An epigenetic approach to understanding (and predicting?) environmental effects on gene expression

Transcription

1 An epigenetic approach to understanding (and predicting?) environmental effects on gene expression Philippe Collas University of Oslo Institute of Basic Medical Sciences Stem Cell Epigenetics Laboratory Norwegian Center for Stem Cell Research

2 High-order folding of the genome Had Leonardo da Vinci figured it out? Coiled braids (folded chromatin) Braids (nucleosomal arrays) Untangled hair (DNA strands) Head of Leda, ~yr 1500

3 DNA compaction in a eukaryotic cell A high-order folding of the genome

4 Epigenetic marks lie on top of the DNA code DNA compaction in a eukaryotic cell DNA methylation Histone modifications

5 3-D genome conformation also influences gene expression Genome conformation capture seq (HiC) Sequencing Chromosome interaction maps

6 3-D genome conformation also influences gene expression Genome conformation capture seq (HiC) Sequencing Integration of multiple information layers

7 3-D genome conformation also influences gene expression a dynamic system Stem / progenitor cell

8 Epigenetic changes determine which genes are active or inactive during development Different sets of genes are active in different cell types Identical genes Variable gene expression patterns

9 The environment can affect future generations through the epigenome Mother: 1 st generation Fetus: 2 nd generation Germ cells: 3 rd generation Direct exposure: up to 3 generations

10 The environment can affect future generations through the epigenome Transmission of epigenetic marks through the germline Mother: 1 st generation Fetus: 2 nd generation?????? Germ cells: 3 rd generation 4 th generation?

11 Patterning developmental gene expression by epigenetic marks Leif Lindeman Ingrid Andersen

12 How does the zebrafish embryo programs its developmental gene expression pattern? ZGA 3 h of development until zygotic genome activation (ZGA) Essentially no transcription during this period Great opportunity to test the hypothesis of an epigenetic pre-patterning of developmental gene expression

13 Capturing epigenetic modifications during early zebrafish development x Pre-MBT 2.5 hpf MBT 3.5 hpf Post-MBT 5.3 hpf Chromatin immunoprecipitation: Immuno-affinity enrichment of chromatin domains bearing a specific modification Lindeman et al., PLoS ONE Lindeman et al., Meth Mol Biol Lindeman, Andersen et al., Dev Cell Andersen et al., Genome Biol.

14 Marking of the genome by histone modifications before, during and after onset of ZGA Non-expressed genes RNA-seq (Aanes et al., Genome Res.) Maternal-zygotic genes Zygotic genes

15 Capturing epigenetic modifications during early zebrafish development x Pre-MBT 2.5 hpf MBT 3.5 hpf Post-MBT 5.3 hpf Lindeman, Andersen et al., Dev Cell

16 The zebrafish genome is marked by modified histones before onset of zygotic genome activation Pre ZGA zebrafish embryos Pre ZGA Gene ontology H3K4me3 Homeostasis H3K27me3 Transcription regulation Development H3K4me3 H3K9me3 H3K27me3 Density profiles H3K9me3 Development Transcription regulation Signaling (Metabolism) Chromatin assembly TSS TSS Signaling Sensory perception

17 Epigenetic fate map of genes marked by H3K4me3 pre-zga

18 Epigenetic fate map of genes marked by H3K4me3 pre-zga: Acquisition of bi- and trivalency Pre MBT MBT Post MBT H3K4me3 H3K9me3 H3K27me3

19 H3K4me3-marked genes before ZGA are inactive... suggesting a predictive role of H3K4me3 marking Pre MBT Pre MBT H3K4me3 marked genes are not expressed

20 H3K4me3 marking before ZGA correlates with transcriptional activation after ZGA onset... suggesting an instructive role of epigenetic marking on (later) gene activation Enhanced propensity for expression Enhanced expression level post-mbt

21 The zebrafish genome is marked by modified histones before onset of zygotic genome activation Pre ZGA zebrafish embryos H3K4me3 Pre ZGA Gene ontology Homeostasis H3K27me3 Transcription regulation Development H3K9me3 Development Transcription regulation Signaling (Metabolism) Chromatin assembly TSS Signaling Sensory perception

22 Common epigenetic pattern of transcriptional poising in zebrafish, mouse and man Pre ZGA zebrafish embryos Pre ZGA Gene ontology Human ES cells Mouse embryos: H3K4/H3K27me3 bivalency Development Transcription regulation Signaling (Metabolism) Mikkelsen et al., 2007 Dahl et al., 2010

23 Epigenetic patterning of zebrafish developmental gene expression before ZGA onset Pre MBT MBT Post MBT Pre patterning Priming Activation H3K4me3 H3K27me3 H3K9me3 Hypomethylation TSS RNAPII H3K36me3 Where do chromatin modifications come from?? 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

24 Predictive modeling of gene expression from chromatin states Developing innovative tools to look at things in another way 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 Andrew Reiner

25 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