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Epigenetics - the operating instructions of our genome

Part 1: How environmental factors change our genetic make-up

Epigenetics - what is it? A new promise of healing or does it provide the key to how our genetic makeup is controlled?

The term epigenetics (from Greek: epi = over) refers to molecular mechanisms that help to make our genes stronger or weaker. In this process, the DNA or certain nucleotide sequences are not changed, but enzymes mark certain sections of the DNA. This process takes place "over" or "on" the DNA. For example, the specific cells of our organism control in this way which and how many enzymes are produced for certain metabolic processes. In a way, epigenetics describes the "operational processes" that are stored on the DNA, as follows a meta-level of genetic regulation. In a sense, epigenetics therefore also describes how our genome organizes itself. The totality of these epigenetic states describes the epigenome.

By means of these "operating instructions", the cell nucleus can regulate, under the influence of external factors such as environmental influences, in what way, at what time and in what quantity genes are switched on or off.

Epigenetic mechanisms influence the cell to respond, for example, to change environmental conditions. This is not only the basis of our evolution as a whole, but also has enormous consequences for our genetic makeup, especially in today's constantly changing environment. We think of climate, increasing water scarcity for parts of the world's population, hunger and malnutrition, oversupply of food for other segments of the population and the accompanying metabolic changes, epidemics, environmental degradation, increase in toxic substances, intoxicants and the like.

The epigenetic, regulatory mechanisms biochemically influence how narrow or accessible certain areas of the genome are for further metabolic processes. The access to the "operational" control of the genome is regulated by attaching or detaching certain methyl groups on the DNA. The labeling pattern of the genome modified in this way is subsequently read by specialized enzymes and thus controls further steps, for example to switch genes on or off.

Consequences

The epigenome consists of a set of chemical changes in the organism's DNA and histone proteins. These changes can be passed on to an organism's offspring via transgenerational, epigenetic inheritance. Changes in the epigenome itself can lead to changes in the structure of chromatin and thus to changes in the function of the genome as a whole.

As a consequence of this model, descriptive epigenetics completely overturns the dogma of biology, according to which the genetic material inherited at birth was unalterably determined. In fact, however, epigenetics is capable of describing even subtly altered environmental factors that affect DNA. In many new research approaches, it has been shown that environmental factors, such as toxic substances, have direct access to the operating instructions of our genome. Likewise, it has been shown that even changes in personality traits can be epigenetically influenced. 

Current research

The epigenome is involved in the regulation of gene expression, physical development, tissue differentiation, and suppression of transposable elements. Unlike the underlying genome, which is in fact largely static in an individual, the epigenome can be dynamically altered by environmental and ecological conditions.

As a prelude to a potential human epigenome project, the Human Epigenome Pilot Project aims to identify and catalog methylation variable positions (MVPs) in the human genome. Advances in sequencing technology now allow the study of genome-wide epigenomic states through multiple molecular methods. An international effort to study the epigenome began in 2010 in the form of the International Human Epigenome Consortium (IHEC), whose members aim to generate at least 1,000 reference epigenomes from various normal and disease-associated human cell types.

Epigenetics is by no means a new "promise of salvation", as some popular science media try to explain it, but an almost fantastic tool to investigate, research and identify diseases caused by environmental influences.

Roadmap Epigenomics Project

One goal of the NIH Epigenomics Project roadmap is to generate reference human epigenomes from healthy individuals across a wide variety of cell lines, primary cells, and primary tissues. The data generated by the project and available through the Human Epigenome Atlas are classified into five types that shed light on different aspects of the epigenome of its states (such as gene expression):

Histone Modifications - Chromatin Immunoprecipitation Sequencing (ChIP-Seq) identifies genome-wide patterns of histone modifications by antibodies against the modifications.
DNA methylation - bisulfite-Seq over the whole genome, reduced representation bisulfite-Seq (RRBS), immunoprecipitation sequencing of methylated DNA (MeDIP-Seq) and methylation-sensitive restriction enzyme sequencing (MRE-Seq) determine the DNA methylation of genome areas with different Resolution down to the single base pair.
Chromatin Accessibility - The DNase I hypersensitive sites sequencing (DNase-Seq) uses the DNase-I enzyme to find open or accessible areas in the genome.
Gene Expression - RNA Seq and Expression Arrays determine the level of expression of protein-coding genes.
Small RNA Expression - smRNA-Seq identifies the expression of small, non-coding RNAs, primarily miRNAs.
Reference epigenomes for healthy people should enable the second goal of the Roadmap Epigenomics project, namely to investigate the epigenomic differences that occur in disease states such as Alzheimer's disease occur.

First important research results

The fiber-digesting bacteria present in the large intestine of mice, strongly influence the epigenome. Polysaccharides degraded to fatty acids influence the gene activity and metabolism of the mice; the short-chain fatty acids formed changed the structure of histones, for example. These proteins hold the long DNA chains together in the cell nucleus. Human tumors undergo extensive disruption of DNA methylation and histone modification patterns. The abnormal epigenetic landscape of the cancer cell is characterized by epigenomic hypo- and hypermethylation of CpG island promoters of tumor suppressor genes, altered histone code for critical genes, and global loss of monoacetylated and trimethylated histone H4.

Oncologist David Gorski and geneticist Adam Rutherford cautioned against the presentation and dissemination of false and pseudoscientific conclusions by New Age authors such as Deepak Chopra and Bruce Lipton. Such conclusions, they said, owe much to the early stages of epigenetics as a science and the spin surrounding it.

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