1. Epigenetics
04/04/16

2. A single genome gives rise to distinct cell-types
About 210 human cell-types

4. An example from Andrew Baccerelli; Ode to Joy

5. 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

6. Epigenetic mechanisms
Nucleosome positions
Histone modification
DNA methylation

7. 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

8. 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

9. 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

12. Aberrant DNA Methylation Pattern in Cancer
Irizarry, Feinberg

13. Transcription regulation
ACATGT TF
RNA

14. ChIP-seq analysis

15. Peak Calling Methods MACS (MACS2) – Liu Lab Peakseq – Gerstein Lab
SPP – Park Lab
GEM – Gifford Lab

16. Epigenetic patterns are dynamic
Human Umbilical Vein Endothelial Cells: HUVEC; GM12878; lymphoblastoid cell.

17. Epigenetic patterns are dynamic

18. Epigenetic patterns are dynamic

19. Epigenetic patterns are dynamic

20. Epigenetic patterns are dynamic
Aberrant patterns are found in cancer and many other diseases

21. Enhancers regulate gene expression from a distance

22. Super-enhancers
Whyte et al., Cell 2013

23. Target super-enhancer in cancer
James Bradner

24. 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:

25. Promoter is relatively stable; enhancer is more dynamic
Can chromatin state really define cell-identity?
Ernst et al., Nature 2011

26. (Fine, Tishby 1998)
Chromatin Domain DO
chromHMM

27. 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

29. Comparison with chromHMM
(Fine, Tishby 1998)
Dom
Nuc
HHMM
chromHMM

30. Variation of genetic information may predict disease risk
wikipedia
What is the mechanism?

31. Noncoding GWAS are enriched with enhancer elements
Murrano et al., Science 2012

32. Identifying disease-relevant cell-types
Murrano et al., Science 2012

33. Source: yewbiotech

35. BCL11A is a master regulator for globin switch
Bauer et al. 2012, Blood

36. BCL11A erythroid enhancer is required for HbF repression
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

37. CRISPR/cas9 genome editing

38. Identifying critical sequences within BCL11A erythroid enhancer
Canver et al. Nature 2015

39. Identifying critical sequences within BCL11A erythroid enhancer

40. Identifying critical sequences within BCL11A erythroid enhancer

41. Species divergence at the BCL11A erythroid enhancer
Human
Mouse
essential
essential
dispensable
partially dispensable
largely dispensable
largely dispensable
These results show the

42. Identifying critical sequences within BCL11A erythroid enhancer

43. 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.