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

We studied functional and structural features of mouse and human SINE repeat elements-derived RNAs in SINEUP long non-coding RNAs which upregulate the translation of the target protein coding gene. To check the interaction of functional SINE RNAs with ribosomal RNAs, we created PARIS2 (psoralen analysis of RNA interactions and structures) libraries from SINEUP (with embedded mouse SINEB2 or human FRAM repeat) and the target sense GFP plasmids co-transfected human cells. HEK293T/17 cells were co-transfected with sense EGFP and SINEUP-GFP (with SINEB2) or miniSINEUP-GFP FRAM plasmids. After 24h of transfection, cells were crosslinked by Amotosalen and UV treatment, total RNA was extracted for PARIS2 library preparation. Two biological replicates, each for SINEUP-GFP and miniSINEUP-GFP FRAM were prepared.