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PHD Credit Seminar 2 Punjab Agricultural University, Ludhiana
PHD Credit Seminar 2 Punjab Agricultural University, Ludhiana
DNMT1
Histones
DNA
Epigenetics in Cancer
Sushant Dhar
PhD Microbiology
L-2013-BS-82-D
Epigenetics
Conrad Waddington introduced the term epigenetics in the 1940s.
'Epigenetics' refers to heritable changes in gene
expression that do not result from alterations in the
gene nucleotide sequence.
Changes in gene expression independent of DNA sequence
alterations.
DNA methylation and histone modification are considered the
two main epigenetic mechanisms.
Epigenetics
The NIH "Roadmap Epigenomics Project," ongoing as of 2014, uses
the following definition: Epigenetics refers to both heritable
changes in gene activity and expression (in the progeny of
cells or of individuals) and also stable, long-term alterations in
the transcriptional potential of a cell that are not necessarily
heritable.
Cold Spring Harbor meeting, 2008: Stably heritable phenotype
resulting from changes in a chromosome without alterations in
the DNA sequence"
Epigenetics
Euchromatin
Heterochromatin
Inactive DNA
Methylation
Structural Protein
Epigenetic Modifications
DNA Methylation
Post-translational histone modifications
Non-coding RNAs
Histone variants
Chromatin remodeling
Aberrations in Epigenetics
Acet. Histone
Deacet. Histone
Activator
s
Transcr. Ready
Gene
CpG
Unmet
h
Repress
ors
Unmethylated Promoter
Activators and repressors in steady state
CpG
Heavily
meth
Transcriptional Activators
dispersed
Steady sate
silencing
Repressor
tightly
tethered to
DNA
Aberrant Hypermethylation
DNA Methylation
CpG island
CpG islands located in areas downstream of promoters have been found to
be methylated in some normal somatic tissues whereas the 5 CpG islands of
most widely expressed housekeeping genes are usually unmethylated.
29,000 CpG islands in human genome (~60% of all genes are associated with
CpG islands)
Genes with 5 CpG islands do not normally rely on DNA methylation for the
control of their gene expression because the islands are unmethylated
regardless of expression level.
Epigenetics in Cancer
Distinct methylation patterns are established during embryogenesis
and are mitotically heritable.
Epigenetics in Cancer
Change of DNA methylation pattern in CpG islands was the first and most
significant abnormal epigenetic change identified in cancerous cells.
The following 3 mechanisms have been suggested for DNA hypomethylation: (a) the
increased instability of the genome, (b) the reactivation of factors that are capable
of movement on DNA, and (c) the functional defect in elements related to genome.
leads
to
inactivation
of
tumor
suppressor
genes.
The
DNA methylation may affect the transcription of genes in two ways. First,
other chromatin
remodeling proteins
that
can
Although CIMP has been associated with environmental and lifestyle factors,
the molecular basis for CIMP is only beginning to be explored. The first clues
came from two studies showing that glioblastomas with a hypermethylator
phenotype
are
associated
with
somatic
mutations
in
isocitrate
RB in Retinoblastoma
MLH1 in colorectal cancer
BRCA1 in Breast Cancer
RUNX3 in Oesophageal Cancer
GATA4 and GATA5 in Gastric Cancer
Carcinoma
Normal
Epithelia
Dysplasia
Carcinoma
in situ
Metastasis
Carcinoma
Normal
Epithelia
Dysplasia
Carcinoma
in situ
Metastasis
Carcinoma
Normal
Epithelia
Dysplasia
Carcinoma
in situ
Metastasis
Normal
CG
CpG island
Hypermethylation
M
Cancer
CG
CG
CG
Genome Wide
Hypomethylation
CGMCG MCG
CG
CG
CG
4
C: cytosine
m
C: methylcytosine
CG
Normal
Region-Specific
Hypermethylation
Cancer
Accumulation of
alities
m
r
o
n
b
A
ic
t
e
n
e
Epig
lysine
or
arginine
residue
on
histone
tails.
Histone
Contd.
Histone Modifications
Acetylation
Ac
Me
Ub
Methylation
Ubiquitination
Su
P
Sumoylation
Phosphorylation
Me
Histone Code
Acetylation of Lysines
Acetylation of the lysines
at the N terminus of
histones removes positive
charges, thereby reducing
the affinity between
histones and DNA.
This makes RNA
polymerase and
transcription factors easier
to access the promoter
region.
Histone acetylation
enhances transcription
while histone deacetylation
represses transcription.
Cancer
Histone hypoacetylation
Overexpression of HDACs
Important
Modifications that represent an active transcription include acetylation of
H3 and H4, and di- or tri-methylation of H3 at lysine 4 (H3K4me2 or me3).
On the contrary, methylation at H3K9 and H3K27 represents an
inactivation of transcription
Important
Histone methylation, which can be associated with transcriptional
activation or repression based on the specific residue methylated.
Inactive Transcription
Active Transcription
RB1 gene was cloned and found to undergo biallelic inactivation in virtually
all retinoblastoma tumors (Friend SH, Dunn JM 1988)
Function of Rb (Retinoblastoma
protein) is to prevent excessive cell
growth by inhibiting cell cycle
progression
Continue
Continued
Aneuploidy- Chromosome
number is abnormal
Fig. RB1 has been implicated in regulating most major epigenetic processes.
Loss of RB1 leads to chromatin remodeling, in which oncogenes that are normally
repressed switch to active chromatin, tumor suppressors that are normally
actively transcribed are repressed, or both. Abbreviation: meDNA, methylated
DNA.
including
MicroRNAs in Cancer
Members of the let-7 family are among the most widely studied tumor
expressed
in
retinoblastoma.
Studies
have
demonstrated
that
p53
status
of
nine
genes:
p16INK4A,
MGMT,
GSTP1,
IMPORTANT
A promoter methylation analysis of the tumor suppressor p16INK4A
showed hypermethylation in most retinoblastoma tumors that also exhibited
p16INK4A protein downregulation. Furthermore, in over half of these cases,
the same alteration in p16INK4A expression was observed in the parents
of these patients, suggesting that this alteration could be a novel inheritable
susceptibility marker for retinoblastoma.
with
global
methylation
of
histone
H3
Lys9.
DNA
?????????????
What determines which CpG islandassociated genes are
susceptible to hypermethylation and histone modification in
different cancer types?
What dictates epigenetic silencing and what protects some
islands from methylation?
New insights into the mechanisms and the role of CpG island
for
cellular
differentiation
during
development
via
locus
involved
in
the
silencing
of Hox gene
expression (Lewis, 1978). Many PcG proteins achieve this control of gene
expression via catalyzing H3K27 methylation. These proteins have been
the subject of intense study as it is clear that they are vital for maintenance
of cell-type identity, differentiation, and disease by creating and maintaining
repressive chromatin environments. Most PcG proteins form two major
polycomb repressive complexes (PRC): PRC1, and PRC2.
KRAS?????
GTPase KRas also known as V-Ki-ras2 Kirsten rat sarcoma viral
oncogene homolog and KRAS, is a protein that in humans is encoded by
the KRAS gene. The protein product of the normal KRAS gene performs an
essential function in normal tissue signaling, and the mutation of a KRAS
gene is an essential step in the development of many cancers.
MSI???????
Microsatellite instability (MSI) is the condition of genetic hypermutability
that results from impaired DNA Mismatch Repair (MMR). In other words,
MSI is the phenotypic evidence that MMR is not functioning normally.
Types of genes targeted for DNA methylation in each subgroup and the effects
of DNA hypermethylation on gene
expression
???????????????????
Interestingly, it
was
noticed
that
112
genes
exhibited
DNA
IMPORTANT
Review
The cell-type specific organization of heterochromatin, established upon cell
differentiation, is responsible for maintaining much of the genome in a
repressed state, within a highly compartmentalized nucleus.
peripheral
heterochromatin
compartment,
excluding
access
to
Several studies have found that certain primary breast and ovarian cancer
cells which lack an inactivated X chromosome (Xi) retain at least 2 active X
(Xa) chromosomes.
Two plausible mechanisms for loss of the Barr body have been proposed:
One study
cell
regulatory
processes
and
widely
implicated
in
correlates
with
enhanced
XIST
expression,
Highlight
The
broad
epigenetic
heterochromatin
and
domains
genetic
is
an
impact
of
understudied,
instability
yet
within
widespread
and
highlight
that
loss
of
compartmentalization
of
List Techniques
The actual methylation status can be determined either through direct PCR
product sequencing (detection of average methylation status) or sub-cloning
sequencing (detection of single molecules distribution of methylation patterns) .
Moreover, bisulfite sequencing analysis can not only indentify DNA methylation
status along the DNA single strand, but also detect the DNA methylation patterns
of DNA double strands since the converted DNA strands are no longer selfcomplementary and the amplification products can be measured individually.
Transcrip.
Factor
binding lost
Deacet.
Via PML
Continued in Text
(a) A conceivable model behind aberrant DNA methylation in AML with inactivating
mutations. Recent studies suggest that transcription factors protect their binding sites
from DNA hypermethylation. Once transcription factor binding is lost, DNA
methylation occurs.
TET2 ????????????
miR-210- microRNA
regulates
gene expression