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’

Mutations at 5’ methyl cytosine cannot be identified and repaired

Maintenance of methylation DNMT1

Southern blot based methylation assay Unmethylated site Me Methylated site -+ HpaII Probe Me HpaII Probe -+

Methylation is globally erased during gametogenesis and embryogenesis

DNA demethylation of early embryos 3h 6h P M P M P M P M 8hAphidicolinFirst met. 22h 2 cells45h 4 cells

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 imprinting Some 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)MaternalPaternal

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, (2005). Griffiths chapter 12 - genomics