Augmenting and directing long-range CRISPR-mediated activation in human cells

Epigenetic editing is an emerging technology that uses artificial transcription factors (aTFs) to regulate expression of a target gene. Although human genes can be robustly upregulated by targeting aTFs to promoters, the activation induced by directing aTFs to distal transcriptional enhancers is substantially less robust and consistent. Here we show that long-range activation using CRISPR-based aTFs in human cells can be made more efficient and reliable by concurrently targeting an aTF to the target gene promoter. We used this strategy to direct target gene choice for enhancers capable of regulating more than one promoter and to achieve allele-selective activation of human genes by targeting aTFs to single-nucleotide polymorphisms embedded in distally located sequences. Our results broaden the potential applications of the epigenetic editing toolbox for research and therapeutics. Long-range CRISPR activation can be enhanced by concurrent recruitment of artificial TFs to the enhancer and promoter of a target gene. This CRISPR activation system can be employed to achieve allele-selective gene upregulation by differentially targeting single-nucleotide polymorphisms embedded in enhancers or other distally located sequences.