Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery: Nature Biotechnology

A.M. Chiarella, K.V. Butler, B.E. Gryder, D. Lu, T.A. Wang, X. Yu, S. Pomella, J. Khan, J. Jin, N.A. Hathaway

Research output: Contribution to journalArticlepeer-review


Gene expression can be activated or suppressed using CRISPR­–Cas9 systems. However, tools that enable dose-dependent activation of gene expression without the use of exogenous transcription regulatory proteins are lacking. Here we describe chemical epigenetic modifiers (CEMs) designed to activate the expression of target genes by recruiting components of the endogenous chromatin-activating machinery, eliminating the need for exogenous transcriptional activators. The system has two parts: catalytically inactive Cas9 (dCas9) in complex with FK506-binding protein (FKBP) and a CEM consisting of FK506 linked to a molecule that interacts with cellular epigenetic machinery. We show that CEMs upregulate gene expression at target endogenous loci up to 20-fold or more depending on the gene. We also demonstrate dose-dependent control of transcriptional activation, function across multiple diverse genes, reversibility of CEM activity and specificity of our best-in-class CEM across the genome. © 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.
Original languageEnglish
Pages (from-to)50-55
Number of pages6
JournalNat. Biotechnol.
Issue number1
Publication statusPublished - 2020


  • Chemical activation
  • Computational electromagnetics
  • Machinery
  • Molecules
  • Proteins
  • Dose-dependent
  • FK506-binding proteins
  • Regulatory protein
  • Small molecules
  • Target genes
  • Transcriptional activations
  • Transcriptional activators
  • Transcription
  • cem 114
  • cem 87
  • cem 88
  • chemokine receptor CXCR4
  • CRISPR associated endonuclease Cas9
  • fk 506 binding protein
  • guide RNA
  • interleukin 1 receptor blocking agent
  • ligand
  • MyoD1 protein
  • octamer transcription factor 4
  • tacrolimus
  • unclassified drug
  • BRD4 protein, human
  • cell cycle protein
  • transcription factor
  • chromatin
  • clustered regularly interspaced short palindromic repeat
  • controlled study
  • dose response
  • epigenetics
  • gene activation
  • gene expression
  • gene function
  • gene locus
  • gene targeting
  • genetic transfection
  • HEK293T cell line
  • human
  • human tissue
  • Letter
  • nonhuman
  • priority journal
  • process optimization
  • promoter region
  • protein expression level
  • transcription initiation
  • upregulation
  • CRISPR Cas system
  • gene expression regulation
  • genetic epigenesis
  • genetics
  • HEK293 cell line
  • human genome
  • metabolism
  • time factor
  • Cell Cycle Proteins
  • Chromatin
  • CRISPR-Cas Systems
  • Epigenesis, Genetic
  • Gene Expression Regulation
  • Genome, Human
  • HEK293 Cells
  • Humans
  • RNA, Guide
  • Time Factors
  • Transcription Factors


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