JoVE Logo
Faculty Resource Center

Sign In





Representative Results






Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published: September 20th, 2018



1Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Curriculum in Genetics and Molecular Biology, University of North Carolina, 2College of Arts and Sciences, Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, 3Chemical Biology and Drug Discovery, Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 4Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, University of North Carolina

Regulation of the chromatin environment is an essential process required for proper gene expression. Here, we describe a method for controlling gene expression through the recruitment of chromatin-modifying machinery in a gene-specific and reversible manner.

Regulation of chromatin compaction is an important process that governs gene expression in higher eukaryotes. Although chromatin compaction and gene expression regulation are commonly disrupted in many diseases, a locus-specific, endogenous, and reversible method to study and control these mechanisms of action has been lacking. To address this issue, we have developed and characterized novel gene-regulating bifunctional molecules. One component of the bifunctional molecule binds to a DNA-protein anchor so that it will be recruited to an allele-specific locus. The other component engages endogenous cellular chromatin-modifying machinery, recruiting these proteins to a gene of interest. These small molecules, called chemical epigenetic modifiers (CEMs), are capable of controlling gene expression and the chromatin environment in a dose-dependent and reversible manner. Here, we detail a CEM approach and its application to decrease gene expression and histone tail acetylation at a Green Fluorescent Protein (GFP) reporter located at the Oct4 locus in mouse embryonic stem cells (mESCs). We characterize the lead CEM (CEM23) using fluorescent microscopy, flow cytometry, and chromatin immunoprecipitation (ChIP), followed by a quantitative polymerase chain reaction (qPCR). While the power of this system is demonstrated at the Oct4 locus, conceptually, the CEM technology is modular and can be applied in other cell types and at other genomic loci.

Chromatin consists of DNA wrapped around histone octamer proteins that form the core nucleosome particle. Regulation of chromatin compaction is an essential mechanism for proper DNA repair, replication, and expression1,2,3. One way in which cells control the level of compaction is through the addition or removal of various post-translational histone tail modifications. Two such modifications include (1) lysine acetylation, which is most commonly associated with gene activation, and (2) lysine methylation, which can be associated with either gene activation or repression, depe....

Log in or to access full content. Learn more about your institution’s access to JoVE content here

1) Cell Line Culture for Producing Lentivirus

  1. Grow fresh, low-passage (less than passage 30) 293T human embryonic kidney (HEK) cells in high-glucose Dulbecco's modified Eagle's medium (DMEM) base media supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, 1x non-essential amino acids (NEAA), Pen/Strep, 2-mercaptoenthanol in a 37 °C incubator with 5% CO2. Split the cells every 3 - 5 d and before they become > 95% confluent.
  2. Passage 293T HEK cells with 18 x 106<.......

Log in or to access full content. Learn more about your institution’s access to JoVE content here

We recently developed CEMs and demonstrated that this technology can be applied to regulate gene expression and the chromatin environment at a reporter locus in a dose-dependent and reversible manner. In Figure 1, a model of the lead CEM, CEM23, is shown. HDAC machinery is recruited to the reporter locus by the HDAC inhibitor which, in this case, is the GFP reporter inserted at the Oct4 locus.

Log in or to access full content. Learn more about your institution’s access to JoVE content here

Here, we described the recently developed CEM system being applied to regulate gene expression and chromatin environment at a specific gene in a dose-dependent manner. We provide an accurate method to study the dynamics involved in regulating gene expression through the selective recruitment of specific endogenous chromatin regulatory proteins. This is a highly modular technology that can be applied to investigate how different protein- and chromatin-modifying complexes work in concert to properly regulate the chromatin .......

Log in or to access full content. Learn more about your institution’s access to JoVE content here

The authors would like to thank the members of the Hathaway and Jin laboratories for their helpful discussions. The authors also thank Dan Crona and Ian MacDonald for their critical reading of the manuscript. This work was supported in part by Grant R01GM118653 from the U.S. National Institutes of Health (to N.A.H.); and by Grants R01GM122749, R01CA218600, and R01HD088626 from the U.S. National Institutes of Health (to J.J.). This work was also supported by a tier 3 and a student grant from the UNC Eshelman Institute for Innovation (to N.A.H and A.M.C, respectively). Additional funding from a T-32 GM007092 (to A.M.C) supported this work. Flow cytometry data was obtain....

Log in or to access full content. Learn more about your institution’s access to JoVE content here

Name Company Catalog Number Comments
DMEM Corning 10-013CV
NEAA Gibco 11140-050
HEPES (for tissue culture) Corning 25-060-Cl
BME (2-Mercaptoethanol) Gibco 21985-023
FBS Atlantic Biologicals S11550 Individual lots tested for quality
Covaris tubes ThermoScientific C4008-632R
Covaris caps ThermoScientific C4008-2A
PEI (polyethylenimine) Polysciences 23966-1
Transfection media (Opti-mem) Gibco 31985070
Virus centrifuge tubes Beckman Coulter 344058
Virus filter membrane Corning 431220
Polybrene Santa Cruz Biotechnology SC134220
0.25 % Trypsin Gibco 25200-056 with EDTA
0.05 % Trypsin Gibco 25400-054 with EDTA
Puromycin InvivoGen ant-pr
Blasticidin InvivoGen ant-bl
SYBR Green Master Mix (asymmetrical cyanine dye) Roche 4913914001
H3K27ac antibody Abcam ab4729
(ChIP kit) ChIP-IT High Sensitivity Kit Active Motif 53040
Sonicator Covaris E110
Ultracentrifuge Optima XPN-80
SW-32 centrifuge rotor Beckman Coulter 14U4354
SW-32 Ti centrifuge buckets Beckman Coulter 130.2
LentiX 293 Human Embryonic Kidney Clontech 632180
PBS Corning 46-013-CM
BSA Fisher BP9700
EGTA Sigma E3889
EDTA Fisher S311-100
NaCl Fisher S271-1
Glycerol Fisher G33-1
Tris Fisher BP152
NP40 Roche 11754599001
Triton MP Biomedicals 807426
Glycine Fisher BP381-500
TE buffer Fisher BP2474-1
HEPES (for ChIP) Fisher BP310-100
Gelatin Sigma G1890
Flow cytometer, Attune NxT Thermo Fisher A24858
FKBP-Gal4 plasmid Addgene 44245
psPAX2 plasmid Addgene 12260
pMD2.G plasmid Addgene 12259
Nanodroplets MegaShear N/A
DNA Nanodrop Thermo Fisher ND1000
Protease Inhibitors (Leupeptin) Calbiochem/EMD 108975
Protease Inhibitors (Chymostatin) Calbiochem/EMD 230790
Protease Inhibitors (Pepstatin) Calbiochem/EMD 516481
CiA:Oct4 mESC The kind gift of G. Crabtree
Lif-1C-alpha - producing Cos cells The kind gift of J. Wysocka

  1. Alabert, C., Groth, A. Chromatin replication and epigenome maintenance. Nature Reviews Molecular Cell Biology. 13 (3), 153-167 (2012).
  2. Venkatesh, S., Workman, J. L. Histone exchange, chromatin structure and the regulation of transcription. Nature Reviews Molecular Cell Biology. 16 (3), 178-189 (2015).
  3. Bannister, A. J., Kouzarides, T. Regulation of chromatin by histone modifications. Cell Research. 21 (3), 381-395 (2011).
  4. Gräff, J., Tsai, L. -. H. Histone acetylation: molecular mnemonics on the chromatin. Nature Reviews Neuroscience. 14 (2), 97-111 (2013).
  5. Verdin, E., Ott, M. 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond. Nature Reviews Molecular Cell Biology. 16 (4), 258-264 (2015).
  6. Hathaway, N. A., et al. Dynamics and memory of heterochromatin in living cells. Cell. 149 (7), 1447-1460 (2012).
  7. Ren, J., Hathaway, N. A., Crabtree, G. R., Muegge, K. Tethering of Lsh at the Oct4 locus promotes gene repression associated with epigenetic changes. Epigenetics. 13 (2), 173-181 (2018).
  8. Stanton, B. Z., Hodges, C., et al. Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nature Genetics. 49 (2), 282-288 (2017).
  9. Koh, A. S., Miller, E. L., et al. Rapid chromatin repression by Aire provides precise control of immune tolerance. Nature Immunology. 19 (2), 162-172 (2018).
  10. Chen, T., Gao, D., et al. Chemically Controlled Epigenome Editing through an Inducible dCas9 System. Journal of the American Chemical Society. 139 (33), 11337-11340 (2017).
  11. Braun, S. M. G., et al. Rapid and reversible epigenome editing by endogenous chromatin regulators. Nature Communications. 8 (1), 560 (2017).
  12. Butler, K. V., Chiarella, A. M., Jin, J., Hathaway, N. A. Targeted Gene Repression Using Novel Bifunctional Molecules to Harness Endogenous Histone Deacetylation Activity. ACS Synthetic Biology. 7 (1), (2018).
  13. Kasoji, S. K., et al. Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath. PLoS ONE. 10 (7), 0133014 (2015).
  14. Chiarella, A. M., et al. Cavitation enhancement increases the efficiency and consistency of chromatin fragmentation from fixed cells for downstream quantitative applications. Biochemistry. 57 (19), 2756-2761 (2018).
  15. Gao, Y., et al. Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nature Methods. 13 (12), 1043-1049 (2016).

This article has been published

Video Coming Soon

JoVE Logo


Terms of Use





Copyright © 2024 MyJoVE Corporation. All rights reserved