Epigenetics Quiz on DNA Methylation

Epigenetics Introduction

• Epigenetics is the study of heritable changes in gene expression or the phenotype.
• These changes occur without alterations to the underlying DNA sequence.
• Epigenetic changes are influenced by factors beyond DNA sequence, such as environment.
• The term "Epi" means on top of/above.
• Epigenetics was first coined by C.H. Waddington.
• He used it to explain cell differentiation beyond genetics.
• Waddington's work included genetic assimilation.
• This involved the acquisition of inherited characteristics through environmental influences.
• An example of Waddington's work was the crossveinless trait in Drosophila.

Questions Related to Epigenetics

• Different adult stem cells have specific fates.
• Myoblasts form muscle and keratinocytes form skin cells.
• Identical twins can have different hair and eye colors due to epigenetic changes.
• Identical twin littermates can have different coat colors because of epigenetic changes.
• Imprinting can silence one parental allele.
• X-inactivation is a type of dosage compensation.

Packing DNA into Chromatin

• Each base pair in DNA is 0.34 nm long.
• The human body has billions of base pairs per cell.
• A typical cell has 2 meters of DNA, yet the nucleus measures only 2-10 μm.
• Humans have approximately 50 trillion cells.
• The DNA in a human body is 100 trillion meters long.
• The distance between the Sun and Earth is 150 billion meters.
• Each person's DNA could stretch from Earth to the Sun and back over 300 times.
• Chromatin compacts DNA within the nucleus.

Nucleosomes

• The nucleosome is the fundamental unit of chromatin.
• It is composed of histone octamer and 147 base pairs of DNA.
• Histone proteins include H2A, H2B, H3, H4 (core histones) and H1 (linker histone).
• It compacts DNA structure within the nucleus.
• It associates with transcription.

Mechanisms of Epigenetics

• There are three main mechanisms of epigenetics:
• 1. DNA methylation
• 2. Histone modification
• 3. Non-coding RNA

DNA Methylation and Histone Modifications

• DNA methylation involves methyl groups attached to specific DNA bases.
• This often silences gene activity.
• Histone modifications include various molecules attaching to histone tails.
• These modifications alter the activity of the DNA around histones.

Cytosine Methylation

• Cytosine methylation involves adding a methyl group to cytosine bases in DNA.
• Methylation commonly occurs at CpG sites.
• The universal methyl donor is S-adenosylmethionine (SAM).

CpG Islands

• CpG islands are clusters of CpG sites often found near gene promoters.
• A CpG island should have at least 200 base pairs and over a 60% GC content.
• They are important for gene regulation.
• Most CpG islands are unmethylated in normal cells.
• They play a role in many processes, including cancer.

Methylation Patterns in Diseases (e.g., Cancer)

• Abnormal methylation patterns are associated with diseases like cancer.
• This includes both global hypomethylation and focal hypermethylation of genes.
• Dysregulation of tumor suppressor genes (TSGs) and oncogenes can be affected.

Progressive Alterations in DNA Methylation in Cancer

• Cancer development is associated with gradual changes in DNA methylation.
• This encompasses shifts from global hypomethylation to regional hypermethylation.
• This process involves an accumulation of epigenetic abnormalities.

CpG Island Methylation

• CpG island methylation is a stable, heritable, and detectable epigenetic signal that has important roles in normal development and disease.
• CpG methylation patterns are readily observed and change in step and through the progression in disease.

DNA Methylation in Stem Cells

• DNA methylation differentiates totipotent embryonic stem cells from unipotent adult stem cells. The methylation patterns are different and distinguishable.

How Methylation Inhibits Transcription

• Methylation may inhibit the binding of regulatory factors to the DNA promoter region.
• Methylation can prevent the binding of activator proteins to enhancer elements.
• Methylation can cause proteins called methyl-CpG-binding proteins (MBPs) to bind.
• These proteins recruit other proteins that then rearrange the chromatin to a less accessible conformation (often repressed).

Establishment and Maintenance of Cytosine Methylation

• De novo methylation occurs via DNMT3a and DNMT3b enzymes.
• Maintenance methylation is aided by DNMT1.
• These enzymes are vital for the regulation of epigenetic modifications.

Bisulfite Sequencing

• Bisulfite treatment is a DNA sequencing method for detecting methylation patterns.
• The treatment will convert cytosine to uracil.
• 5-methylcytosine nucleotides are unaffected.

IncRNA and Epigenetics

• Non-coding RNAs, including IncRNAs, influence epigenetics.
• IncRNAs are associated with DNA methylation and histone modifications, and thereby regulate transcription.
• IncRNAs can either activate or repress transcription.

Chromatin Structure

• Euchromatin: Active genes, accessible DNA, light-staining, open conformation.
• Heterochromatin: Silent genes, inaccessible DNA, dark-staining, closed conformation.

Core Histones

• Core histone proteins (H2A, H2B, H3, H4) are highly conserved and enriched in basic amino acids.
• These are important for DNA packaging.

Histone Modifications

• Histone modifications (methylation, acetylation, phosphorylation, ubiquitination, sumoylation, and other modifications) regulate gene expression.

Methylation of Histone H3-K27

• H3K27 methylation is associated with gene silencing
• The enzyme EZH2 and Polycomb Repressive complexes (PRCs) mediate this methylation.

Chromatin Modifications

• Various modifications are associated with specific biological processes.
• These include methylation of cytosine (DNA), acetylation or phosphorylation of lysines (histones), and methylation of arginines (histones).

Maternal Behavior and Epigenetics

• Maternal behaviors affect methylation patterns in offspring's brains.
• Attentive or inattentive mothering can affect epigenetic modifications in offspring brains.

Rainbow and Copycat Cats

• Random X chromosome inactivation patterns result in distinctive coat patterns.
• Coat coloring in calico cats due to stochastic inactivation.

Xist RNA and Epigenetics

• Xist IncRNA functions in cis to silence the X chromosome.
• Xist interacts with transcriptional regulators via the chromatin.

Histone Modifications and Modifiers

• Histone modifiers include:
• Writers (acetylases, methylases, phosphorylases)
• Readers (proteins binding to the marks)
• Erasers (deacetylases, demethylases, phosphatases)