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 stages1. Epigenator2. Epigenetic Initiator3. 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…