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Probing the structure of the lncRNA DAMER and its interaction with ATF4 mRNA using SHAPE-MaP

ABSTRACT: This experiment was conducted to obtain direct structural evidence for the base-pairing interaction between DAMER and ATF4 mRNA. In vitro transcribed RNAs (DAMER-WT, ATF4 mRNA, DAMER mutants) were folded either alone or together and subsequently modified with the SHAPE reagent 1-methyl-7-nitroisatoic anhydride (1M7). A DMSO-only reaction served as the negative control. Sites of modification, which indicate flexible nucleotides, were identified as mutations during reverse transcription. The resulting cDNA was used for library construction and deep sequencing. The data were processed using ShapeMapper2 to calculate reactivity profiles and model RNA secondary structures.

ORGANISM(S): Homo sapiens

PROVIDER: GSE309440 | GEO | 2025/10/27

REPOSITORIES: GEO

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