Epigenetics

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Epigenetics Heritable alterations in chromatin
structure can govern gene expression without
altering the DNA sequence.
Viterbo Università degli Studi della Tuscia
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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
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Epigenetic phenomena
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Genic, chromosome or genomic IMPRINTING
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Differential behavior of homologous chromosomes
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)
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Nuclear transplantation in mammals
androgenetic embryos (two male pronuclei)
gynogenetic embryos (two female pronuclei)
Poor development of the embryo proper
Poor development of extraembryonic components
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Angelman, Prader-Willi syndromes

• Usually caused by large (megabase) deletions of
  15q11-q13
• Delete maternal chromosome AS
• Delete paternal chromosome PWS

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

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PWS Mouse model
PWS
AS Mouse model
AS
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Imprinting cycleestablishment, maintenance and
erasure
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What Mendel (fortunately) didnt find in his
experiments with peas
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Does the genomic imprinting falsifies the
Mendels 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
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HETEROCHROMATIN NUCLEATION AND MAINTENANCE
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• 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.

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Position Effect Variegation (PEV)
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• 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

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X chromosome inactivation
The Barr body
XY
XX
XXX
XXXXX
XXXXY
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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)
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imprinted facultative heterochromatization
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Female and male cells from P.citri
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PARAMUTATION Alexander Brink
x
B-I
B
x
B/B-I
B-I
B/B-I
B-I/B-I
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MOLECULAR MECHANISMS OF EPIGENETICS
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The chromatin
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nucleosomes
Histone protein modifications
DNA
histones
DNA modifications
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HISTONE PROTEIN MODIFICATIONS
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Acetylation Phosforylation Methylation
Ubiquitination H3 H4 H2A H2B
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HP1 and modified histone tails interactions
during heterochromatin formation
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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.
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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.
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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.
2003425475-9.
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DNA MODIFICATIONS
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Imprinting cycle/DNA metylation
cycleestablishment, maintenance and erasure
Maternal genome Paternal genome
zygote
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Heterochromatin, HP1 and histone tail
modifications
Histone H3 lysine 9 methylation