Fig. 3: SINEUP structure dynamics and interaction with HNRNPK in the nucleus and cytoplasm. | Nature Communications

Fig. 3: SINEUP structure dynamics and interaction with HNRNPK in the nucleus and cytoplasm.

From: Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation

Fig. 3

a Normalized icSHAPE reactivity score profiles of mouse antisense (AS) Uchl1 SINEB2 RNA in the nucleus and cytoplasm and b related 2D-structure models created from icSHAPE data. SINEUP motifs from M1 to M7 are indicated by dashed squares. c Normalized icSHAPE reactivity score profiles of human SINE RNA FRAM in the nucleus and cytoplasm and d their respective 2D-structure models. Different structural regions between the compartments are shaded in blue boxes. e seCLIP data for HNRNPK binding to SINEUP-GFP RNA (of AS Uchl1 SINEB2) in the nuclear and cytoplasmic fractions of HEK293T cells. IP, immunoprecipitation against HNRNPK; input, not immunoprecipitated, contains all RNA–protein complexes in the given fraction. Normalized peak regions representing significant enrichment of HNRNPK binding site in IP compared to input are indicated as horizontal bars. Identified HNRNPK binding sites are marked by a red line on 2D-structure models of AS Uchl1 SINEB2 in (b).

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