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.