Long-range regulation of transcription scales with genomic distance in a gene-specific manner

Abstract

Although critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here, we bypass the need for sequence-specific transcription factors (TFs) and recruit activators directly using a chimeric array of gRNA oligos to target dCas9 fused to the activator VP64-p65-Rta (CARGO-VPR). We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible when targeted with a single guide. We utilize CARGO-VPR across the Prdm8-Fgf5 locus in mouse embryonic stem cells (mESCs), where neither gene is expressed. Although activator recruitment to any tested region results in the transcriptional induction of at least one gene, the expression level strongly depends on the genomic distance between the promoter and activator recruitment site. However, the expression-distance relationship for each gene scales distinctly in a manner not attributable to differences in 3D contact frequency, promoter DNA sequence, or the presence of repressive chromatin marks at the locus. • dCas9 targeting with single gRNAs often fails to result in detectable dCas9 binding • CARGO-VPR achieves effective activator recruitment to arbitrary genomic sites • Expression decays with genomic distance between the promoter and activator binding site • Distance-transcription relationship scales in a gene-specific manner Jensen et al. show that targeting dCas9-VPR using a multiplexed array of RNA guides results in effective activator recruitment to promoter-distal, previously inaccessible genomic sites, allowing for long-range transcriptional activation. The transcriptional response decays with genomic distance between the promoter and activator recruitment site, but the scaling of this relationship is gene specific.

Topics & Concepts