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In-cell RNA secondary structure analysis of functional SINE transcripts

ABSTRACT: SINEUPs are long non-coding RNAs which contain a functionally crucial SINE repeat element and positively regulate target mRNA translation at post-transcription level. To study secondary (2D) structure of these functional SINE-derived RNAs, various SINEUP-GFP plasmids containing different mouse SINEB2 repeat elements or human SINE FRAM repeat were transfected along with sense EGFP plasmid in HEK293T/17 cells. Total RNA in transfected cells were probed at flexible regions with NAI-N3 reagent and icSHAPE (in-vivo click selective hydroxyl acylation and profiling experiment) libraries were prepared. To further understand the structure dynamics of SINE transcripts in subcellular locations, cells were fractionated in nuclear and cytoplasmic fractions after 24 h of transfection and fraction-specific icSHAPE libraries were constructed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE224534 | GEO | 2023/02/06

REPOSITORIES: GEO

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RNA-RNA interaction analysis of functional SINE repeat elements-derived transcripts

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