Epigenetic class 1: What is epigenetic?

Different types of epigenetic modifications in the genome.

 

“ Change in phenotype without a change of genotype or change in the phenotype is results from an alteration in gene expression, not by a gene mutation.”

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Alteration in the phenotype of any character is originated from a change in genotype. If any mutation occurs in a gene it influences the phenotype of the related gene but epigenetic change is originated by an alteration in gene expression.

Each somatic cells have the same genetic content but the expression of the different gene is variable depending upon the type of tissue. For example, Skin cells required more melanin during summer, hence gene which codes for melanin is expressed more in skin cells as compared to lung cell or liver cell.

Insulin is produced by the pancreas so the gene which codes for insulin, expressed more in the pancreas as compared with epithelial skin cell.

When the expression of a tissue-specific gene is altered, epigenetic change occurs. Therefore if melanin is underexpressed or overexpressed in the skin cells, it results in epigenetic alteration.

Generally, epigenetic changes are associated with cancer because an alteration in gene expression induces uncontrolled cell growth. p53 gene is a transcriptional factor, alteration in p53 gene expression leads to uncontrolled transcription (because it is a transcriptional factor), results in abnormal cell growth.

Junk DNA is non-coding DNA sequences but it plays a crucial role during transcription and translation. Methylation in the non-coding region of the DNA makes it transcriptionally inactive. Methyl group is added to the C or G base of the non-coding DNA sequences, hence it is not recognized by an enzyme.

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Image represents difference between genetic change vs epigenetic change

During epigenetic alteration, change in methylation pattern does activate or deactivate gene expression. Other epigenetic mechanisms like ubiquitination, Histone modification, non-coding RNA associated gene silencing and chromatin remodelling are responsible for alteration in gene expression.

Read the article: Epigenetic class 2: How epigenetic alteration helps us evolving and surviving in all condition?

Various types of cancer, fragile X syndrome, angelman’s syndrome, prader-willi syndrome, ratt syndrome are occurred due to epigenetic alteration. Epigenetic changes are stable and heritable. Though it might inherit from mother to her child during pregnancy, it may also occur during adulthood or late onset of age.

During embryogenesis, almost all methylated sequences are demethylated first, and then remethylated into embryo. It is just like installing or updating a new program to  mobile or computer.

Methylation of DNA

The function of the gene or gene expression is altered by the addition of methyl group (CH3) by enzyme DNA methyltransferase (DNMTs). DNMT1, DNMT2, DNMT3a and DNMT3b are four major types of enzyme required for maintaining DNA methylation pattern.

DNMT1 is responsible for maintenance of inherited methylation pattern or natural methylation. While DNMT3a and DNMT3b are committed to new methylation.

Generally, in humans, the cytosine base is more prone to methylation. The 5th carbon of cytosine is methylated and is called as 5-mC or 5-methylcytosine. The 5-mC is predominantly observed in CpG Island of junk DNA. Methylation in CpG Island near promoter region results in underexpression of a gene.

Read further,

  1. Proteinase K DNA extraction method
  2. Phenol chloroform DNA extraction: Basics, preparation of chemicals and protocol
  3. Different types of DNA extraction methods
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The image represents DNA methylation and histone modification along with micro RNAs. Image credit: www.mcb.asm.org

Demethylation is also an important phenomenon for maintaining epigenetic changes. The methyl group is removed by the same enzyme- DNMTs.  DNA hypomethylation and DNA hypermethylation is the most common type of epigenetic alterations in the nature.

A classical example of methylation is inactivation of X chromosome in a female. Female has two X chromosomes, so the genetic composition of X chromosome is twice in female as compared with the male. For maintaining constant gene expression the whole X chromosome becomes methylated and remain inactive.

Histone modification

Histones are protein molecules which help to arrange DNA into systemic manner. Histone H1, H2a, H2b, H3 and H4 are major histone subtypes which helps DNA to organize on the chromosomes. Histone provides the structural identity to DNA which helps DNA to fit inside the cell nucleus.

Fore more detail on DNA packaging read the article: DNA packaging in eukaryotes

Modification in histone arrangement hinders DNA packaging. Post translational modification of histone includes methylation, acetylation, ubiquitylation and phosphorylation are involved in epigenetic alterations.  It alters gene expression by altering chromatin structure (For more detail on chromosome arrangement and chromatin structure read the article: Story of a chromosome).

Modification of histone-DNA packaging activates or inactivates transcription process. Histone H3 is the major site of modification. Several major modifications are listed below:

Modification

Histone

Amino acid

Position of amino acid

methylation

H3

Arginine

2

lysine

4, 9, 27, 36, 79

Phosphorylation

H3

serine

10, 28

threonine

3,11

Acetylation

H3

lysine

9, 14, 18, 23, 56

Methylation

H4

Arginine

3

lysine

20

Phosphorylation

H4

serine

1

Acetylation

H4

lysine

5, 8,

  • Acetylation of histone

Acetyl co- enzyme A actively involved in acetylation and deacetylation. Acetyl (COCH3) group from acetyl co-A is added to histone during acetylation and histone acetyltransferase (HAT) is an enzyme actively involved in this process.

Histone deacetylase (HDAC) enzyme is responsible for deacetylation. More than 20 HATs are identified till date. HATs and HDACs enzymes control modification process by addition or deletion of –COCHgroup to the histon. if the mechanism is imbalanced it will result in epigenetic alteration.

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The image represents the process of Acetylation and deacetylation of histone. Image credit: www.eurheartj.oxfordjournals.org

Processes of apoptosis, DNA replication, DNA repair, cell cycle and transcription are highly regulated by acetylation of histone, so change in the acetylation pattern of histone will influence any of the process listed above and it will result in altered gene expression.

Read more,

  1. Role of Telomeres in ageing
  2. The XX chromosome in male: A case of sex reversal
  3. DNA digital data storage
  • Methylation of histone

Histone methyltransferase (HMT) enzyme regulates histone methylation by the addition or deletion of a methyl group.

Alteration in methylation pattern of histone which is bounded with a specific gene will activate or deactivate that particular gene. Modification at that site will change the gene expression of the DNA sequence associated with histone.

Different types of HMTs have specific activity on different sites of the histone. Methylation in histone H3 at 2nd position of amino acid arginine and 4th, 9th, 27th position of amino acid lysine, are the most common type of modifications. It is involved in transcription, cell proliferation and differentiation. Imbalance in histone methylation causes oncogenic activity.

  • Histone phosphorylation

Phosphorylase enzyme regulates the process of modification through histone phosphorylation. It is induced by the response of DNA damage. Diverse DNA damage responds during cell division leads to activate histone phosphorylation.

After the DNA repair, the site of histone is dephosphorylated. If the mechanism of phosphorylation is dysregulated, it will modify the DNA repair mechanism. Down-regulation or up-regulation of histone phosphorylation will increase or decrease transcriptional activity of a gene. Hence gene expression is altered.

Histone phosphorylation plays important role in cell signalling, DNA repair, apoptosis and transcription.

Chromatid remodelling

A nucleosome, histone-DNA assembly arranged systematically into chromatin. If nucleosome assembly is tightly packed, it will not allow transcriptional factor to binds with DNA. Here tightly wrapped histone molecules resist transcription.

Loosely arranged chromatid facilitate transcriptional factors to bind with DNA and allow transcription. Tightly packed chromatid regions are called as heterochromatin and are transcriptionally inactive. DNA in heterochromatin region is methylated and histones are modified which creates a dense, tight arrangement of DNA- histone complex.

A loosely packed region of chromatin is transcriptionally active and called as euchromatin region. Imbalance in euchromatin and heterochromatin arrangements results in epigenetic alteration.

Chromatin modelling and remodelling process are highly conserved and tightly regulated, error in chromatin modelling results in alteration of gene expression.


Attend class: Immunogenetics


Non coding RNA (ncRNA)

Yes, it cannot build any protein. ncRNAs are transcribed into RNA but not involved into translation. Hence it cannot code for protein. ncRNAs are sort RNA sequences which can be miRNA, piRNA, siRNA or long ncRNAs.

microRNAs (miRNAs) are shorter (up to ~30nt long) RNA molecules which involved in mRNA silencing. It binds to the complementary sequences present on mRNA and degrades or cleaves mRNA and blocks translation.

Short interfering RNAs (siRNA) are also a shorter type of ncRNA which mediates post-transcriptional gene silencing. Here siRNA cleaves mRNA molecule and induces heterochromatin formation by RNA induced transcriptional silencing complex. It promotes methylation and condensation chromatin which blocks translation.

Long ncRNAs are ~200nt long non-coding RNA molecules which exhibits catalytic activity similar to shorter ncRNAs. Long ncRNA creates a complex with the protein involved in chromatin modification. It modifies chromatin state and influence gene expression.

X chromosome inactivation is mediated by long ncRNA. Xist (X- inactive specific transcript gene) actively involved in x chromosome inactivation. 

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The image represents an epigenetic profile of genome. Image credit: www.janewhitney.com

Even though the epigenetic profile in highly conserved and maintained from the evolution, Our life style has a major influence on it. Food, bad habits like smoking and tobacco eating, adverse environment, exercise, sleeping habits all type of un-natural conditions or adverse lifestyle results in epigenetic alterations.

 

Article written by: Tushar Chauhan

 

Read next:

Story of Chromosome

Story of DNA

Story of Gene