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Epigenetics…
We inherit more than just the DNA sequence
Definition
Gene functions can be altered by more than just
change in DNA sequence.
“An Epigenetic trait is a stably heritable phenotype
resulting from changes in a chromosome without
alterations in the DNA sequence”
Mechanism of Epigenetic process
It can be divided into 3 stages
1. Epigenator
2. Epigenetic Initiator
3. Epigenetic Maintainer
Epigenator
Triggers that changes the environment of the cell to create a
epigenetic phenotype.
It can be anything – like nutrition, toxin, radiation, hormones
etc.
Epigenator signals are transient, they remain in the cell
environment long enough to trigger the epigenetic process.
They are not necessary for the subsequent process.
Epigenetic initiator
 Translates the Epigenator signal to mediate the epigenetic effect on
chromatin.
 Priming of epigenetic initiator by Epigenator –> Initiator identifies location
on a chromosome where epigenetic state is to be established.
 Initiator could be a DNA-binding protein, a noncoding RNA, or any other
entity that can define the coordinates of the chromatin structure to be
assembled.
 unlike the Epigenator, the Initiator may not dissipate after its
action, but rather may persist with the Maintainer.
 Initiator will in general be a signal that requires self-reinforcement
and self-renewal through positive feedback mechanisms.
Epigenetic Maintainer
 Signals that sustains the epigenetic chromatin state created by
initiators.
 Maintainers do not have absolute DNA sequence specificity.
Consequently, they could operate at any chromosomal location to
which they are recruited by an Initiator.
 This signals involves many different pathways, including DNA
methylation, histone modifications, histone variants, nucleosome
positioning, and others.
DNA methylation
 Oldest epigenetic mechanism known
 Addition of methyl group at cytosine
residue at CpG dinucleotides.
 These methyl groups project into the
major groove of DNA and inhibit
transcription.
 Methylation is mostly observed at non-coding regions and interspersed
repetitive elements. NOT seen in CpG islands of active gene.
 The addition of methyl groups is controlled at several different levels in
cells and is carried out by a family of enzymes called DNA
methyltransferases (DNMTs). It can be de novo or maintenance, following
DNA replication.
 Three DNMTs (DNMT1, DNMT3a and DNMT3b) are required for
establishment and maintenance of DNA methylation patterns.
 DNMT1 - for the maintenance of established patterns of DNA
methylation
 DNMT3a and 3b - new or de novo DNA methylation patterns.
Effects of DNA methylation:
1. deactivation of parasitic Transposons
2. Somatic hyper-mutations at Ig locus in B and T cells
3. embryonic development and growth
4. Genomic imprinting
5. X-chromosome inactivation
Dysregulation in methylation process result in many disorders like ICF
(Immunodeficiency, centromeric instability and facial abnormalities),
cancers (deactivation of Tumor suppressor genes) etc.
Histone modification
Modification Writer Eraser
Acetylation HAT HDAC
Methylation HMT HDM
Phosphorylation PK PP
 Effects of histone modifications:
Cis effect – alter inter-nucleosomal contacts and spacing
Trans effect – altered histone-non histone protein associations
 Pattern of histone modification may provide ON or OFF epigenetic
signature mark
Acetylation – a/w active chromatin domain
Phosphorylation – a/w condensed chromatin which generally fails to
support transcriptional activity.
H3K4Me3 and H3K36Me3 – a/w active transcription
H3K27Me3, H3K9Me2/3 and H4K20Me3 – a/w repressed genes
Nucleosome positioning, Chromatin
remodeling complex and histone variants
 Sometimes nucleosomes are bound by repressive chromatin associated
factors  Transcription machinery is not able to gain access to binding
site
 It is solved by Chromatin remodeling enzymes.
 Categorized in two families;
1. SNF2H or ISWI – mobilizes nucleosome along the DNA
2. SWI/SNF or Brahma – alter the structure of nucleosome and hence
DNA:histone contacts
Additionally there are some ATP dependent “exchanger complexes” –
replace core histone with histone variants
Histone variants
 Histones are synthesized and deposited only during S phase
 Replacement with histone variant is independent of cell cycle stage
 Take immediate effect in response to transcriptional activity or
stress signals
 Replacement of H3 by H3.3 and H2A by H2A.Z is better studied and
they are correlated with transcriptional activities
 Specific exchanger complexes are observed for histone variants
RNAi and Heterochromatin formation
EPIGENETIC INHERITENCE
 epigenetic marks are erased during two phases of the life cycle –
Firstly, just after fertilisation
Secondly, in the developing primordial germ cells
 Cellular mechanisms may allow for co-transmission of some epigenetic
marks
 During replication, DNA polymerases working on the leading and lagging
strands are coupled by the DNA processivity factor proliferating cell nuclear
antigen (PCNA),
 PCNA is implicated in patterning and strand crosstalk that allows for copy
fidelity of epigenetic marks
 children who were conceived during a harsh wartime famine in the
Netherlands in the 1940s are at increased risk of diabetes, heart disease and
other conditions — possibly because of epigenetic alterations to genes
involved in these diseases
 poor people living in inner cities, where cycles of drug addiction,
neuropsychiatric illness and other problems often seem to recur in parents
and their children.
 laboratory mice trained to fear the smell of acetophenone, a chemical the
scent of which has been compared to those of cherries and almonds. He and
Dias wafted the scent around a small chamber, while giving small electric
shocks to male mice. The animals eventually learned to associate the scent
with pain, shuddering in the presence of acetophenone even without a shock.
This reaction was passed on to their pups.
Effect of environmental chemicals on
Epigenetics
 Cadmium – interact with the methyltransferase DNA binding domain -
interference in enzyme-DNA interaction - reduces genome methylation
 Arsenic – Detoxification of As is by enzymatic methylation using SAM -
depressed SAM levels - global DNA hypomethylation
 Nickel - replace magnesium in DNA interactions, enhance chromatin
condensation, and trigger de novo DNA methylation - leading to the
inactivation of the gene
Also increases global H3K9 mono- and dimethylation, a/w increased DNA
methylation and long-term gene silencing.
 Chromium - reduce in-vitro H3 phosphorilation and trimethylation, and
acetylation marks in H3 and H4 – a/w lung cancers
Effect of nutrition on Epigenetics
 Folate, vitamin B-12, methionine, choline (Soymilk, broccoli ), and betaine
(Wheat Bran, Spinach, Sweet Potato, beef etc.)can affect DNA methylation
and histone methylation through altering 1-carbon metabolism.
 Pantothenic acid is a part of CoA to form acetyl-CoA, which is the source of
acetyl group in histone acetylation.
 Genistein (soyabean, coffee) and tea catechin affects DNA
methyltransferases (Dnmt)
 Resveratrol (grape, blueberry, raspberry, mulberry), butyrate (released by
gut bacteria), sulforaphane (broccoli), and diallyl sulfide (garlic and onion)
inhibit HDAC and curcumin inhibits histone acetyltransferases (HAT).
Thank
you…

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Epigenetics : overview and concepts

  • 1. Epigenetics… We inherit more than just the DNA sequence
  • 2. Definition Gene functions can be altered by more than just change in DNA sequence. “An Epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence”
  • 3. Mechanism of Epigenetic process It can be divided into 3 stages 1. Epigenator 2. Epigenetic Initiator 3. Epigenetic Maintainer
  • 4. Epigenator Triggers that changes the environment of the cell to create a epigenetic phenotype. It can be anything – like nutrition, toxin, radiation, hormones etc. Epigenator signals are transient, they remain in the cell environment long enough to trigger the epigenetic process. They are not necessary for the subsequent process.
  • 5. Epigenetic initiator  Translates the Epigenator signal to mediate the epigenetic effect on chromatin.  Priming of epigenetic initiator by Epigenator –> Initiator identifies location on a chromosome where epigenetic state is to be established.  Initiator could be a DNA-binding protein, a noncoding RNA, or any other entity that can define the coordinates of the chromatin structure to be assembled.
  • 6.  unlike the Epigenator, the Initiator may not dissipate after its action, but rather may persist with the Maintainer.  Initiator will in general be a signal that requires self-reinforcement and self-renewal through positive feedback mechanisms.
  • 7. Epigenetic Maintainer  Signals that sustains the epigenetic chromatin state created by initiators.  Maintainers do not have absolute DNA sequence specificity. Consequently, they could operate at any chromosomal location to which they are recruited by an Initiator.  This signals involves many different pathways, including DNA methylation, histone modifications, histone variants, nucleosome positioning, and others.
  • 8. DNA methylation  Oldest epigenetic mechanism known  Addition of methyl group at cytosine residue at CpG dinucleotides.  These methyl groups project into the major groove of DNA and inhibit transcription.
  • 9.  Methylation is mostly observed at non-coding regions and interspersed repetitive elements. NOT seen in CpG islands of active gene.  The addition of methyl groups is controlled at several different levels in cells and is carried out by a family of enzymes called DNA methyltransferases (DNMTs). It can be de novo or maintenance, following DNA replication.  Three DNMTs (DNMT1, DNMT3a and DNMT3b) are required for establishment and maintenance of DNA methylation patterns.  DNMT1 - for the maintenance of established patterns of DNA methylation  DNMT3a and 3b - new or de novo DNA methylation patterns.
  • 10. Effects of DNA methylation: 1. deactivation of parasitic Transposons 2. Somatic hyper-mutations at Ig locus in B and T cells 3. embryonic development and growth 4. Genomic imprinting 5. X-chromosome inactivation Dysregulation in methylation process result in many disorders like ICF (Immunodeficiency, centromeric instability and facial abnormalities), cancers (deactivation of Tumor suppressor genes) etc.
  • 11. Histone modification Modification Writer Eraser Acetylation HAT HDAC Methylation HMT HDM Phosphorylation PK PP
  • 12.
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  • 15.  Effects of histone modifications: Cis effect – alter inter-nucleosomal contacts and spacing Trans effect – altered histone-non histone protein associations  Pattern of histone modification may provide ON or OFF epigenetic signature mark Acetylation – a/w active chromatin domain Phosphorylation – a/w condensed chromatin which generally fails to support transcriptional activity. H3K4Me3 and H3K36Me3 – a/w active transcription H3K27Me3, H3K9Me2/3 and H4K20Me3 – a/w repressed genes
  • 16. Nucleosome positioning, Chromatin remodeling complex and histone variants  Sometimes nucleosomes are bound by repressive chromatin associated factors  Transcription machinery is not able to gain access to binding site  It is solved by Chromatin remodeling enzymes.  Categorized in two families; 1. SNF2H or ISWI – mobilizes nucleosome along the DNA 2. SWI/SNF or Brahma – alter the structure of nucleosome and hence DNA:histone contacts Additionally there are some ATP dependent “exchanger complexes” – replace core histone with histone variants
  • 18.  Histones are synthesized and deposited only during S phase  Replacement with histone variant is independent of cell cycle stage  Take immediate effect in response to transcriptional activity or stress signals  Replacement of H3 by H3.3 and H2A by H2A.Z is better studied and they are correlated with transcriptional activities  Specific exchanger complexes are observed for histone variants
  • 20. EPIGENETIC INHERITENCE  epigenetic marks are erased during two phases of the life cycle – Firstly, just after fertilisation Secondly, in the developing primordial germ cells  Cellular mechanisms may allow for co-transmission of some epigenetic marks  During replication, DNA polymerases working on the leading and lagging strands are coupled by the DNA processivity factor proliferating cell nuclear antigen (PCNA),  PCNA is implicated in patterning and strand crosstalk that allows for copy fidelity of epigenetic marks
  • 21.  children who were conceived during a harsh wartime famine in the Netherlands in the 1940s are at increased risk of diabetes, heart disease and other conditions — possibly because of epigenetic alterations to genes involved in these diseases  poor people living in inner cities, where cycles of drug addiction, neuropsychiatric illness and other problems often seem to recur in parents and their children.  laboratory mice trained to fear the smell of acetophenone, a chemical the scent of which has been compared to those of cherries and almonds. He and Dias wafted the scent around a small chamber, while giving small electric shocks to male mice. The animals eventually learned to associate the scent with pain, shuddering in the presence of acetophenone even without a shock. This reaction was passed on to their pups.
  • 22. Effect of environmental chemicals on Epigenetics  Cadmium – interact with the methyltransferase DNA binding domain - interference in enzyme-DNA interaction - reduces genome methylation  Arsenic – Detoxification of As is by enzymatic methylation using SAM - depressed SAM levels - global DNA hypomethylation  Nickel - replace magnesium in DNA interactions, enhance chromatin condensation, and trigger de novo DNA methylation - leading to the inactivation of the gene Also increases global H3K9 mono- and dimethylation, a/w increased DNA methylation and long-term gene silencing.  Chromium - reduce in-vitro H3 phosphorilation and trimethylation, and acetylation marks in H3 and H4 – a/w lung cancers
  • 23. Effect of nutrition on Epigenetics  Folate, vitamin B-12, methionine, choline (Soymilk, broccoli ), and betaine (Wheat Bran, Spinach, Sweet Potato, beef etc.)can affect DNA methylation and histone methylation through altering 1-carbon metabolism.  Pantothenic acid is a part of CoA to form acetyl-CoA, which is the source of acetyl group in histone acetylation.  Genistein (soyabean, coffee) and tea catechin affects DNA methyltransferases (Dnmt)  Resveratrol (grape, blueberry, raspberry, mulberry), butyrate (released by gut bacteria), sulforaphane (broccoli), and diallyl sulfide (garlic and onion) inhibit HDAC and curcumin inhibits histone acetyltransferases (HAT).

Editor's Notes

  1. TDG – thymine DNA glycosylase TET- 10 11 translocation 5caC carboxylcytosine 5fc formylcytosine