Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins

Nat Commun. 2025 Aug 26;16(1):7948. doi: 10.1038/s41467-025-63167-x.

Abstract

Programmable epigenome editors modify gene expression in mammalian cells by altering the local chromatin environment at target loci without inducing DNA breaks. However, the large size of CRISPR-based epigenome editors poses a challenge to their broad use in biomedical research and as future therapies. Here, we present Robust ENveloped Delivery of Epigenome-editor Ribonucleoproteins (RENDER) for transiently delivering programmable epigenetic repressors (CRISPRi, DNMT3A-3L-dCas9, CRISPRoff) and activator (TET1-dCas9) as ribonucleoprotein complexes into human cells to modulate gene expression. After rational engineering, we show that RENDER induces durable epigenetic silencing of endogenous genes across various human cell types, including primary T cells. Additionally, we apply RENDER to epigenetically repress endogenous genes in human stem cell-derived neurons, including the reduction of the neurodegenerative disease associated V337M-mutated Tau protein. Together, our RENDER platform advances the delivery of CRISPR-based epigenome editors into human cells, broadening the use of epigenome editing in fundamental research and therapeutic applications.

MeSH terms

  • CRISPR-Cas Systems* / genetics
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism
  • DNA Methyltransferase 3A
  • Epigenesis, Genetic*
  • Epigenome Editing
  • Epigenome* / genetics
  • Gene Editing* / methods
  • HEK293 Cells
  • Humans
  • Mixed Function Oxygenases
  • Neurons / metabolism
  • Proto-Oncogene Proteins
  • Ribonucleoproteins* / genetics
  • Ribonucleoproteins* / metabolism
  • tau Proteins / genetics
  • tau Proteins / metabolism

Substances

  • Ribonucleoproteins
  • DNA Methyltransferase 3A
  • DNMT3A protein, human
  • TET1 protein, human
  • tau Proteins
  • DNA (Cytosine-5-)-Methyltransferases
  • Mixed Function Oxygenases
  • Proto-Oncogene Proteins