Decoding the epigenome to navigate human health
Transcript of Decoding the epigenome to navigate human health
EPINOMICS 2
Epigenome is the instructions for using genome hardware
Hardware Software
Genome Epigenome
EPINOMICS 3
Instructions encoded within non-coding sequence
Genes
98% 2%
Approximately 40% of genome encodes for the
regulation of gene expression
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Techniques for measuring epigenomic features
Output Direct measures
RNA DNA
Methylation
Protein-DNA
Mapping
Accessibility
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Landscape of technologies for measuring epigenome
TECHNOLOGY LANDSCAPE
Co
st
Sequencing
Microarray MeDIP
Bisulfite
conversionChIP
DNase
hypersenitivity
?
RNADNA
Methylation
Protein
Mapping
Open or active
regions
Scop
e
Static ~1% of genome Dynamic
Output of
epigenome
Assay only single
epigenetic factor
All bound
TFs
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✔
✔
✔
Rapid and efficient technology for profiling the epigenome
ChIP-seq DNase-seq ATAC-seq
Input
requirement107 cells 107 cells 100-50,000 cells
Sample prep
time
2 days 4 days 2 hours
(30 min hands-on)
Outputs
• Measures single
factor only
• High skills required
to reproduce
• All proteins bound to
genome in 1 reaction
• Limited factors
can be probed
• Higher-order
chromatin compaction
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Types of epigenomic features measured using ATAC-seq
DNA-binding proteins
Chromatin compaction
Active regulatory elements
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Identification of active regulatory elements from limited number of cells
Closed Active
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Active regulatory elements are fingerprint of cell identity
TET2 TET2 mRNA
HSC
CMP
GMP
MEP
CD8+ T cells
NK cells
100 kb0 5000
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Rapid and sensitive detection of epigenomic modulationC
D4
+ T
ce
ll a
cti
va
tio
n
PM
A/io
no
myc
in
0 hr
1 hr
2 hr
4 hr
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Rapid and efficient technology for profiling the epigenome
DNA-binding proteins
Chromatin compaction
Active regulatory elements
Implications
Dynamic readout of cell
state and functioning
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Binding locations of hundreds of factors read out at once
ATAC-seq
Ge
no
me
-wid
e C
TC
F m
oti
fs
Bound
Unbound
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Detection of therapeutic modulation of epigenomic factors
Resting
Distance from binding site (bp)
Bin
din
g s
co
re
NFAT
CD4+ T cell activation
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Detection of therapeutic modulation of epigenomic factors
Resting
Activated
Distance from binding site (bp)
Bin
din
g s
co
re
NFAT
CD4+ T cell activation
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Rapid and efficient technology for profiling the epigenome
DNA-binding proteins
Chromatin compaction
Dynamic
readout of all
protein-DNA
interactions
Active regulatory elements
Implications
Dynamic readout of cell
state and functioning
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Single basepair resolution nucleosome positioning
Detection of nucleosome
organization at transcription start
sites
Detection of nucleosome
positioning with loss of chromatin
remodeling complex
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Real time monitoring of epigenomic changes in patients
Week 0
Patient treatment
time course
Pati
en
t 20
Week 1
Week 2
Week 3 *Vo
rin
osta
t
* Treatment stopped
50 Fragment length (bp) 600
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Rapid and efficient technology for profiling the epigenome
Chromatin compaction
Implications
Determination of
functional epigenetic
states
DNA-binding proteins
Dynamic
readout of all
protein-DNA
interactions
Active regulatory elements
Implications
Dynamic readout of cell
state and functioning
Mapping epigenomic landscape to create purposeful navigation
EPINOMICS 26
Reference Maps
• Genome variants (1000 Genomes)
• Many regulators (ENCODE)
• Many many regulatory elements
Navigation
• Fast: clinical time scale
• Sensitive: clinical samples
• Actionable: clinical decision criteria
Measuring impact of environmental factors using plant epigenomics
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• Continuously sample soil, air and water
• Material relative easy and inexpensive to obtain
• Able to sample from same plant over time
• Can perform follow-up experiments in controlled lab environment
Acknowledgements
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Team
Fergus Chan - Co-founder
Tracy Nance, PhD - Bioinformatics
Marie Brennan, MD/PhD - Physician
John Latham, PhD - Scientist
Matt Negulescu, Software engineer
Anupama Joshi, Software engineer
Advisers
Howard Chang, MD/PhD - Stanford
Will Greenleaf, PhD - Stanford
Mike Snyder, PhD - Stanford
Anshul Kundaje, PhD - Stanford
Robert Tibshirani, PhD - Stanford
Joseph Ecker, PhD - Salk