Extended Data Fig. 8: isASO-ID. Wing chemistry determines the ASO-protein interactome.
From: Profiling the interactome of oligonucleotide drugs by proximity biotinylation
SILAC-MS/MS for either BG-ASO or CA-ASO (20mer containing either MOE or LNA wings) at 25 nM against Lipofectamine 3000. Plotted was the normalized enrichment (log2) of replicate 1 against replicate 2 with swapped SILAC labels. In a), b), d) and e) all proteins enriched >2-fold in both replicates are highlighted and colored according to their RNA- and/or DNA-binding function (blue = RNA-binding, orange = DNA binding). Furthermore, selected paraspeckle core proteins (brown), P-body components (gold), and ribosomal proteins (purple) are highlighted as well as selected known ASO interactors not passing the threshold. In c) and f) the same proteins annotated in a), b), d) and e) are highlighted regardless their enrichment in this particular part of the experiment. a) Enrichment with 25 nM BG-ASO (20mer MOE) over Lipofectamine 3000 b) Enrichment with 25 nM BG-ASO (20mer LNA) over Lipofectamine 3000. c) Enrichment with 25 nM BG-LNA (20mer) over 25 nM BG-MOE (20mer). d) Enrichment with 25 nM CA-MOE (20mer) over Lipofectamine 3000. e) Enrichment with 25 nM CA-LNA (20mer) over Lipofectamine 3000. f) Enrichment with 25 nM CA-LNA (20mer) over 25 nM CA-MOE (20mer). For the isASO-ID SILAC-MS/MS experiments in panel a-f, detected proteins were colored according to their biological function as P-body component (gold), paraspeckle protein (red) and the annotated GO terms DNA binding (orange) and RNA binding (blue). Ribosomal proteins were colored in purple. Proteins passing the applied enrichment threshold (>1 log2 unit) are represented as filled squares. Carboxylases are highlighted as filled black squares and represent unregulated control proteins.
