Epigenetic phenomena

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 inactivationthe 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 Xautosome 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
Fathers imprint on his daughters thinking?

• Why are boys more likely to have autism (and
  other disorders of social function) than girls?
• Turners 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
  11.22 in Hartl
• Methylation of a genes promoter tends to switch
  it off, due to binding of a specific protein to
  methylated DNA

9
Determination of methylation

HpaII
CCGG GGCC
CCGG GGCC
CCGG GGCC
MspI



10
Gel electrophoresis of fragments
MspI
HpaII
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
• Heterochromatins 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.