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DMS-MaPseq: A genome-wide or targeted approach for RNA structure probing in vivo

ABSTRACT: DMS-MaPseq: A genome-wide or targeted approach for RNA structure probing in vivo

OTHER RELATED OMICS DATASETS IN: GSE84537

PROVIDER: PRJNA329551 | ENA |

REPOSITORIES: ENA

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Probing in vivo RNA structure with optimized DMS-MaPseq in rice

Project description:Here, we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). Our study presents an optimized DMS-MaPseq for probing in vivo RNA structure in rice.

2022-04-05 | GSE197245 | GEO

DMS-MaPseq: A genome-wide or targeted approach for RNA structure probing in vivo

Project description:Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features for each molecule, and allows genome-wide studies as well as focused investigations of low abundance RNAs. We apply DMS-MaPseq to Drosophila melanogaster ovaries—the first experimental analysis of RNA structure in an animal tissue—and demonstrate its utility in the discovery of a functional RNA structure involved in the non-canonical GUG translation initiation of the human FXR2 mRNA. Additionally, we use DMS-MaPseq to compare the in vivo structure of messages in their pre-mRNA and mature forms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand our ability to monitor RNA structure in vivo.

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Probing in vivo RNA structure with optimized DMS-MaPseq in rice

Project description:Probing in vivo RNA structure with optimized DMS-MaPseq in rice

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Targeted DMS probing of SF3A3 5' UTR

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DMS-MapSeq Analysis of Antisense Oligonucleotide Binding to lncRNA PANDA

Project description:While various methods exist for examining and visualizing the structure of RNA molecules, dimethyl sulfate-mutational profiling and sequencing (DMS-MaPseq) stands out for its simplicity and versatility. This technique has proven effective for studying RNA structures both in vitro and in complex biological settings. We've updated the protocol for using DMS-MaPseq, and it can also be employed to identify the binding of antisense oligonucleotides (ASOs) to RNA. By applying this updated protocol, we successfully characterized the structural ensemble of the HIV1 Rev Response Element (RRE), along with its two alternative structures. The findings align with previously published research. Additionally, we resolved the structure of the long non-coding RNA PANDA, which was previously unknown. Moreover, we used PANDA as a basis for designing ASOs and confirmed their binding through a substantial decrease in DMS-reactivities at the anticipated ASO binding locations.

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Project description: Not available

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Project description:Targeted DMS probing of SF3A3 5' UTR

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