Transcriptomics

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SmartSHAPE: a low-input method for transcriptome-wide RNA structure probing uncovers RNA structure landscape in mouse colonic macrophages


ABSTRACT: Here, we report the development and application of smartSHAPE, a SHAPE-like RNA structure probing method that requires low amounts of input due to the largely reduced artefact signals of premature RT stops and increased efficiency of library construction. We used smartSHAPE to profile the global RNA secondary structures of two subtypes of mouse colonic macrophages upon inflammation, and provided evidence that RNA conformational changes at protein binding sites regulate gene expression and, in turn, immune responses. We predicted functional RNA structure elements based on smartSHAPE structure data, and discovered that PD-L1 contains a YRY-motif stem-loop structural element within the 3’UTR, which triggers RNA degradation mediated by Regnase-1.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE155961 | GEO | 2021/03/31

REPOSITORIES: GEO

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