an epigenetic approach to understanding (and predicting ... seminar august... · pre-mbt 2.5 hpf...
TRANSCRIPT
Philippe CollasUniversity of Oslo
Institute of Basic Medical SciencesStem Cell Epigenetics Laboratory
Norwegian Center for Stem Cell Research
An epigenetic approach to understanding(and predicting?) environmental effects on
gene expression
www.collaslab.com
Untangled hair(DNA strands)
Head of Leda, ~yr 1500
Braids(nucleosomal arrays)
Coiled braids(folded chromatin)
Had Leonardo da Vinci figured it out?
High-order folding of the genome
DNA compaction in a eukaryotic cell
A high-order folding of the genome
DNA compaction in a eukaryotic cell
Epigenetic marks lie on top of the DNA code
DNA methylation
Histone modifications
Genome conformationcapture–seq (HiC)
3-D genome conformation also influences gene expression
Sequencing Chromosome interaction maps
Genome conformationcapture–seq (HiC)
3-D genome conformation also influences gene expression
SequencingIntegration of multiple information layers
3-D genome conformation also influencesgene expression – a dynamic system
Stem /progenitor cell
Epigenetic changes determine which genes are active or inactive during development
Identical genes Variable gene expression
patterns
Different sets of genes are active in different cell types
The environment can affect future generations through the epigenome
Mother:1st generation
Fetus:2nd generation
Germ cells:3rd generation
Direct exposure: up to 3 generations
Mother:1st generation
Fetus:2nd generation
Germ cells:3rd generation
?? ?
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Transmission of epigenetic marks through the germline
The environment can affect future generations through the epigenome
4th generation?
Patterning developmental gene expression by epigenetic marks
Leif LindemanIngrid Andersen
• 3 h of development until zygotic genome activation (ZGA)• Essentially no transcription during this period• Great opportunity to test the hypothesis of an epigeneticpre-patterning of developmental gene expression
How does the zebrafish embryo programs itsdevelopmental gene expression pattern?
ZGA
Capturing epigenetic modifications during earlyzebrafish development
xPre-MBT2.5 hpf
MBT3.5 hpf
Post-MBT5.3 hpf
Lindeman et al., 2010. PLoS ONELindeman et al., 2010. Meth Mol BiolLindeman, Andersen et al., 2011. Dev CellAndersen et al., 2012. Genome Biol.
Chromatinimmunoprecipitation:
Immuno-affinity enrichment ofchromatin domains bearing a
specific modification
Marking of the genome by histone modificationsbefore, during and after onset of ZGA
RNA-seq(Aanes et al., 2011. Genome Res.)
Non-expressed genes
Maternal-zygotic genes Zygotic genes
Capturing epigenetic modifications during earlyzebrafish development
xPre-MBT2.5 hpf
MBT3.5 hpf
Post-MBT5.3 hpf
Lindeman, Andersen et al., 2011. Dev Cell
Homeostasis
Transcription regulationDevelopment
Development Transcription regulationSignaling(Metabolism)
Chromatin assembly
Gene ontologyPre‐ZGA
TSS
H3K4me3
H3K9me3
H3K27me3
SignalingSensory perception
The zebrafish genome is marked by modified histonesbefore onset of zygotic genome activation
Pre‐ZGA zebrafish embryos
Density profiles
H3K4me3H3K9me3
H3K27me3
TSS
Epigenetic fate map of genes marked by H3K4me3 pre-ZGA
Epigenetic fate map of genes marked by H3K4me3 pre-ZGA:Acquisition of bi- and trivalency
Pre‐MBT
H3K27me3H3K9me3H3K4me3
MBT
Post‐MBT
Pre‐MBT
Pre‐MBT H3K4me3‐marked genes are not expressed
H3K4me3-marked genes before ZGA are inactive... suggesting a predictive role of H3K4me3 marking
Enhanced propensity for expression Enhanced expression level post-MBT
H3K4me3 marking before ZGA correlates with transcriptionalactivation after ZGA onset
... suggesting an instructive role of epigenetic marking on (later) gene activation
Homeostasis
Transcription regulationDevelopment
Development Transcription regulationSignaling(Metabolism)
Chromatin assembly
Gene ontologyPre‐ZGA
TSS
H3K4me3
H3K9me3
H3K27me3
SignalingSensory perception
The zebrafish genome is marked by modified histonesbefore onset of zygotic genome activation
Pre‐ZGA zebrafish embryos
Human ES cells
Mikkelsen et al., 2007
Mouse embryos:H3K4/H3K27me3 bivalency
Dahl et al., 2010
Gene ontologyPre‐ZGA
Development Transcription regulationSignaling(Metabolism)
Common epigenetic pattern of ’transcriptional poising’ in zebrafish, mouse and man
Pre‐ZGA zebrafish embryos
Epigenetic patterning of zebrafish developmental gene expression before ZGA onset
Pre‐MBT MBT Post‐MBT
H3K4me3
H3K27me3H3K9me3
H3K36me3RNAPII
TSS
Pre‐patterning Priming Activation
Hypomethylation
Our data currently support two models:
• transgenerational inheritance of chromatin marks?
• post-fertilization removal & reconstitution of epigenetic marks based on DNA sequence rather than through a copy of histone modifications – inherent instructive property of DNA?
Both models are compatible with a de novo epigenetic marking of genes post-fertilization
?Where do chromatin modifications come from?
Predictive modeling of gene expression from chromatin states
Goal: to correlate epigenetic profiles at specific developmental stages to patterns of gene expression across stages
• Characterize epigenetic modifications throughout the genome• Find interrelations among the marks by assigning ‘chromatin states’• Do this for each developmental stage• Correlate developmental expression patterns with epigenetic patterns across the
states• Find epigenetic pattern changes which predict expression fate across
developmental stages• Find epigenetic patterns that are predictive of biological process (Gene Ontology)
and anatomically-specific (Zfin) expression
Atlas of zebrafish developmental epigenetics with prediction value
Apply to other species or fields
Developing innovative tools to look at things in another way
Andrew Reiner
Implications for CERAD
What you’re going to do to an adult organism (bearing gametes) or an embryo is going to affect, through changes in the epigenome, gene expression
patterns, phenotype, behavior, health, etc.
These epigenetic changes may have a predictive value on gene expression later in life
Need: a robust assay to survey epigenetic changes in early (fish) embryos
Fish’n ChIPs protocol – Dr. Leif Lindeman