Transcript Group meeting on 10.28.04

Epigenetics
Slides by GC Yuan
3/28/12
One genome, Many cell-types
•The genome is constant
across all cell types.
•Tissue specific gene
expression cannot be
explained by the DNA
sequence alone.
•Epigenetics provides an
addition layer of
regulatory control.
•errraticwisdom.com
Epigenetics
• Epigenetics refers to changes in phenotype
(appearance) or gene expression caused by
mechanisms OTHER THAN changes in the
underlying DNA sequence.
• In the most stringent sense, epigenetics only
refers to heritable changes --- those can be
passed on to daughter cells (somatic) or next
generation (germline).
• In common usage of the term, epigenetics does
not have to be heritable.
Epigenetic mechanisms
• Nucleosome positions
• Histone modification
• DNA methylation
Chromatin
• DNA is packaged into
chromatin.
• Nucleosome is the
fundamental unit of
chromatin. It wraps
146 bp DNA.
• Higher-order
organization is still
poorly understood.
Felsenfeld and Groudine 2003
DNA in the nucleus is
complexed with histones to form
nucleosomes
10,000 nm
11 nm
30nm
1bp (0.3nm)
Individual histone proteins
Complete nucleosome
with DNA
Richard Wheeler
Histone modification
The amino acids on the N-terminus of
histones can be covalently modified
at multiple locations in multiple ways.
Felsenfeld and Groudine 2003
Histonations???
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Acetylation
Methylation (me1, me2, me3)
Phosphorylation
Ubiquitination
Sumoylation
Citrulination
ADP-ribosylation
Histone variants
The core histone proteins have a number of
variants.
• H2A.Z
(early embryonic development?)
• H2A.X
(maybe DSB repair???)
• H3.3
(???)
• CENP-A
(centromeres)
• …
Mapping
histones
by ChIP-seq
•Extract proteinbound DNA by
chromatin
immunoprecipitation
•Detect the
nucleotide sequence
of the ChIP-DNA by
next generation
sequencing
technology.
•Park 2009, Nature Rev Gen
Euchromatin and heterochromatin
Euchromatin
Heterochromatin
Heterochromatin is enriched near
centromeres and telomeres.
The action’s in the middle – sequence signatures
are used to regulate nucleosome placement
Segal 2006
The action’s in the middle – sequence signatures
are used to regulate nucleosome placement
Segal 2006
DNA methylation
DNA methylation
normally occurs only at
CpG dinucleotides and
can be inherited during
cell-division.
Alberts et al.
Molecular Biology of the Cell
More “track” data, typically % methylation
Weber 2005
Rauch 2007
Lister/Ecker 2011
Genome-wide DNA methylation detection
• Bisulfite sequencing
– Convert unmethylated C to U
(RNA version of T).
– Sequence the original and converted
sequences and look for differences.
• Methylated DNA immunoprecipitation (MeDIP)
– Similar to ChIP, but use antibodies against methyl-C
instead, followed by microarray or sequencing.
• Endonuclease digestion
– Digest by methylation-sensitive, sequence-specific
enzymes followed by sequencing.
Epigenetic Regulation of
Transcription
Promoter DNA methylation is negatively
correlated with gene expression
Lister et al. 2009, Nature
DNA methylation pattern in genomic regions
(of ES cells) is unique
Lister et al. 2009
Genome-wide nucleosome positions
Genome-wide nucleosome positions can be identified by
MNase based tiling array or DNA sequencing methods
Most promoters contain nucleosome depleted regions
before TSS.
Yeast
Lee et al. 2007
Human
Schones et al. 2008
Transcription factor binding sites (TFBSs)
are likely to be nucleosome-depleted
TFBSs tend to be
nucleosome-depleted.
Motif sites that are
unbound in our condition
but bound in other
conditions also tend to be
nucleosome depleted.
Motif sites that are
always unbound do not
have nucleosomedepletion property.
Yuan et al. 2005
Transcriptional regulation by
nucleosome and histone modification
• Nucleosome positioning
is mainly repressive
• Histone modification can
be either active or
repressive
TF
TF
H3K9ac
Ace
TFTF
TF
TF
H3K27me3
TF target site
Correlation between gene expression and
different histone modification patterns
Barski et al. 2007
Histone code hypothesis
“… multiple histone modifications, acting in a combinatorial
or sequential fashion on one or multiple histone tails,
specify unique downstream functions …”
― Strahl and Allis,
Nature, (2000)
Role of Epigenetics in
Development
Polycomb family proteins silence
developmental genes
(DNA methyltransferases)
Sparmann and Lohuizen Nature Reviews Cancer 6, 846–856 (November 2006) | doi:10.1038/nrc1991
Polycomb binding represses gene expression
•Polycomb complexes repress gene expression
through H3K27me3.
Ac
Suz12
Eed
Jmj
Ezh2
PRC2
me
Bmi1
HPC
HPH
Ring1
PRC1
Polycomb targets developmental genes in ES
expressed
Oct4
Nanog
Sox2
repressed
Polycomb
Kim et al. 2008, Cell
Enrichment in Polycomb
ChIP-bound gene functions
Boyer et al. 2006, Cell
Bivalent domains in ES cells
ES cells contain many
bivalent domains: H3K4me3
(active mark) and H3K27me3
(repressive mark)
These genes are
“poised for activation.”
High/intermediate/low CpG content
Mikkelsen et al. 2007
Lineage-specific epigenetic patterns
activation
repression
Housekeeping
Neural TF
Neurogenesis
Adipogenesis
Epigenetic patterns
change during cell
differentiation.
Mikkelsen et al. 2007
Neural progenitor
Brain/lung TF,
multiple TSSs
Epigenetics and Diseases
General DNA methylation signature of cancer
• (Many) CpG islands are (usually)
unmethylated in normal cells.
• In cancer, some of the CpG islands are
hypermethylated, repressing some tumor
repressor genes.
• But the overall level of DNA methylation is
typically decreased.
The CpG Island Methylator Phenotype (CIMP)
Toyota M et al. PNAS 1999;96:8681-8686
Jean-Pierre Issa. Nature Reviews Cancer 4, 988-993 2004
Methylator subtype of brain cancer
Laird 2010
Methylator subtype is associated with survival
Laird 2010
Over-expression of Ezh2 in advanced
prostate cancer
Oncogenes/
metastasis
promoters
Varambelly et al. 2002
Why does this matter?
Epigenetic reprogramming can modify
tumorigenesis
Genetics are tough to modify;
epigenetics aren’t (as much).
1.
Gives us a way to “cure
cancer” and
2.
Links cancer to
developmental biology!
In SCID mice
Partially tumor-derived
Control
Hochedlinger et al.
Genes & Dev, (2004)
An ESC signature of high-grade breast cell cancers
More epigenetic
suppression
More
“stemmy”
“Worse” tumors →
Ben-Porath et al. 2010
ES-signature is negatively associated with survival
Stemness is good when you’re an embryo,
bad when you’re a tumor
Ben-Porath et al. 2010
Maybe
New debate of ESC signature of cancer
• “ESC” signature associated with cancer can be
explained by Myc activity
• ESC signature contains three modules:
core, Polycomb, and Myc.
• The ESC signature associated with cancer can be
explained by Myc signature.
Kim et al. 2010
But in all fairness, epigenetics
matter for more than just cancer…
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Lung
Cardiovascular
Diabetes
Ageing
Post Traumatic Disease
Social Behavior
…
Epigenetics and Environment
Epigenetic changes are reversible
• Epigenetic changes can be induced by
environmental changes.
• Unlike genetic mutations, epigenetic changes
are reversible.
• Ideal for therapeutic targets, IF we know how
epigenetic patterns are regulated.
Jirtle and Skinner 2007
Environment
Diet
Environment
Diet
Immune
function
Baccarelli 2010
Baccarelli 2010
Nutrition affects skin color
Skin color is controlled
by DNA methylation
Genetically identical
Mother mouse was fed with methyl-enriched diet during pregnancy
Jirtle and Skinner 2007
NIH Epigenome Roadmap
• Five-year initiative starting from 2008
• It will generate reference epigenome for
hundreds of cell-types in human
• The data will be made publicly available
immediately.
• New technologies will be developed to detect
novel epigenomic marks
• Population-level studies will be carried out to
detect epigenetic changes associated with
various diseases.
This is an exciting time to do research in
epigenomics!
To learn more...
• Bernstein et al. “The mammalian epigenome”
Cell. 2007 Feb 23;128(4):669-81.
• Jones and Baylin, “The epigenomics of cancer”,
Cell. 2007 Feb 23;128(4):683-92.
• Jirtle and Skinner, “Environmental epigenomics and
disease susceptibility.”,
Nat Rev Genet. 2007 Apr;8(4):253-62.
• NIH Epigenome Roadmap
– http://www.roadmapepigenomics.org/
• NIH ENCODE Project
– http://www.genome.gov/10005107