Genome-wide Programmable Transcriptional Memory by CRISPR-based Epigenome Editing

General approaches for heritably altering gene expression would enable many discovery and therapeutic efforts. Here, we present CRISPRoff— a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks enabled us to explore the rules for heritable silencing. We identify sgRNAs capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. Our finding that targeted DNA methylation outside of CGIs leads to memorized gene silencing expands the canonical model of methylation-based silencing and broadly enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance. RNA-seq, ChIP-seq, and Whole Genome Bisulfite Sequencing samples to characterize CRISPRoff knockdown efficiency and offtargets.