The Epigenome (Genomics)

The epigenome refers to all the heritable changes in the genome that do not involve alterations in the DNA sequence but affect gene expression.

It is crucial for regulating gene expression.

Epigenetic mechanisms such as DNA methylation, histone modification, X-inactivation, and genomic imprinting control gene expression patterns.

The genome is packaged into the nucleosome, where histone proteins and DNA form the first level of packing.

Nucleosomes are further wound into 30nm fibers.

These fibers are packaged with scaffold proteins to form higher-order structures, with chromosomes being the densest form of genomic DNA.

DNA methylation, which regulates gene expression.

Histone modification, which affects chromatin structure and gene expression.

X-inactivation, which silences one of the X chromosomes in females.

Genomic imprinting, where the expression of certain genes depends on the parent of origin.

Pharmacoepigenetics, which studies how epigenetic changes influence drug response.

Euchromatin is gene-rich and transcriptionally active.

It has a dispersed appearance under a microscope.

It contains unique DNA sequences.

Heterochromatin is gene-poor and less transcriptionally active.

It has a condensed appearance.

It contains repetitive DNA sequences.

The epigenome refers to the sum of all heritable changes in the genome that do not occur in the primary DNA sequence.

These changes affect gene expression and result in a change in phenotype but not genotype.

DNA methylation

Histone modification

X-inactivation

Genomic imprinting

The nucleosome is the first level of DNA packing, formed by histone proteins and DNA.

It plays a crucial role in the compacting of the genome into higher-order chromatin structures.

Nucleosomes are wound up to form 30nm fibers.

These fibers are then further wound up with scaffold proteins.

This process generates higher-order structures that lead to the formation of chromosomes.

Euchromatin: Gene-rich, transcriptionally active, dispersed appearance, and unique DNA sequences.

Heterochromatin: Gene-poor, less transcriptionally active, condensed appearance, and repetitive DNA sequences.

DNA methylation is the addition of a methyl group to the 5' position of a Cytosine.

This process is catalyzed by DNA methyltransferase enzymes (DNMT1, DNMT3a, DNMT3b).

S-Adenosyl Methionine provides the methyl group required for this modification.

In differentiated cells, DNA methylation occurs in CpG dinucleotides.

DNA methylation patterns change during development and play a crucial role in controlling gene expression.

Histone modification is the addition of chemical groups to the proteins that make up the nucleosome.

There are over 100 known histone modifications, and many are of unknown function.

A large range of enzymes catalyze histone modifications.

Methylation

Acetylation

Phosphorylation

Ubiquitination

Many different amino acids can be modified, and they may have 1 to 4 groups added, leading to a large number of modifications.

How are histone modifications named? (1)

H3K4Me3 means that on Histone 3, the Lysine (K) at position 4 is tri-methylated.

Writers

Erasers

Readers

Histone Acetyltransferase (HAT1)

Histone Methyltransferase (EHMT1)

Histone Deacetylase (HDAC1)

Histone Demethylase (KDM1)

Bromodomain and extra-terminal (BET) proteins (BRD2)

Chromodomain proteins (CBX1)

Histone acetylation at Lysine residues relaxes the chromatin structure.

It reduces the positive charge on histones, making it accessible for transcription factors.

Histone methylation is complex.

It can either repress or activate transcription depending on where it occurs.

Concurrent histone modifications can interact and affect gene expression in complex ways.

X-inactivation is the inactivation of one of the two X chromosomes in every somatic cell in females.

The Y chromosome has virtually no genes, so there is only one copy of each X chromosome gene in males (hemizygosity).

X-inactivation ensures that every somatic cell in all humans has the same number of active copies of every gene.

The Xist gene is transcribed as a long noncoding RNA (lncRNA) from the X-inactivation center (Xic).

It binds all over the X-chromosome to initiate X-inactivation.

Histone acetylation is removed.

Histone and DNA methylation occur, contributing to the inactivation of the X-chromosome.

The inactive X-chromosome becomes heterochromatic and forms a Barr body.

Tsix is transcribed in the opposite direction to Xist.

It antagonizes Xist RNA to keep one X chromosome active.

Tortoiseshell cats are female because the coat color is determined by alleles on the X chromosome, and females have two X chromosomes.

One X chromosome carries an orange fur allele.

The other X chromosome carries a black fur allele.

Random X-inactivation in different cells results in patches of orange fur from one X and black fur from the other X.

This causes the characteristic tortoiseshell coat pattern.

Genomic imprinting is the selective expression of genes based on the parental origin of the gene copy.

Every autosomal gene has one paternal and one maternal copy.

The expression of some genes is determined by which parent the gene copy is inherited from.

Imprinted genes are often found in clusters.

There are very few imprinted genes, around 250.

Imprinting is mediated by imprinting control regions (ICRs).

One copy is silenced by DNA methylation, catalysed by DNMT3a.

Histone methylation also contributes to gene silencing.

Long noncoding RNAs (LncRNAs) are essential to the imprinting process.

Imprinting patterns are reset during gamete formation.

DNA methylation.

Histone modification.

X-inactivation.

Genomic imprinting.

Pharmacogenetics refers to the study of how genetic variations affect an individual’s response to drugs.

Relevance to cancer treatment: Epigenetic modifications can influence the efficacy of cancer therapies by altering the way genes are expressed in tumour cells.

Big Pharma is interested in targeting epigenetic pathways to improve drug response and potentially develop better cancer treatments.

Pharmacogenetics focuses on how genetic factors influence drug absorption, distribution, metabolism, and excretion (ADME).

Epigenetics influences gene expression through modifications like DNA methylation, histone modification, etc., without changing the DNA sequence.

In cancer, epigenetic alterations can render tumours more or less responsive to certain treatments.

By understanding pharmacogenetics and epigenetics, more effective drugs can be developed, improving cancer treatment.

Yes, targeting epigenetic enzymes may offer a new approach in cancer treatment.

Epigenetic enzymes regulate DNA and histone modifications, which are often altered in cancer cells.

Epigenetic therapies aim to reverse these changes, restoring normal gene expression and potentially suppressing tumour growth.

Global DNA methylation is altered in tumour cells, impacting gene expression.

Hypermethylation of tumour suppressor genes leads to their silencing, promoting cancer.

Hypomethylation of tumour-activating genes can lead to their overexpression, aiding tumour growth.

Epigenetic enzymes like DNMT3A and TET1/2, which regulate DNA methylation, are often mutated in cancer cells.

Histone modifications include acetylation, methylation, phosphorylation, and ubiquitination of histone proteins, which regulate gene expression.

Histone Acetyltransferases (HATs) add acetyl groups, often leading to gene activation.

Histone Methyltransferases (HMTs) add methyl groups, which can either silence or activate genes, depending on the specific modification.

Histone Kinases add phosphate groups to histones, affecting chromatin structure and gene expression.

Histone Demethylases remove methyl groups, often activating silenced genes.

Histone Readers are proteins that recognize and bind to specific histone modifications (e.g., acetyl, methyl, or phosphoryl groups).

In cancer, histone readers can help in interpreting and amplifying epigenetic signals, thus contributing to uncontrolled tumour cell growth.

DNMT3A (DNA methyltransferase)

TET1/2 (Ten-Eleven Translocation methylcytosine dioxygenases)

Histone Acetyltransferases (HATs)

Histone Methyltransferases (HMTs)

DNA Methyltransferase Inhibitors (DNMT inhibitors) block the activity of enzymes that add methyl groups to DNA, which can silence genes.

Role in cancer treatment: By inhibiting DNMTs, these drugs aim to reactivate silenced tumour suppressor genes, potentially suppressing cancer cell growth.

Example: 5-Azacytidine (Vidaza) is used in the treatment of myelodysplastic syndrome (MDS), a type of cancer affecting blood cells.

5-Azacytidine (Vidaza) is a DNMT inhibitor that works by blocking DNA methylation.

It is used primarily to treat myelodysplastic syndrome (MDS), a condition that often progresses to leukaemia.

By reactivating silenced genes, it can help prevent the growth of abnormal cells in the bone marrow.

Histone Deacetylase Inhibitors (HDAC inhibitors) block the enzymes that remove acetyl groups from histones, leading to a more relaxed chromatin structure.

This allows tumour suppressor genes to be reactivated, promoting normal cell function and potentially inhibiting tumour growth.

HDAC inhibitors can treat cancers like cutaneous T-cell lymphoma, where gene silencing plays a role in the disease progression.

Romidepsin (Istodax) is a Histone Deacetylase Inhibitor (HDAC inhibitor) that reactivates tumour suppressor genes.

It is approved for the treatment of cutaneous T-cell lymphoma (CTCL), a type of cancer affecting T-cells in the skin.

By inhibiting HDACs, Romidepsin restores gene expression and can slow the progression of cancer.

Seven drugs have been FDA-approved so far that target epigenetic mechanisms.

These drugs include DNA Methyl Transferase Inhibitors (e.g., 5-Azacytidine) and Histone Deacetylase Inhibitors (e.g., Romidepsin), and they are used to treat various cancers, such as myelodysplastic syndrome and cutaneous T-cell lymphoma.