An SMN2 splicing-correcting antisense oligonucleotide promotes gene looping and transcription activation

We have previously proposed a combined therapy for spinal muscular atrophy based on the upregulation of exon 7 (E7) inclusion into SMN2 mRNA by the antisense oligonucleotide nusinersen (ASO1) together with histone deacetylase inhibitors (HDACi). Using a CRISPR/deadCas-based strategy, we show here that targeting histone acetylation at the SMN2 E7 region duplicates the HDACi effect, which overcomes pleiotropic effects. Most noticeably, targeted acetylation at the E7 region causes acetylation and activation of the 30-kbp-distant promoter. Since E7 and the nusinersen target site map near the SMN2 gene 3'-end, this cross-talk between the two ends of the gene prompted us to use chromosome conformation analysis (3C) to find that ASO1 promotes gene looping. This unpredicted property of ASOs in modulating chromatin 3D configuration depends on cohesin, CTCF, cleavage/polyadenylation factors and a canonical poly(A) signal, and causes promoter activation at a long distance, which expands the therapeutic potential of splicing-correcting ASOs.