All the cells in the organism have the same DNA DNA is packed together with histones and other proteins into chromatin. Chromatin is a highly dynamic.

All the cells in the organism have the same DNA

• DNA is packed together with histones and other proteins into chromatin.

• Chromatin is a highly dynamic material which carries a substantial amount of epigentic information.

• All cells in the organism carry the same genetic material, however each cell type expresses different genes.

Epigenetics

• Epigenetics - Heritable changes in gene expression that operate outside of changes in DNA itself

Chromatin remodeling

• Protein expression can be induced and repressed over many orders of magnitude. An important part of this regulation is exerted via chromatin remodeling by DNA methylation and numerous modifications mainly of the N-termini of histones - acetylation, methylation, phosphorylation and ubiquitilation. There might be up to about 150 different such modifications !!!!

Epigenetic chromatin regulation

A. Modification at the DNA level

cytosine methylation

The five nucleotides that make up the DNA

CpG dinocleotides are palindromic

5’ CpG 3’3’ GpC 5’

CpG dinocleotides are palindromic

5’ CpG 3’3’ GpC 5’

To be recognized as a CpG island, a sequence must satisfythe following critera:

1. (G+C) content of 0.50 or greater2. an observed to expected CpG dinucleotide ratio of 0.60 or greater3. and both occurring within a sequence window of 200 bp or greater.

CpGs are vastly underrepresented genome-widecompared to what would be expected by chance (0.23 inthe human genome and 0.19 in the mouse genome,respectively) This is because deamination of cytosine givesrise to uracil, which is easily recognized as foreign withinthe DNA strand and replaced, whereas deamination ofmethylcytosine gives rise to thymine, which is less readilyrecognized as foreign and therefore prone to mutationand depletion in the genome.

CpG island definition based on sequence compositionidentifies these elements at the promoter sites ofapproximately half of the genes in the human genome,most of which are expressed in most or all tissues, hencetheir designation as ‘housekeeping’ genes.

Mutations at 5’ methyl cytosine cannot be identified and repaired

Maintenance of methylation

Brandeis, M., Ariel, M. & Cedar, H. (1993) Bioessays 15, 709-713.DNMT1

Southern blot based methylation assay

Unmethylated site

Me

Methylated site

- +

HpaII Probe MeHpaII Probe

- +

Methylation is globally erased during gametogenesis and embryogenesis

Kafri, T. , Ariel, M., Brandeis, M., Shemer, R., Urven, L., McCarrey, J ., Cedar,H. & Razin, A. (1992) Genes Dev 6, 705-714.

DNA demethylation of early embryos 3h 6h

P

M

P

M

P

M

P

M

8h Aphidicolin First met.

22h 2 cells 45h 4 cellsMayer, W., Niveleau, A., Walter, J ., Fundele, R. & Haaf, T. (2000) Nature403, 501-2

Establishment of DNA methylation pattern

• The methylation pattern of the genome is established anew every generation. In that sense methylation is an epigentic phenomenon - it influences the genetic material but it is not inherited from one generation to another.

• All methylation (or at least almost all) is erased during early embryogenesis and reestablished

DNMT3

Roles of DNA methylation

• Transcriptional silencing

• Protecting the genome from transposition

• Genomic imprinting

• X inactivation

• Tissue specific gene expression

Histone code or language ?

Role of histone acetylation

• Acetylated histones open up the chromatin and enable transcription. Histones are acetylated by HAT (histone acetylases) which are parts of many chromatin remodeling and transcription complexes.

Role of histone de-acetylation

• Deacetylated histones are tightly packed and less accessible to transcription factors.

• Histones are deacetylated by HDAC (histone de-acetylase) proteins.

Epigenetic chromatin regulation

A. Modification at the DNA level

1. cytosine methylation

B. Histone modification - the histone code

1. Histone acetylation

2. Histone methylation

3. Histone phosphorylation

4. Histone ubiquitilation

5. Different types of histones

Mono-allelic expression

Smell

Immune system

X chromosome

Genomic imprintingSome genes are expressed only from the maternal genome and some only

from the paternal genome

It is estimated that about 80 genes are imprinted and they can be found on

several different chromosomes

For example - igf2, h19, igf2r and genes involved in the Angelman and Prader Willi

syndromes

Control (P+M) Maternal Paternal

Imprinting is maintained by DNA methylation

Obligatory reading:Lande-Diner, L. & Cedar, H. Silence of the

genes--mechanisms of long-term repression. Nat Rev Genet 6, 648-54 (2005).

Griffiths chapter 12 - genomics