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gene expression defects: Epigenetic Editing to mimic and reverse cancer‐associated epigenetic mutations
‐ genomics: genome‐wide sequencing
‐ epigenomics:
DNA (de)methylation
histone modifications
…
‐ transcriptomics
Marianne Rots
Professor of Molecular Epigenetics
Epigenetic Editing
Dept of Pathology and Medical Biology
University Medical Center Groningen
The Netherlands
Edvard Munch,
m.g.rots@umcg.nl
expressionist
Epigenetics:
heritable, yet reversible changes in gene expression,
not encoded in the naked DNA sequence
Chromatin: packaging of DNA
Nobel prize 2012:
Sheep Dolly, 1996
Molecular Biology of the Cell (© Garland Science 2008)
Epigenetic modifications
on the packaging proteins of the DNA (HISTONES)
Epigenetics in Health and Disease
on the DNA molecule
• development, imprinting, …
• normal cellular functioning
• memory
• ageing
• regenerative medicine
Kim et al, 2013
5-methylcytosine
5-hydroxymethylcytosine
5-formylcytosine
5-carboxylcytosine
•
•
•
•
•
diabetes
asthma
psychiatric
cancer
…
=> diagnostic, prognostic, therapeutic…
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Epigenetics in Toxicology
writers
erasers
Epigenetic marks are stable =>
maintained by epigenetic enzymes (writers, erasers)
Epigenetic Editing: the concept
Epigenetic Editing: Editing: targeted rewriting of epigenetic marks
fuse an epigenetic writer or eraser to a engineered DNA binding domain
Epigenetic marks are reversible => adapted by epigenetic enzymes
affected by
• environment,
• food,
• exercise,
• stress,
• toxins,
• …
DNA binding domain + writer = more epi‐marks
indications
transgenerational effects:
- Pesticides
- Plastics
-…
DNA binding domain + eraser = fewer epi‐marks
Human variations, stochasticity, standardized protocols, reproducibility,…
DNA binding domains: designer proteins
The drug-able genome concept
downregulation
• Zinc Finger Proteins:
mammalian transcription factors
clinical trials ongoing
• TALEs
Transcription Activator Like Elements
siRNA:
ATFs:
Artificial Transcription Factor:
A= DNA binding domain
B= Transcription modulator
numerous mRNA molecules
2 DNA molecules
upregulation
cDNA:
ATFs:
plant pathogen
• CRISPRs
but:
Clustered Regularly Interspaced Short Palindromic Repeats
bacterial defense system
limited by cDNA size, isoform choice
all isoforms expressed, in natural ratios
transient -> harmful integrations required
uncontrollable expression induction
Advantages Epigenetic Editing: curable genome
Epigenetic Editing: proof-of-principle
- down:
sustained, inherited without integration
- up:
natural expression control
= closely mimics nature
Endogenous Epigenetic Editing:
pioneering papers
many studies provide proof for
1) cause versus consequence
epi‐mark => gene expression
- targeted DNA methylation= gene repression
(Rivenbark et al., 2012; Siddique et al., 2013, Nunna et al., 2014)
2) accessibility of silenced genes
(reviewed in de Groote et al., Nucl Acids Res 2012)
- targeted DNA de-methylation= gene activation
(Gregory et al., 2013; Maeder et al., 2013, Chen et al., 2014)
- targeted histone modifications= gene repression
VEGF-A (Snowden et al., 2002)
her2/neu (Falahi et al., 2013);
several genes (Konermann et al., 2013)
enhancers (Mendelhall et al., 2013)
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induction of
repressive marks
gene repression
and growth inhibition
Summary
Epigenetic Editing= targeted overwriting of epigenetic marks
=> feasible and effective
• as research tool: mimic or reverse epigenetic mutations
• as biomedical tool: towards a cure for the uncurable
Falahi et al., 2013
Acknowledgments
COLLABORATORS
Local collaborators
(RA Bank, M Hylkema, A vd Berg, GAP Hospers, AGJ vd Zee, GBA Wisman, E Schuuring, …)
Acknowledgments
EPIGENETIC EDITING LAB:
David Cano Rodriguez
Hui Chen
Jelleke Dokters
MHJ Ruiters, Synvolux Inc, Groningen
PJ Verschure, Neth Inst for Systems Biology, UvA
A Jeltsch, T Jurkowsky, Stuttgart, Germany
E Weinhold, Aachen, Germany
A Kiss, Szeged, Hungary
DJ Segal, Davis, CA, USA
B van Zundert, Santiago, Chili
P Blancafort, Perth, Australia
GL Xu, SIBS, Shanghai, China
Fahimeh Falahi
Ieneke (B)TF van der Gun
Rutger AF Gjaltema
Christian Huisman
Pytrick Jellema
Sabine Stolzenburg
Roelien Smouter-Vos
Monique GP van der Wijst
New:
J Song
M Winkle
J Rendon
Former:
TM Geel
ML de Groote
F Bustos
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