epigenetics 12/05/07. epigenetic regulation is critical for cell differentiation
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Epigenetics
12/05/07
Epigenetic regulation is critical for cell differentiation
Gene imprinting
More examples of epigenetic regulation
Epigenetic mechanisms
• DNA methylation
• Histone modification
• Nucleosome positions
DNA methylation
Alberts et al. Molecular Biology of the Cell
Methylated genes are silenced
Probable mechanisms for DNA methylation induced siliencing
• The DNA methylation marker directly interferes with TF binding.
• The DNA methylation marker is recognized by proteins that cause chromatin structure changes.
1bp (0.3nm)
10,000 nm
30nm
11 nm
DNA in the nucleus is complexed with histones to
form nucleosomes
Histone modification
Felsenfeld and Groudine, Nature, (2003)
AcetylUbiquitylMethylPhosphoryl
Histone tails can be covalently modified in multiple ways at multiple sites
Luger et al. Nature, (1997)
How histone modfication is inherited
• Histone methylation marks may be inherited by local concentration.
• The exact mechanism for inheritance is unknown.
• Even if histone modification is inherited is not proved.
Transcriptional regulation by chromatin
• Nucleosome positioning • Histone modification
TF
TF
TF target site
TF
TF
DNA methylation
histone modification
chromatin
H3K9m
e3
H3K9me3
H4K16ac
HP1
Epigenetic reprogramming during development
• Methylation marks are erased during cleavage. – Methylation of the maternal genome is actively
stripped within hours of fertilization.– Maternal genome is passively erased at a slower rate.
• de novo methylation after implantation. • Another round of demethylation during
differentiation.• DNA methylation is essential for development.
Epigenetic reprogramming can reverse tumorgenesis
Hochelinger et al. Genes & Dev, (2004)
Cancer and histone modification
Chin, Nature (1998)
Cancer and chromatinBRG1, the motor component of the SWI/SNF chromatin complex, is mutated in multiple cell lines (Wong et al. 2000)
• prostate DU145;
• lung A-427;
• prostate TSU-Pr-1;
• lung NCI-H1299;
• breast ALAB;
• lung NCI-H1299;
• pancreas Hs 700T
•…
suggesting BRG1 may be a tumor repressor protein
Genomic-view of epigenetic regulation
• How to detect genome-wide patterns of epigenetic markers?
• How do epigenetic factors regulate genome-wide gene expression?
• How is the distribution of genome-wide epigenetic markers regulated?
1.Tile microarray– 20 bp offset, 50-mers– Chr III + 233 promoters
2.Hybridize– mononucleosomal DNA– vs naked genomic DNA
3.Compute
Log (mononuc/genomic)
Yuan et al., Science, (2005)
Nucleosome positioning in yeast
MAT
MATa
MAT nucs
predictedpositioned nucs
literaturepositioned nucs
fuzzy nucs
MFA2 HIS3
CHA1 centromere
Yuan et al., Science, (2005)
Average signal (aligned by ATG codon) shows regular pattern.
Stereotyped pattern
Aligned by ATG
95% CI
Distance to ATG
Log
2
Ra
tio
Yuan et al., Science, (2005)
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 nucleosome-depletion property.
Yuan et al., Science, (2005)
Histone modification in yeast
Liu et al., PLoS Biology, (2005)
Co-regulated histone modifications
Liu et al., PLoS Biology, (2005)
Nucleosome positioning in human
Ozsolak et al., Nat Biotech, (2007)
Histone modification in human
Guenther et al., Cell, (2007)
Distinct histone modification pattern in Embryonic Stem (ES) cells
Gene
ES
Differentiated cell type 1
Differentiated cell type 2
Bernstein et al. Cell (2006)
H3K27M: repressiveH3K4M: active
Differentiated cell type n
ES cells contain both repressive and active markers
Differentiated cells contain either repressive or active markers but not both
Euchromatin and heterochromatin
http://respiratory-research.com
Large–scale chromatin domain
Rinn et al. Cell (2007)
Large-scale chromatin domain
ENCODE, Nature, 2007
Large-scale chromatin domain
ENCODE, Nature, 2007
Open Closed
Large-scale chromatin domain
ENCODE, Nature, 2007
Open Closed
DNA methylation in human
Eckhardt et al. Nat Gen. (2007)
DNA-methylation pattern in human
Eckhardt et al. Nat Gen. (2007)
Histone modification
Felsenfeld and Groudine, Nature, (2003)
AcetylUbiquitylMethylPhosphoryl
Histone tails can be covalently modified in multiple ways at multiple sites
Luger et al. Nature, (1997)
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)
• Integrative analysis using multiple genomic data resources
(sequence, gene expression, histone modification)
• Linear regression model
yi expression; Aij acetylation; Si promoter sequence
• Key is to estimate sequence dependent regulatory effects.
j
iiijji SfAy )(
Statistical assessment of the global impact of histone acetylation on gene expression
Yuan et al. Gen Bio (2006)
Estimating sequence dependent regulation effects
Linear regression model with transcription factor binding motifs
Sij motif score
•Scan motif (MDscan, AlignAce)
•Filter out insignificant motifs (RSIR)
linear f(Si)
j
ij
ijjijji SAy
Yuan et al. Gen Bio (2006)
Performance of the linear regression model
Performance of the linear regression model
Performance of the linear regression model
Cumulative effect of histone acetylation
Test whether including quadratic interaction between different acetylation sites would improve model performance
quadratic interaction
j
ij jk
ikijjkj
ijjijji AASAy
p-value for quadratic interaction coefficients (jk)
statistically insignificant
Reading List
• Strahl and Allis 2000;– Proposed histone code hypothesis
• Bernstein et al. 2007– An up to date review of epigenomics
• Yuan et al. 2005;– Nucleosome positions in yeast
• Yuan et al. 2006;– Statistical analysis of histone related gene
expression.