CRISPR-mediated synergistic epigenetic and transcriptional control

Targeted activation of endogenous genes is an important approach for genome engineering. Here we report that the nuclease-deactivated dCas9 fused to a transcriptional activator (VPR) and an epigenetic effector (the catalytic domain of histone acetyltransferase p300core) simultaneously, sequentially, or as a quadripartite effector, can lead to synergistic activation of target genes. The composite activator, VPRP, behaves more efficiently than individual activators across a set of genes in various cell types. We report unintended off-target changes to chromatin acetylation and transcription from expression of p300core. Our work demonstrates that transcriptional and epigenetic effectors can synergize with enhanced gene activation and highlights the need for optimization of epigenetic effectors to reduce off-targets for further applications. Overall design: For RNA-seq, 12 samples were sequenced with paired-end sequencing. The set contains 6 groups, each containing two biological replicates. For H3k27Ac ChIP-seq, 10 samples were sequenced. The set contains 5 groups, each containing two biological replicates.