Lecture 14: Epigenetics

1. Epigenetics

Epigenetics is defined as an INHERITABLE effect that influences gene activity but does NOT  INVOLVE a change in DNA sequence.

In practice epigenetics is the study of gene expression or phenotype changes. The meaning of this term is simple and is comprised of two words:epi- (Greek:- over, above) and genetics. The term  Epigenome refers to the overall epigenetic state of a cell genome [1].

Epigenetics include two predominant mechanisms:histone modifications and DNA methylation. Specific processes linked with epigenetics are described in this article:[1]: imprinting, gene silencing, paramutation, X chromosome inactivation, position effect, reprogramming, maternal effects, carcinogenesis, heterochromatin and histone modifications, parthenogenesis and cloning [1]. The molecular basis of epigenetics is very complex [1-4].

 Picture  1. Two main components of the epigenetic code. Source -Nature 441, 143-145 (11 May 2006) [14].

Epigenetic changes play crucial role in imprinting, differentiation of cells, cell dividing, metastasis formation. What is more -  transcriptional silencing of selected genes caused by DNA methylation plays a crucial role in development and progression of human cancers(TSGs are inactivated by gene mutation, deletion or DNA methylation [5]). Epigenetic changes may be inherited and may be reversible.Somatic epigenetic inheritance, particularly through DNA methylation and chromatin remodeling, is crucial  in the development of eukaryotic organisms and differentiation of cells.

In some diseases a single gene knock out is sufficient to cause a disease. Most cases require both copies to be knocked out. Epigenetics play a role in congenital genetic disease, Angelman Syndrome, Prader-Willi Syndrome, Beckwith-Wiedemann syndrome (syndromes associated with genomic inprinting - phenomenon in mammals where the father and mother contribute different epigenetic patterns) and as said above -cancer.

 2. DNA methylation and cancer

Epigenetics in cancer and developmental abnormalities.

A variety of compounds are considered as epigenetic carcinogens(heavy metals – including nickel, diethylstilbestrol, arsenite, hexachlorobenzene.Developmental abnormalities may be caused by epigenetic changes induced by teratogens.

Transcriptional silencing of selected genes caused by DNA methylation plays a crucial role in development and progression of human cancers.TSGs may be  inactivated by gene mutation, deletion or DNA methylation.About half of TSGs mutated in familial cancer syndromes have been shown to be inactivated by promoter methylation:

-RB1  (retinoblastoma)

-VHL (kidney cancer)

-APC, hMLH1 (MSI-high cancer phenotype)

- p16 (pancreatic cancer, melanoma)

-CDH1 (inherited diffused gastric cancer)

-BRCA1 (breast/ovarian cancer)

Picture 2. Methylation blocks transcription of TSGs.

There are two types of methylation in cancer:

TYPE A – age-related , borders of CpG islands (p16, hMLH1)– most common. Caused by inflammation, virial infections and AGE – colorectal cancer.

TYPE C – cancer-specyfic methylation – CpG island densely methylated – concordant methylation of multiple genes (hMLH1, p16, CDH1)– caused by genetic defect (eg. Mutation of DNA-MT). colorectal cancer, gastric cancer, liver tumors, pancreatic cancer.

Picture 3. Age, methylation and cancer.

An excellent example of gene inactivation by promoter methylation is CDH1 gene. It encodes E-cadherin protein. In gastric carcinoma, two important mechanisms of E-cadherindown-regulation have been described to date:mutations (germ-line and sporadic) and methylation of the 5’ CpG island in the promoter region, which may cause transcriptional repression of the CDH1 gene [6].

Picture 4. CpG island in CDH1 promoter region.

E-cadherin plays a crucial role in: the normal tissue functions, right cell morphology and cell differentiation. Changes in E-cadherin function/expression may be linked with aberrant cell-to-cell adhesion (that is why diffused gastric cancer may be a result of decreased expression of E-cadherin) , especially during metestasis formation.

Picture 5: Changes in E-cadherin function/expression may be linked with aberrant cell-to-cell adhesion, especially during metastasis formation.

3. Epigenetic research and diagnostics:

Epigenetic diagnostics and research uses a wide range of molecular biologic techniques including: cheap but not precise MSP (methylation specyfic PCR)[7], popular chromatin immunoprecipitation [8](with its large-scale analysis on  ChIP-on-chip and ChIP-seq),bisulfite sequencing,FISH, methylation-sensitive restriction enzymes, DNA adenine methyltransferase identification. The use of bioinformatic  methods is playing an increasing role in computational epigenetics.

The important role of epigenetic defects analysis in cancer opens up new, exciting  opportunities for improved diagnosis and therapy (de-methylation drugs - including Decitabine)[9]. With no doubts we may use bioinformatic methods to improve diagnosis and therapy by detecting and classifying cancer types and subtypes [10]. Hovewer, still we have to careful talking about epigenetic treatment. Up to date such treatment strategies are not fully convincing and may cause hypomethylation effects  in genes where hypomethylation may become dangerous for the cell and may contribute to malignancies.

4. Bioinformatics in Epigenetics: data processing and analysis [11].

With no doubts well equipped laboratory where researchers seriously think about epigenetics need a full time expert in bioinformatics. This is why because diagnostics and research in computational epigenetics comprises the application (or often development) of bioinformatic methods for computational data analysis/modeling.

High- throughput epigenetics techniques have been developed recently for genome-wide mapping of epigenetic information. Such methods include  bisulfite sequencing, ChIP-on-chip and  ChIP-seq. These methods generate huge amount of data. Thus epigenetic analysis needs professional bioinformatics experts dedicated to data processing and quality control by bioinformatic methods.

Bioinformatics in Epigenetics – Practical applications:

There are several applications in Epigenetics  where bioinformatics experts are urgently needed:epigenetic regulatory circuitry,population epigenetics (regulatory mechanisms from the integration of gene expression profiles with epigenome data and maps of haplotypes),evolutionary research,medicine (epigenome regulation in human and its medical consequences), theoretical modeling, genome browsers. Here you can find useful Epigenetics Databases [12]: