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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 satisfy
the following critera:
1. (G+C) content of 0.50 or greater
2. an observed to expected CpG dinucleotide ratio of 0.60 or greater
3. and both occurring within a sequence window of 200 bp or greater.
CpGs are vastly underrepresented genome-wide
compared to what would be expected by chance (0.23 in
the human genome and 0.19 in the mouse genome,
respectively) This is because deamination of cytosine gives
rise to uracil, which is easily recognized as foreign within
the DNA strand and replaced, whereas deamination of
methylcytosine gives rise to thymine, which is less readily
recognized as foreign and therefore prone to mutation
and depletion in the genome.
CpG island definition based on sequence composition
identifies these elements at the promoter sites of
approximately half of the genes in the human genome,
most of which are expressed in most or all tissues, hence
their designation as ‘housekeeping’ genes.
Mutations at 5’ methyl cytosine
cannot be identified and repaired
Maintenance of methylation
DNMT1
Brand eis, M., Ariel, M. & Cedar, H. ( 1 99 3 ) Bioessays 1 5 , 70 9-71 3.
Southern blot based methylation
assay
Unmethylated site
Methylated site
Me
Probe
HpaII
-
+
Me
HpaII
-
Probe
+
Methylation is globally erased during
gametogenesis and embryogenesis
Kafri, T., Ariel, M., Brand eis, M., Sh emer, R., U rven, L., McCarrey, J., Cedar,
H. & Razi n, A. (199 2) Genes Dev 6, 705-714.
DNA demethylation of early embryos
3h
6h
8h
Aphidicolin First met.
P
P
P
M
M
M
P
M
22h 2 cells
Mayer, W., N iveleau, A., W alt er, J., Fund ele, R. & Haaf , T. ( 20 00) Natu re
40 3, 501-2
45h 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)
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