1. Epigenetic phenomena
Epigenetics refers to genetic inheritance that is not coded by the DNA sequence
It includes changes in gene expression due to modification of DNA or change in its chromatin state (facultative heterochromatin)
Lecture will illustrate this with various examples

2. X chromosome inactivation
In female mammals with 2 X chromosomes, one X is inactivated, i.e. all its genes are switched off, and it forms the Barr body
This is to prevent a double dose of X-chromosome gene products relative to that in male cells
Which of the 2 X chromosomes is inactive in a cell line, is usually randomly determined early in development

3. The calico cat
The calico cat is an example of X-chromosome inactivation
She is heterozygous for a gene on the X, one allele gives orange fur, the other black
Random X-inactivation in cells early in development gives patches with either the orange or black allele active
White patches are due to an autosomal gene, “spotting”

4. Consequences of X inactivation: the calico cat

5. Muscular dystrophy in girls
Duchenne muscular dystrophy (DMD) is an X-linked recessive disease, usually only affects boys
The karyotype of girls with DMD sometimes shows an X:autosome translocation
In this case, X-inactivation is not random - the normal X is always inactivated, because the translocation interferes with the inactivation process
Therefore, the normal DMD gene is switched off, and the other one is disrupted by the translocation
So these girls show the symptoms of DMD

6. Genomic imprinting
Usually it does not make any difference from which parent you got a particular gene
But with some genes it does matter - this is called genomic (or genetic) imprinting
Example:
Prader-Willi syndrome (PWS): small stature, obesity, learning difficulties
Angelman syndrome (AS): epilepsy, learning difficulties, unsteady gait, “happy” appearance
PWS often caused by deletion of a gene “SNRPN” on paternal chromosome 15
AS often caused by deletion of the same gene, but the maternally-derived one
Therefore the gene must be expressed differently depending on which parent it came from

7. Father’s imprint on his daughter’s thinking?
Why are boys more likely to have autism (and other disorders of social function) than girls?
Turner’s syndrome (45XO) girls are of normal intelligence but often have social function problems
Their single X can be either maternal or paternal in origin
The ones with a maternal X are much more likely to have the social problems
All boys have a maternally-derived X
So, there could be imprinted gene(s) on the X, which are involved in social function
When maternally inherited this could might contribute to disorders such as autism

8. Mechanism of imprinting
The mechanisms of X-inactivation and imprinting are not fully understood but both involve DNA methylation
DNA can be reversibly methylated on C bases - fig in Hartl
Methylation of a gene’s promoter tends to switch it off, due to binding of a specific protein to methylated DNA

9. Determination of methylation
HpaII m m
CCGG
GGCC
CCGG
GGCC
CCGG
GGCC m m
MspI

10. Gel electrophoresis of fragments
MspI
HpaII 1 2 3 4 1 5
Methylated
sites which
are not present
in HpaII digest
Non-methylated site

11. Is methylation state related to gene activity?
Many sites within a genes are methylated
some sites only in certain tissues
others in all tissues
A minority of sites are methylated in tissues in which the gene is not expressed, but are unmethylated in tissues in which the gene is active
Experiments suggest that these sites are important regulators of gene activity

12. Position-effect variegation (PEV)
State of chromatin (euchromatin, heterochromatin) can affect gene expression
A gene could be moved to a heterochromatic region by an inversion
Heterochromatin’s structure tends to switch off gene expression

13. An example of PEV
A mutant allele of the w gene in Drosophila causes eyes to be white (wild-type is red)
An inversion of part of the X chromosome causes eyes to have red and white patches (fig 7.36 in Hartl)
This is because of PEV switching off w gene in some cell lines in the eye
The boundary between heterochromatin and euchromatin is not exactly the same in all cell lines, hence eyes are mosaic

14. Summary - epigenetic gene regulation
Both mammalian X inactivation and Drosophila position effect variegation are examples of epigenetic gene regulation.
The repressed state caused by the chromatin rearrangement is heritable, but importantly the decision to induce the repressed state is not encoded by the genome.