My presentation for the families of Rett syndrome patients. This serves as a basic primer on what epigenetics is without deep details on the science. Appropriate for all levels of education. For more information contact the author: crwynder@gmail.com

1. 27th Annual
Conference

2. Epigenetics 101
or
How does Rett Syndrome arise
from the mutation
Christopher Wynder

3. Rett syndrome molecules
• 3 genes have been clinically implicated in
Rett syndrome: MeCP2, CDKL-5 & FoxG1
• FoxG1 is a very rare cause of Rett
syndrome (less than 1% of cases)
• 95% of all Rett syndrome cases are
caused by mutations in the MeCP2 gene
• These mutations effectively stop MeCP2
from doing its job

4. A step back: what is DNA and how
does it relate to genes
A gene is a DNA word
Word: a series of
letters that have a
meaning.
DNA is the
material that is
passed from
parent to child.
DNA is a 4
letter code that
provides the
parts list and
instruction
manual for life
T
AC
G T
AC
G
C G C G
P P PP P

5. Genes
• Genes are words.
• As with language a word by itself is not
very useful.
• However when mixed in the correct order
(grammar) they can be very powerful.
• When used inappropriately they can
change meaning or be meaningless

6. Gene grammar
• There are approx. 15 000 genes.
• Each one has a specific use and time when it should be
used.
• In scientific parlance gene grammar is called
“Epigenetics” from the greek “epi”-above.
• In Epigenetics, we study how genes are organized and
how a cell decides which ones to use at a particular point
in time.
See Jane Stop make Run destroy brain Skinheart jeans workcells
See Jane Stop make Run destroy brain Skinheart jeans workcells

7. Organizing 15000 genes
Purified DNA from a cell1. Organization of the genome
1. The length of DNA from a cell is
about 2 metres (6 feet)
2. The size of a cell is about 100 mM (1
millionth of a metre)
3. The cell needs a mechanism to
package DNA to fit it into its nucleus
1. The cell packages its DNA into
organizational units
2. Each unit can be further broken
down to further organanizational
units

8. Compacting and organizing the genome
• Cells use special
proteins called
histones to compact
DNA into
manageable size.
• These proteins are
part of the epigenetic
machinery

9. What is MeCP2
• MeCP2: Methyl CpG binding Protein #2
What does the name tell us?
1. It’s a protein
2. Its job in the cell is to bind “stuff”
3. The thing that it binds is “methylated”
DNA

10. What is Methyl-CpG?
• CpG: is shorthand used to describe a
special “kind” of DNA sequence
• This DNA is a series of C’s and G’s [i.e.
CGCGCGCG]
• Methyl CpG sequences occur in discrete
“islands”
• CpG “islands” appear to be used to
regulate gene expression
C G C G
P P PP P

11. Grammar and Access
• To use the words (i.e. genes) the cell must
move the histones.
• There are times when certain words just
cannot be used.
• These words receive a methyl “bookmark”
• Hence methyl CpG
• MeCP2 binds to meCpG to act as a glue
to ensure that word is not used.

12. MeCP2 & Epigenetics
The big picture questions:
How does the cell decide who to bookmark?
Answer: Through other sets of bookmarks
and readers
What does this mean for a cell?
Answer: Each cell can have a unique set of
words that it uses
Epigenetics is the study of what the bookmarks are and how the cell responds

13. Epigenetics:so what
• Epigenetics is
responsible for the
variation seen in
nature amongst
close relations
Epigenetics also
explains how dogs
have so much
variation

14. Female specific Epigenetics
• Calico cats are always female.
• All cells in their fur have the same
colour genes.
• But they don’t have access to all of
them.
• This is because fur colour genes
are on the X chromosome.
• Each female has 2 X chromosomes.
• Some genes on the X need to have
low expression.
• Therefore 1 copy of the X
chromosome is turned off-
“inactivated”

15. X inactivation and DNA methylation
• X inactivation
spreads by a
molecule known as
Xist.
• Xist acts as a guide
telling the cell
where to put
methly-CpG.
Me-CpG
MeCP2 MeCP2

16. MeCP2 is a X chromosome gene
Random Inactivation
2 copies of fully functional MeCP2
Doesn’t matter which X is inactive
The cell can do all of the normal
MeCP2 tasks
Random Inactivation
1 copy of fully functional MeCP2
In cells with the MeCP2 inactive
some functions are lost.
This cell specific

17. brainlung
Heart
MeCP2
In the Brain
During development
Brain
So what: What does MeCP2 do
in a cell?
Controls access to the instructions to different tissues

18. Neuron
(brain cell)
So what: What does MeCP2 do
in a cell?
Tu parle
francais?
Do you
speak
english?
Yes

19. MeCP2 turns genes off
DNA in the cell is ALWAYS found in
association with histones.
The cell takes advantage of this to
set bookmarks and reminders
(e.g. methyl CpG)
There are another whole set of
bookmarks that occur on the
histone proteins themselves.
These bookmarks are put onto
place by enzymes. These enzymes
are the writers and erasers of
epigenetic regulation.
They are also a source of possible
therapeutic targets
(making a gene)

20. Example of how Histone modifications
relate to MeCP2
HAT
HDM
MeCP2
• Writers:
1. HAT
2. HMT
• Erasers:
1. HDAC*
2. HDM
• Readers:
1. HP1
2. MeCP2

21. Why target these proteins?
HDAC inhibitors- stops inappropriate
bookmarking of needed genes
(already FDA approved for cancer, 1 is a
anti-epileptic)
HDM inhibitors-stops inappropriate use of
specific words and chapters
The biology suggests that these may be
able to “replace” MeCP2 lost function

22. Certain HDM inhibitors mimic
MeCP2 function
meH3K4
meH3K27
Requires a HDM 1st
Then a HMTinhibitor HDM
Normally blocking this
HDM is MeCP2’s job
Another strategy is to “turbocharge” HDMs that remove meH3K4

23. Why is RTT mainly the brain?
• MeCP2 is part of a
family.
• This whole family does
the same job.
• Each family works in a
specific tissue.
• Similar mutations in the
other family members
cause specific types of
cancer or “wasting”
disorders not related to
Rett syndrome.

24. How does MeCP2 effect the brain
function?
• Through it’s job as a reader of
epigenetic bookmarks
• The wide array of functions that
MeCP2 performs ALL
contribute to Rett syndrome.
• The different mutations have
different effects on the
presentation of the disease.
• In addition since each person is
different based on their
personal epigenetics, the
disease will be individual as
well.
Change its ability to “see” meCpG
Genes do not get turned off
appropriately
Change its ability to interact
with the writers and erasers
Genes do not stay off

25. MeCP2 has multiple jobs in the
brain
Undecided
cell
During development, MeCP2
has role in what kind of neurons
In the brain, MeCP2 has role in
how neurons communicate with
each other
Each different neuron uses different genes
To define themselves.
In the absence of MeCP2 individual
neurons “talk” with a different language
than their neighbours

26. How do we “know” these things?
• Mouse work and genetic sequencing by
pioneers such as Adrian Bird and Huda
Zoghbi i.e. “in vivo” models
• Recently a new model has surfaced:
iPSCs-induced pluripotent stem cells. An
in vitro model
In vivo- used to describe research done in a whole organism
(e.g. in a mouse mutant)
In vitro- any other model including cells in a dish.

27. What are Stem cells?
• Stem cells have the ability to differentiate into all cell lineages and self renew
• Recent advances have allowed us to convert skin into stem cells
• Since Rett syndrome mutations happen in all cells we can take skin and make stem cells
by epigenetically re-programming the skin
• iPS can be used as a model system to monitor neural differentiation to test where the
errors are and possibly what effect therapeutics have on these errors
Endoderm
Mesoderm
Ectoderm
Neurons
RBC
Skeletal system
Pancreatic
cells
Skin cells
Stem cell
Stomach cell

28. Modeling Rett syndrome in human
cells

29. In vitro model confirms mouse
models
Funded by IRSF

30. Current therapeutic models

31. Epigenetics and RTT
• MeCP2 is a epigenetic regulator
• It has diverse jobs in brain cells
• Some of these jobs involve other
epigenetic regulators
• New models based on new technologies
are showing a possible role for novel
therapeutics based on epigenetics