Epigenetics

The study of changes in phenotype without changes in genotype. Breakthroughs have allowed us to enable the possiblity of genome-wide epigenetic research e.g. mapping the human genome-wide DNA methylation, Pioneering work started in 1869-1928. 

Techiques include

• DNA methylation 
• Histone modifciation 
• Chromatin conformations 

It is the study of heritable phenotype changes that is brought about by modification of gene expression, but do not involve alterations in the DNA sequences. This can tell you the follwing information:

• cell type 
• disease 
• developing stage 
• envriomental stage 

!869 -1928 by Miesher, Flemming, Kosseland Heitz defined nucleic acids, chromatin and histone proteins, which leas to the cytological distinction between euchromatin and heterochromatin. 

This led to the development of X-chromosome inactivation and imprinting which led to the idea of swithcing genes on and off

• Heritable  during mitosis leasding to acquired phenotyoe
• Reversible 
• Changed by enviroments e.g, Diet, drugs & aging 

Drvien by changes in the chromatin structure, which alters gene expression. This is regulated by interactions between differnet features of DNA. 

Epigenetics defines the process by which organisms access and use the information stored in DNA, Cells in an organism have identical DNA sequences yet maintain different terminal phenotypes - called nongenetic cellular memory. This records development and enviromental cues. 

The epigenome is complex and diverse. 

• histone tail modification
• DNA methylation 
• Chromatin looping
• Topologically associating domains

Epigenetic arks and gene expression are altered by transcriptiom factors. 

• DNA methylation
• Chromarin remodelling
• Histone Variation 
• Covalent histone modications 
• Regulatory RNA

DNA methylation is an epigenetic mechanism that occurs by the addition of a methyl (CH3) group to DNA, thereby often modifying the function of the genes and affecting gene expression. The most widely characterized DNA methylation process is the covalent addition of the methyl group at the 5-carbon of the cytosine ring resulting in 5-methylcytosine (5-mC). These methyl groups project into the major groove of DNA and inhibit transcription.

DNA demethylation is the removal of a methyl group from DNA.

DNA methylation is controlled by three types of enzyme

• De novo methyltransferase: it adds a methyl group to an unmethylated target sequence on DNA. 
• Maintenance methyltransferase: it converts hemimethylated sites to fully methylated sites by
• Demethylase: it removes a methyl group, typically from DNA, RNA, or protein

Patterns of DNA methylation in the genome and the topology of chromatin structure and composition are tightly linked. DNA methylation and histone methylation/ acetylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function

Further roles of DNA methylation

• Cellular defence mechanism against the activity of foreign genes 
• During the embryonic development of mammals,
• High levels of DNA methylation in repetitive DNA sequences act as nucleation centres for heterochromatin formation
• X chromosome inactivation
• Genome stability 
• Imprinting

Imprinting occurs in the germline and it affects few hundred genes (usually located in clusters). Accompanied by heavy methylation –different methylation in female and male germline (sex specific). Once imprinted and methylated, silenced genes remain transcriptionally inactive during embryogenesis – only one copy of the gene is active in embryogenesis 

Histone tails are subject to post-translational modifications.

The enzymes that catalyses histone modifications are the following:

·       HAT: histone acetyl transferase

·       HDAC: histone deacetylase

·       HMT: histone methylase

·       HDM: histone demethylase

·       Kinase

·       Phosphatase

Proteins recognize a specific histone code. Proteins with specific binding domains recognise specific modifications and thereby influence chromatin  structure and function.

Short-term effects

•       Ongoing processes

•       Transcription, replication, repair

Long-term effects

•       Heritable changes

•       Cellular memory

The dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins or to the replication machinery

DNA wrapped within nucleosomes becomes accessible to regulatory elements, such as transcription factors and the replication machinery. Chromatin remodelling can result from covalent modification of histones by histone acetyltransferases, histone deacetylases, histone methyltransferases or kinases, and by ATP-dependent protein complexes that physically remodel, move or remove nucleosomes.

Chromatin remodeling is an active process. The energy-dependent displacement or reorganization of nucleosomes that occurs in conjunction with activation of genes for transcription. 

All remodeling complexes contain a related ATPase catalytic subunit, and are grouped into subfamilies containing more closely related ATPase subunits.

• Nucleosome organization and assembly
• Chromatin access
• Nucleosome editing

A non-coding RNA (ncRNA) is a functional RNA molecule that is transcribed from DNA but not translated into proteins. Epigenetic related ncRNAs include miRNA, siRNA, piRNA and lncRNA.

In general, ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. 

Those ncRNAs that appear to be involved in epigenetic processes can be divided into two main groups; the short ncRNAs (<30 nts) and the long ncRNAs (>200 nts). 

The three major classes of short non-coding RNAs are microRNAs (miRNAs), short interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs).

Both major groups are shown to play a role in heterochromatin formation, histone modification, DNA methylation targeting, and gene silencing.

Epigenetic effects may be inherited through generations (transgenerational epigenetics).

Acetylated histones are conserved and distributed at random to the daughter chromatin fibers at replication.

•   Aging
•   Exercise
• Diet
• Epigenetic Drugs 
•  transgenerational epigenetic inheritance
• Environment influences gene expression and epigenetic marks

In contrast to 'hard' alterations of the DNA sequence (mutations), 'soft' adaptations of the chromatin template (modifications) are potentially all reversible. This distinction represents one of the key hallmarks of epigenetic control, providing a basis for 'epigenetic therapies'.

Hypermethylation of promoter regions in tumor suppressor genes can inactivate many tumor suppressor functions.

•       Dysregulation of miRNAs in cancer

•       Altered pattern of histone modifications in different types of cancer

Epigenetic modifications have a considerable effect on cancer.  Methylation levels play an important role in cell divisions, DNA repair, differentiation, apoptosis, angiogenesis, metastasis, growth factor response, detoxification, and drug resistance.

Such features have promoted huge advances in the early detection of cancer using methylation levels.  HDACs, specifically HDAC1, can often be identified in elevated quantities in prostate and gastric cancer patients.

•       The term ‘epigenetic clock’ is used to denote two distinct but related things.

•       First it is as a synonym of a highly accurate age estimator based on DNA methylation levels

•       Second it is the concept of an innate process in the body that continues inexorably, resulting in ageing.

Overview of epigenetic changes during aging. In young individuals, the cells within each cell type have a similar pattern of gene expression, determined in large part by each cell having similar epigenetic information. During aging, the epigenetic information changes sporadically in response to exogenous and endogenous factors. The resulting abnormal chromatin state is characterized by different histone variants being incorporated, altered DNA methylation patterns, and altered histone modification patterns, resulting in the recruitment of different chromatin modifiers

EWAS: epigenome-wide association study is an examination of a genome-wide set of quantifiable epigenetic marks, such as DNA methylation, in different individuals to derive associations between epigenetic variation and a particular identifiable phenotype/trait.

Epigenetic therapy is the use of drugs or other epigenome-influencing techniques to treat medical conditions. Many diseases, including cancer, heart disease, diabetes, and mental illnesses are influenced by epigenetic mechanisms, and epigenetic therapy offers a potential way to influence those pathways directly:

•       DNA Methyltransferase Inhibitors: nucleoside analogues, such as 5-azacytidine (cytosine analogue, used in myelodysplastic syndrome treatment). The drug acts to inhibit DNA methylation as it becomes incorporated into DNA during DNA replications, blocking DNA methyltransferase activity which can help to reactivate genes which have been silenced. It inhibits DNMTs by irreversible covalent binding

•       Histone Deacetylase Inhibitors: SAHA is a histone deacetylase inhibitor used in the treatment of cutaneous T-cell lymphoma. This drug prevents the removal of acetyl groups added to histone tails which would usually cause DNA decondensation. By halting this profile, chromatin would be in a more open conformation, allowing the activation of genes.