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

Christina L Jensen; Liang-Fu Chen; Tomek Swigut; Olivia J Crocker; David Yao; Mike C Bassik; James E Ferrell Jr; Alistair N Boettiger; Joanna Wysocka

doi:10.1016/j.molcel.2024.10.021

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

Mol Cell. 2024 Nov 19:S1097-2765(24)00861-X. doi: 10.1016/j.molcel.2024.10.021. Online ahead of print.

Authors

Christina L Jensen¹, Liang-Fu Chen², Tomek Swigut¹, Olivia J Crocker³, David Yao³, Mike C Bassik³, James E Ferrell Jr⁴, Alistair N Boettiger⁵, Joanna Wysocka⁶

Affiliations

¹ Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
² Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
³ Department of Genetics, Stanford University, Stanford, CA 94305, USA.
⁴ Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
⁵ Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
⁶ Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institutes, Stanford University, Stanford, CA 94305, USA. Electronic address: wysocka@stanford.edu.

PMID: 39626660
DOI: 10.1016/j.molcel.2024.10.021

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.

Keywords: CRISPR activation; dCas9; enhancer; gene regulation; genomic distance; promoter.

Grants and funding

R35 GM131792/GM/NIGMS NIH HHS/United States