Epigenetics 04/04/16
A single genome gives rise to distinct cell-types About 210 human cell-types
An example from Andrew Baccerelli; Ode to Joy
Definition Epigenetics refers to changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence. These changes may remain through cell divisions for the remainder of the cell's life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism. Non-genetic factors cause the organism's genes to behave (or "express themselves") differently. wikipedia
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. The chromatin structure is hierarchical. Felsenfeld and Groudine 2003
Nucleosome and histone modification First layer chromatin structure looks like “beads-on-a-string”. A nucleosome is made of core histone proteins. The amino acids on the N-terminus of histones can be covalently modified. Felsenfeld and Groudine 2003
DNA methylation DNA methylation normally occurs at CpG dinucleotide only and can be inherited during cell-division. Alberts et al. Molecular Biology of the Cell
Aberrant DNA Methylation Pattern in Cancer Irizarry, Feinberg
Transcription regulation ACATGT TF RNA
ChIP-seq analysis
Peak Calling Methods MACS (MACS2) – Liu Lab Peakseq – Gerstein Lab SPP – Park Lab GEM – Gifford Lab
Epigenetic patterns are dynamic Human Umbilical Vein Endothelial Cells: HUVEC; GM12878; lymphoblastoid cell.
Epigenetic patterns are dynamic
Epigenetic patterns are dynamic
Epigenetic patterns are dynamic
Epigenetic patterns are dynamic Aberrant patterns are found in cancer and many other diseases
Enhancers regulate gene expression from a distance
Super-enhancers Whyte et al., Cell 2013
Target super-enhancer in cancer James Bradner
Chromatin state segmentation methods ChromHMM (Ernst&Kellis); Segway (Hoffman&Noble). Both are based on hidden Markov models (HMM). histone mark intensities chromatin state Data are binned. Assumptions Markov property: Independent obs:
Promoter is relatively stable; enhancer is more dynamic Can chromatin state really define cell-identity? Ernst et al., Nature 2011
(Fine, Tishby 1998) Chromatin Domain DO chromHMM
diHMM domain-level state nuc-level state histone mark intensities Each domain-bin corresponds to a block of nuc-bins. nuc-level state histone mark intensities Additional Assumptions Obs is determined only by nuc-level state depends on the domain-level state n Nuc-level transition is domain dependent Domain-level transition can only occur at the end of a block only when i is multiple of block size Marco et al. under review
Comparison with chromHMM (Fine, Tishby 1998) Dom Nuc HHMM chromHMM
Variation of genetic information may predict disease risk wikipedia What is the mechanism?
Noncoding GWAS are enriched with enhancer elements Murrano et al., Science 2012
Identifying disease-relevant cell-types Murrano et al., Science 2012
Source: yewbiotech
BCL11A is a master regulator for globin switch Bauer et al. 2012, Blood
BCL11A erythroid enhancer is required for HbF repression 55 58 62 This modest affect on BCL11A expression and HbF level is just a minimal estimate of the impact of the underlying element. Deletion of the enhancer results in profound loss of BCL11A expression. Hardison and Blobel. Science 2013; Bauer et al. Science 2013
CRISPR/cas9 genome editing
Identifying critical sequences within BCL11A erythroid enhancer Canver et al. Nature 2015
Identifying critical sequences within BCL11A erythroid enhancer
Identifying critical sequences within BCL11A erythroid enhancer
Species divergence at the BCL11A erythroid enhancer Human Mouse essential essential dispensable partially dispensable largely dispensable largely dispensable These results show the
Identifying critical sequences within BCL11A erythroid enhancer
Summary Epigenetics play an important role in gene regulation in development and diseases. Epigenetic regulation provides mechanistic understanding of disease associated genetic variants. Predicted function of regulatory elements can be experimentally tested by CRISPR/cas9 genome-editing.