2. Epigenetics represents the science for the studying
heritable changes of DNA, not involving changes
in DNA sequence that regulate gene expression.
6. The 30nm fiber is
organized to loops that
can be opened up
individually
7. The association of the histone octamer with the DNA is
inherently dynamic. In addition, there are factors that act on
the nucleosome to increase or decrease the dynamic nature of
this association. Together, these properties allow changes in
nucleosome position and DNA association in response to the
frequently changing needs for DNA accessibility.
The dynamic nature of DNA binding to the histone core
structure is important, because many DNA-binding proteins
strongly prefer to bind to histone-free DNA. Such proteins can
recognize their binding site only when it is released from the
histone octamer or is contained in linker or nucleosome-free
DNA.
Early studies of chromosomes divided chromosomal regions
into two categories: euchromatin and heterochromatin.
8. Heterochromatin was characterized by dense staining
with a variety of dyes and a more condensed appearance,
whereas euchromatin had the opposite characteristics,
staining poorly with dyes and having a relatively open
structure.
It became clear that heterochromatic regions of
chromosomes had very limited gene expression. In
contrast, euchromatic regions showed higher levels of gene
expression , suggesting that these different structures were
connected to global levels of gene expression.
9.
10. Chromatin remodelling
DNA methylation and demethylation
Histone acetylation and deacetylation.
Histone methylation and demethylation
Phosphorylation and dephosphorylation of histones and
non- histone proteins
11. Chromatin remodeling is principally carried out by 1)
covalent histone modifications by specific enzymes, e.g.,
histone acetyltransferases (HATs), deacetylases,
methyltransferases, and kinases, and 2) ATP-dependent
chromatin remodeling complexes which either move, eject or
restructure nucleosomes.
Chromatin remodeling is the rearrangement
of chromatin from a condensed state to a transcriptionally
accessible state, allowing transcription factors or other DNA
binding proteins to access DNA and control gene expression.
Chromatin remodeling is highly implicated in epigenetics.
Epigenetic modifications to histone proteins such as
methylation/demethylation and acetylation/deacetylation can
alter the structure of chromatin resulting in transcriptional
activation or repression.
12. The presence of 5-
methylcytosine leads to the
silencing of genes in that
local area of the
chromosome.
MT = DNA
methyltransferase .
HDAC = Histone
deacetylase
MeCP2 = Methyl-CpG-
binding protein
Deacetylase
13. DNA methylation is a common epigenetic event that occur
in genome which plays key role in silencing genes for
tissue specific expression.
It is determined during embryogenesis and passed to all
differentiating cells and tissues.
DNA methylation is a covalent modification of DNA that
does not change the DNA sequence, but has an influence on
gene activity.
DNA is modified in post replicative process that results in 3
methylated bases:C5 methyl cytosine N4 methyl cytosine
N6 methyl adenine.
DNA methylation does not change DNA sequence but
influence gene activity.
Occurs almost exclusively at cytosines that are followed
immediately by a Guanine- CpG Dinucleotide.
14. CpG islands are located near or in the promoter region.
Enzymes involved in DNA methylation :DNA
METHYLTRANSFERASES(DNMTs)DNMTs catalyze this
reaction at different times during the cell cycle.
DNMT1- Maintainance methylase , DNMT 2, DNMT3a
and DNMT3b- ‘ de novo ’methylases , DNMT3L
DNMT1:maintains the pattern of DNA methylation after
DNA replication.requires a hemi-methylated DNA substrate
and will faithfully reproduce the pattern of DNA
methylation on the newly synthesized strand . DNA
methylation- ‘an automatic semi conservative mechanism’
DNMT3a and DNMT3b: Will add methyl groups to CG
dinucleotides which are previously unmethylated on both
the strands. Re-establish the methylation pattern.
15. The methylation pattern of the genome is
established anew every generation. In that
sense methylation is an epigentic phenomenon
- it influences the genetic material but it is not
inherited from one generation to another except
for the imprinted region.
All methylation (or at least almost all) is erased
during early embryogenesis and reestablished
16.
17. CpG Islands
Promoter
site
Non-
promoter site
Non- methylated Methylated
TF binding
Non- methylated Methylated
Transcription
Transcription
inhibition
Silencing of
transcription
Transcription Stability of
genome
TF binding
Silencing of parasitic
recombination sites
18. Enzymes providing histone modifications
Acetylation: HATs - CBP,p300, GCN5, ATF2, Tip 60…
Deacetylation: HDACs- class I and II
Methyaltion:
Lysine : SET-domain HMTase and non-SET domain
HMTase (Dot1)
Arginine: PRMT family, CARM1
Demethylation: LSD1
Ubiquitination: ubiquitin conjugase Rad6/ligase Bre1for
H2B
De-Ubiquitination: SAGA-associated Ubp10
19. “Histone Code” hypothesis
1. Modifications of the Histone tails act as marks that can be read
by other proteins to control the expression or replication of
chromosomal regions. The coding in the histones may be
heritable.
2. Combinations of these modifications are thought to constitute the
so-called “histone code” which can be read and interpreted by
different cellular factors leading to transcriptional activation or
repression. For example, a general characteristic of euchromatin
is tri-methylation at lysine residues of histone H3 – lysine 4
(K4), lysine 36 (K36), and lysine 79 (K79) and a high level of
histone acetylation, while heterochromatin is characteristically
enriched in trimethylation of other histone H3 lysine residues
K9, K20, and K27.
3. Generally, histone acetylation is associated with transcriptionally
active genes.
4. Deactylation is associated with inactive genes (= gene silencing)
20. • It is the introduction of an Acetyl functional group
to the Lysine amino acid of the histone tail.
• These reactions are catalyzed by enzymes with
"histone acetyltransferase" (HAT)
21. Acetylation has the effect of changing the overall charge of the
histone tail from positive to neutral. Nucleosome formation is
dependent on the positive charges of the H4 histones and the
negative charge on the surface of H2A histone fold domains.
Acetylation of the histone tails disrupts this association, leading
to weaker binding of the nucleosomal components. By doing this,
the DNA is more accessible and leads to more transcription
factors being able to reach the DNA. Thus, acetylation of
histones is known to increase the expression of genes through
transcription activation.
22. Deacetylation performed by HDAC molecules has the
opposite effect. By deacetylating the histone tails, the DNA
becomes more tightly wrapped around the histone cores,
making it harder for transcription factors to bind to the
DNA. This leads to decreased levels of gene expression
and is known as gene silencing.
There are a total of four classes that categorize Histone
Deacetylases (HDACs). Class I includes HDACs 1, 2, 3,
and 8. Class II is divided into two subgroups, Class IIA
and Class IIB. Class IIA includes HDACs 4, 5, 7, and 9
while Class IIB includes HDACs 6 and 10. Class III
contains the Sirtuins and Class IV contains only HDAC11.
23. Both lysine and arginine residues are known to be
methylated.
Methylated lysines are the best understood marks of the
histone code, as specific methylated lysine match well with
gene expression states. Methylation of lysines H3K4 and
H3K36 is correlated with transcriptional activation while
demethylation of H3K4 is correlated with silencing of the
genomic region. Methylation of lysines
H3K9 and H3K27 is correlated with transcriptional
repression.[4] Particularly,
H3K9me3 is highly correlated with constitutive
heterochromatin.[5]
