Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

Summary

Gene silencing is instrumental to interrogate gene function and holds promise for therapeutic applications. Here, we repurpose the endogenous retroviruses’ silencing machinery of embryonic stem cells to stably silence three highly expressed genes in somatic cells by epigenetics. This was achieved by transiently expressing combinations of engineered transcriptional repressors that bind to and synergize at the target locus to instruct repressive histone marks and de novo DNA methylation, thus ensuring long-term memory of the repressive epigenetic state. Silencing was highly specific, as shown by genome-wide analyses, sharply confined to the targeted locus without spreading to nearby genes, resistant to activation induced by cytokine stimulation, and relieved only by targeted DNA demethylation. We demonstrate the portability of this technology by multiplex gene silencing, adopting different DNA binding platforms and interrogating thousands of genomic loci in different cell types, including primary T lymphocytes. Targeted epigenome editing might have broad application in research and medicine.

Graphical Abstract

Highlights

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  Repurposing the ERV silencing machinery for targeted epigenetic gene silencing

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  Hit-and-run delivery of combinations of engineered transcriptional repressors (ETRs)

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  Inheritable and stimulation-resistant silencing of endogenous genes by DNA methylation

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  Portable to different cell types and DNA binding platforms and amenable to multiplexing

Abstract

Transient co-expression of engineered transcriptional repressors (ETRs) allows for stable and highly specific epigenetic silencing of endogenous genes, which is amenable to multiplexing and can be reverted by targeted DNA demethylation.