Fig. 2: In-cell SINE structures and conserved motifs in functionally active SINEUPs.

a Antisense (AS) Uchl1 SINEB2 RNA secondary structure based on icSHAPE data (right) is compared with the one previously identified using chemical footprinting¹¹. In icSHAPE-based structure, squares highlight the common sequences and structure motifs in in-cell structures of SINE, with their corresponding motif number. AGG (blue) and UGG (red) motifs are shown. Location of SINEUP motifs in icSHAPE-derived structures of functionally active SINE RNAs from (b) antisense Txnip SINEB2, (c) antisense Uxt SINEB2-b and (d) human SINE element FRAM. e icSHAPE-derived RNA secondary structures and local SINEUP motifs (colors as in Fig. 2a) of functionally dormant wild-type antisense Gadd45α SINEB2-a and its deletion mutant antisense Gadd45α SINEB2-a [Δ27–36] with gained SL1. f Effect of antisense Gadd45α SINEB2-a deletion mutants on GFP protein expression as measured by Western blot. An empty vector was used as the negative control. Four mutants with random deletion, as listed in the Figure, were compared with the full-length construct (Full). N = 3 biologically independent experiments, data are mean values ± standard deviation, P value by two-tailed Student’s t-test. AS antisense, Δ deletion, SL1 stem-loop 1. Source data for (f) are provided as a Source Data file.