1. Epigenetics
Heritable alterations in chromatin structure can govern gene
expression without altering the DNA sequence.
Viterbo
Università degli Studi della Tuscia

2. Epigenetics denotes all those hereditary
phenomena in which the phenotype is not only
determined by the genotype (the DNA
sequence itself) but also by the
establishment over the genotype
(in greek “epi” means “over”) of an
imprint that modulates its
functional behavior

3. Invertebrates and Plants Polycomb group proteins
Epigenetic phenomena
Vertebrates,
Invertebrates and Plants
Genic, chromosome and genomic imprinting
Heterochromatin formation
Centromere function
RNA interference (PTGS)
Paramutation
RIP e MIP (Quelling)
Polycomb group proteins
Transvection
Eukaryotes
Mammals
Drosophila
Eukaryotes
Drosophila
Plants
Fungi

4. Genic, chromosome or genomic
IMPRINTING

5. x A x x x A x A zygote Differential behavior of homologous chromosomes
maternal genome
paternal genome
zygote x A
Sciara coprofila x x
Differential
behavior of homologous chromosomes
embryo x A
embryo x A
The chromosome which passes through the male germ line aquires an imprint that results in behaviour exactly opposite to the imprint
conferred on the same chromosome by the
female germ line
(H. Crouse, 1960)

6. Nuclear transplantation in mammals
zygote P M M P
androgenetic embryos
(two male pronuclei)
gynogenetic embryos
(two female pronuclei)
Poor development of the embryo proper
Poor development of extraembryonic
components

7. Angelman, Prader-Willi syndromes
Usually caused by large (megabase+) deletions of 15q11-q13
Delete maternal chromosome = AS
Delete paternal chromosome = PWS

8. Prader-Willi Syndrome - obesity, mental retardation,
short stature.
Angelman Syndrome - uncontrollable laughter, jerky
movements, and other motor and
mental symptoms.

9. PWS
Mouse
model
PWS AS
Mouse
model AS

11. Imprinting cycle establishment, maintenance and erasure

12. What Mendel (fortunately) didn’t find in his experiments with peas
1:1

13. NO Does the genomic imprinting falsifies the Mendel’s rules?
Neither the segregation of single gene alleles, nor the indipendent
behavior of different genes are affected by the existence
of imprinting
What the imprinting may mask are the dominance relations
between alleles, and hence only the phenotypic output of a cross

14. NUCLEATION AND MAINTENANCE
HETEROCHROMATIN
NUCLEATION AND MAINTENANCE

15. In 1928, Heitz defined the heterochromatin as regions of chromosomes
In 1928, Heitz defined the heterochromatin as regions of chromosomes that do not undergo cyclical changes in condensation during cell cycle as the other chromosome regions (euchromatin) do.
Heterochromatin is not only allocyclic but also very poor of active genes, leading to define it as genetically inert (junk DNA).
Heterochromatin can be subdivided into two classes: constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin indicates those chromatin regions that are permanently heterochromatic. These regions occupy fixed sites on the chromosomes of a given species, are present in both homologous chromosomes, throughout the life cycle of the individual.
Facultative heterochromatization is a phenomenon leading to the developmentally or tissue-specific co-ordinate reversible inactivation of discrete chromosome regions, entire chromosomes or whole haploid chromosome sets.

16. Position Effect Variegation (PEV)
White+
pericentric
heterochromatin
Drosophila melanogaster X chromosome W+ W- Y
inversion
White+
Wm4
Wm4 W- Y

17. In all cases an inversion or translocation changed the position of
the gene from a euchromatic to heterochromatic position
this results in variegation
Some rearrangements gave large patches of red facets adjacent to
large patches of white
Conclusion: Decision on expression of white is made early during
tissue development and maintained through multiple cell divisions
Gene is not mutated – movement of the rearranged allele away
from heterochromatin can restore expression
PEV is not limited to Drosophila: see telomeric silencing in yeast

18. X chromosome inactivation
The Barr body XY XX
XXX
XXXXY
XXXXX

19. Genotype is Xyellow/Xblack Yellow patches: black allele is inactive
In mammals the dosage compensation of the X chromosome products, between XX females and XY males is achieved by inactivating one of the two Xs in each cell of a female (Mary Lyon, 1961)
Genotype is Xyellow/Xblack
Yellow patches: black allele is inactive
Black patches: yellow allele is inactive
Xyellow/Xblack

20. imprinted facultative heterochromatization
Coccid chromosome system
zygote
maternal chromosomes
paternal chromosomes
imprinted facultative
heterochromatization
embryo
embryo
Planococcus citri (2n=10)

21. Female and male cells from P.citri

22. PARAMUTATION
Alexander Brink x B’
B-I x
B’/B-I*
B-I
B’/B-I
B-I*/B-I

23. MOLECULAR MECHANISMS
OF EPIGENETICS

24. The chromatin

25. Histone protein modifications DNA modifications
nucleosomes
Histone protein
modifications
DNA
histones
DNA
modifications

26. HISTONE PROTEIN
MODIFICATIONS

27. H3 H4 H2A H2B Acetylation Phosforylation Methylation Ubiquitination
4KMe
…4KMe
…9KMe
9KMe
…16KAc
16KAc
…20KMe
20KMe
euchromatin
heterochromatin
chromatin

28. HP1 and modified histone tails interactions during heterochromatin formation
non histone chromatin
proteins: HP1
euchromatin
heterochromatin
9KMe

29. Histone Code and Transcriptional Silencing
Epigenetic modifications leading to gene silencing.
(A) Gene repression through histone methylation.
Histone deacetylase deacetylates lysine 9 in H3,
which can then be methylated by HMTs. Methylated
lysine 9 in H3 is recognised by HP1, resulting in
maintenance of gene silencing.
B) Gene repression involving DNA methylation. DNA
methyltransferases methylate DNA by converting SAM
to SAH, a mechanism that can be inhibited by DNMT
inhibitors (DNMTi). MBPs recognise methylated DNA
and recruit HDACs, which deacetylate lysines in the
histone tails, leading to a repressive state.
(C) Interplay between DNMTs and HMTs results in
methylation of DNA and lysine 9 in H3, and consequent
local heterochromatin formation. The exact mechanism
of this cooperation is still poorly understood.

30. Histone Code and Transcriptional Activation
Epigenetic modifications leading to gene activation.
(A) Setting 'ON' marks in histone H3 to activate gene
transcription. Lysine 4 in H3 is methylated by HMT (for
example MLL) and lysine 9 is acetylated by HAT, allowing
genes to be transcribed. It is not known, if HMTs and HATs
have a direct connection to each other.
(B) In the postulated 'switch' hypothesis, phosphorylation
of serines or threonines adjacent to lysines displaces
histone methyl-binding proteins, accomplishing a binding
platform for other proteins with different enzymatic
activities. For example, phosphorylation of serine 10 in
H3 may prevent HP1 from binding to the methyl mark on
lysine 9. Other lysines in H3 may be acetylated by HATs,
therefore overwriting the repressive lysine 9 methyl mark
and allowing activation.
(C) Although there is no HDM identified to date, one can
speculate that, if this enzyme exists, serine 10 phosphorylation
in H3, for example, by Aurora kinases, can lead to recruitment
of HDMs that in turn demethylate lysine 9 in H3. Histone
acetyltransferases might then acetylate lysine 9 and HMTs
methylate lysine 4, resulting in the loosening of the chromatin
structure and allowing gene transcription.

31. Histone Modification Cassettes
Methylation of Lys-9 by DIM-5 (SUVAR39H1) recruits HP1 via its chromodomain.
In turn, HP1 can recruit additional SUVAR39H1 and other silencing proteins to
establish heterochromatin.
Phosphorylation of Ser-10 abolishes methylation of Lys9 by DIM-5 (SUVAR39H1) and
binding of the HP1, thereby blocking heterochromatin formation.
Phosphorylation of Ser-10 can modestly stimulate acetylation of Lys14 by GCN5,
thus promoting transcription.
Lys-9 and Ser-10 have been referred to as a methyl/phos switch:
Fischle W, Wang Y, Allis CD. Nature. 2003;425:475-9.

32. DNA MODIFICATIONS

36. maintenance methylase
Imprinting cycle/DNA metylation cycle establishment, maintenance and erasure
Maternal genome
Paternal genome
zygote m
maintenance
embryonic divisions m
maintenance methylase
somatic cells
gametogenesis
reversion
de novo
establishment m
demethylase
de novo methylase
gametes

40. Heterochromatin, HP1 and histone tail modifications
dapi
m9KH3
HP1
merge
Histone H3 lysine 9 methylation
dapi
m9KH3
HP1
merge
Histone H4 lysine 20 methylation