Response written by: Elphège Nora, PhD - postdoctoral researcher in Edith Heard's laboratory, Institut Curie
Each cell of the body produces molecules known as proteins. The structure of proteins...Read more...
Response written by: Elphège Nora, PhD - postdoctoral researcher in Edith Heard's laboratory, Institut Curie
Germ cells of human beings (and all other organism actually) are unfortunately unable...Read more...
Cancer, ageing, stem cells and cloning are just some of the many evokative words that have been associated with epigenetic research. What is epigenetics? What are stem cells? What impact do these things have on ordinary lives? These important FAQs among others are addressed here.
Response written by: Elphège Nora, PhD - postdoctoral researcher in Edith Heard's laboratory, Institut Curie
Each cell of the body produces molecules known as proteins. The structure of proteins is directly encoded by the cells' genes. In humans, genes are very similar from one individual to another but there are not completely identical. This means that the proteins produced by my cells are very similar, but not completely identical to yours.
In our blood some special cells, called the cells of the immune system, have the amazing ability to probe the proteins that are on the outside of almost all the other cells of the body. At the beginning of their life some very important immune cells are trained to become aggressive whenever they meet proteins encoded by foreign genes. Then immune cells migrate through the blood vessels and can reach almost every part of the body, where they meet many other cells. As you can see—not much happens to your immune cells when they meet other cells from your body. However, upon encountering a foreign cell that has foreign proteins because of its foreign genes, your immune cells will become aggressive toward that foreign cell and simply kill it.
Normally this is a good thing, because in most cases these foreign cells are parasites that made their way in our body, such as pathogenic microorganisms. But the problem is that a tissue graft [http://www.merriam-webster.com/dictionary/graft] is, by definition, also made up of foreign cells. In order to prevent the immune system from systematically destroying the graft, doctors typically prescribe drugs that tamper with the action of the immune system so that grafted patients can tolerate the foreign cells in their body. The goal is to tamper with the action of the immune system, but not prevent it from acting completely otherwise grafted patients would not be able to fight against pathogenic microorganisms. Thus, a fine balance has to be reached, and sometime the immune system is still too strong despite of the drugs—and will end up destroying the transplanted tissue.
Germ cells of human beings (and all other organism actually) are unfortunately unable to "copy" the skills and knowledge of their producer. Children/offspring, develop from the fusion of two gametes (germ cells), one from the mother and one from the father. This fusion is actually the end point of germ cell maturation. Thus, each child is a unique mixture of its two parental genomes. However, they are born without any recollection whatsoever of their parent's memory, knowledge, or skills acquired by training during the previous generation. It is indeed a bit discouraging not to be able to transmit the skills we worked so hard to develop directly through our germ cells! However, as humans, we have hopefully developed other ways to transmit our skills and knowledge to our children: though schooling and education. That's another way to transmit skills across generations, and even better, we can transmit these to many more individuals than our biological children!
This is a good question - but difficult to answer! We actually do not really understand how that works, but many researchers are working hard to find out! We do know that it has to do with the way the various neurons in our brain reorganize the contacts they make with each other, and also with the way they send chemical and electrical signals to each other. These properties of brain neurons can be modified by chemical and electrical stimuli they receive from the various sensitive nerves that are connected to the outside world through our eyes, nose, hair etc... Many researchers are working on trying to understand what these nerves really modify in our neurons, down to the molecular level, depending on what sensation we feel and remember. This is surely a very exciting avenue of research!
The 2012 Nobel prize in Physiology or Medicine, to John Gurdon and Shinya Yamanaka, is a very good example of how knowledge about epigenetics can be practically applied. Epigenetics basically aims at understanding how a cell – or an organism – can keep a recollection of what it has experienced, and transmit that recollection to its descendants over many generations. Each cell of our body is an illustration of this kind of process, as a blood cell when dividing will give rise to daughter cells of the blood lineage, skin cells will give rise to other cells of the skin lineage, etc..., because the cellular state (blood, skin, etc...) is somehow instructed from the parental mother cell to the daughter cell. There are many molecular mechanisms that play a role in this process and researchers are actively trying to understand them.
What John Gurdon and Shinya Yamanaka understood is how to actually interfere with this process, and force a cell to "forget" its identity. To be precise the cell actually does not really forget, but is pushed into an embryonic state, gaining the ability to give rise to cells not only of its own cell type, but of almost all the cell types of the body. This phenomenon is sometimes called "de-differentiation" or "reprogramming". Practical applications are obvious: for example you could take some skin cells of a patient who suffered heart-failure, force them to de-differentiate in the dish and then let them re-differentiate, still in the dish, to heart cells and put them back in the diseased heart of the patient. Such manipulation of cell identity for therapeutic purposes is one of the far-reaching practical applications of Epigenetics. For more information check out Sceince's Scitable education resource here.
However don't forget that the nucleus is a crowded place and DNA polymerases are not just floating around. The constantly bump into many, many other molecules, which can actually affect how replication initiates or proceeds. This is an area of very intense research. Also not just humans need to replicate DNA; by definition, all living organisms do it—even the simplest bacteria! Nowadays we understand enough about this process that we can recreate part of it in test tubes in the lab, to make many copies of DNA from a few molecules. In fact, I just did it today; all I needed to mix was a DNA template with the DNA polymerase in a proper water-based chemical buffer plus a few molecules that we chemically synthesized. You can find more information about this amazing experiment by searching for "Polymerase Chain Reaction" on the web.
Strictly speaking, the word "epigenetic" characterizes the mode of inheritance of a given trait, irrespective of the molecular mechanism or process that underlies it. "Epigenetic process" and "epigenetic mechanisms" are synonymous expressions often employed to refer to the molecular process or mechanism that underlies the epigenetic inheritance of a given trait. Now you understand that in order to be perfectly correct one should actually not use the terms "epigenetic process" or "epigenetic mechanism", as strictly speaking it is not the process or mechanism that is epigenetic in essence. "Epigenetic" is instead an adjective characterizing of the mode of inheritance. However "epigenetic process/mechanisms" are convenient words and widely used as it is much easier to talk about your favorite "epigenetic process" that your favorite "process that underlies the epigenetic inheritance of your favorite trait"! But really that big sentence is what one means by "epigenetic process".
Now "Epigenetic tag" is tricky. According to what I just said, what does "epigenetic tag" actually mean then? Is it a molecular tag that is involved in the epigenetic inheritance of a given trait, or is it a tag that is epigenetically inherited? That really is not the same thing! In fact I have met people discussing epigenetic tags (or "Epigenetic marks" in that case), who were arguing and thought they were disagreeing but in the end they realized they were using the same word to talk about two different things. In these conditions the best to avoid confusion is to always remember that "epigenetic" is an adjective qualifying the mode of inheritance, not a molecule, a tag or a mark.
In eukaryotic cells, the DNA is packaged within the nucleus in a structure called chromatin. This structure is a highly dynamic nucleoprotein complex that plays a central role in regulating how and when DNA is copied and transcribed into RNA. Thus chromatin states vary from cell type to cell type and along chromosomes. The epigenome refers to these states at the whole genome level. Typically, a multi-cellurar organism will be characterized by one genome, but by as many epigenomes as there are cell types.
Epigenetics encompasses all processes that lead to heritable changes in gene expression (during development or across generations) without changes in the DNA sequence itself. In eukaryotes, chromatin is at the heart of most epigenetic processes. Thus, the study of epigenetics often crosses that of epigenomes (epigenomics).
So what's the advantage of using stem cells from the embryo that have been reprogrammed in this way? The main advantage is that you can derive a greater variety of cell types. Embryonic stem cells, as they are called, have the potential to be any body cell. Adult stem cells on the other hand have partly committed to different cell fates. So, for example, you can only make muscle cells from adult stem cells found in muscle. The disadvantage to using embryonic stem cells, is that they have the potential to become cancerous. This has not been observed with adult stem cells. When scientists understand how these cells are programmed to become different cell types, embryonic stem cells could be used in therapies. They can also be used to test drugs, which means that animals don't necessarily need to be used.
Scientists can take the nucleus out of a fertilised egg cell, and replace this with a nucleus from the patient. This reprogrammed egg cell can be used to clone more cells with the adult nucleus. The resultant cell line could then be used to treat the patient. Obviously not everyone feels comfortable about this technology, because it involves using embryonic tissue.
Patients' own adult stem cells have been successfully used to treat a number of conditions, like Parkinson's disease and multiple sclerosis. If you take adult stem cells from other people, they might not be genetically compatible with the patient. Transplanted adult stem cells can be rejected. Another way to avoid rejection of stem cell transplants is to use a much more controversial method. The way that Dolly the Sheep was created. Scientists can take the nucleus out of a fertilised egg cell, and replace this with a nucleus from the patient. This reprogrammed egg cell can be used to clone more cells with the adult nucleus. The resultant cell line could then be used to treat the patient. Obviously not everyone feels comfortable about this technology, because it involves using embryonic tissue.
When you cut yourself, your body's defences are rapidly initiated at the wound site. Your own natural stem cells are recruited to make new skin. Different kinds of stem cells are present in each of your body organs to repair damaged tissue. These are adult stem cells. Scientists are excited about harnessing the power within these special cells to create more organic ways of treating different diseases. Reinforcing the body's own therapeutic strategies has many advantages over traditional chemical treatments, for example chemotherapy, which can be devastating for patients.
Eugenics and epigenetics are not interrelated. The term eugenics is derived from Greek and means 'well born' or 'good breeding'. Its concept was first formulated by Charles Darwin´s cousin Sir Francis Galton in 1865, although he didn't use the term eugenics until 1883. Eugenics is a social philosophy which advocates the supposed improvement of human hereditary qualities. Proposed means of doing so have included (but are not limited to) birth control, selective breeding, genetic engineering, racial hygiene, and even extermination.
The molecular mechanisms responsible for imprinting are defined by the inheritance of epigenetic tags (see FAQ 7) from cell generation to cell generation and from the parents to their offspring. Classically, epigenetic imprinting, or silencing, is the suppression of certain genes on chromosomes, depending on from which parent they were received. When DNA is passed to daughter cells after fertilization of an egg by a sperm, certain alleles can become active only if they were received from the mother, others only if they came from the father. If a gene is suppressed through imprinting from one parent, and the allele from the other parent is not expressed because of mutation, neither can act and the child will be deficient. Genetic imprinting has also been defined as the gamete-of-origin dependent modification of phenotype.
Histone proteins can be modified as epigenetic tags by modifying enzymes in a substrate-specific manner. Prominent are methylation, acetylation and phosphorylation of specific Lysines, Arginines and Serines within the aminoacid sequences of the tails of histones. Imprinting, or silencing, is the suppression of certain genes on chromosomes, depending on from which parent they were received. Combinations of these chemical alterations are thought to modify the structure and function of chromatin. The particular combination of these epigenetic tags may represent various types of chromatin and are thought to represent a histone code in analogy to the genetic code.
It is now believed that the first coding nucleotide-chains on earth were RNA molecules. They represented the first replicators in an RNA world roughly 3.5 billion years ago. There are five arguments for an initial RNA world: 1. Prebiotic synthesis of ribose is simpler than synthesis of DNA. 2. The nucleophily of 2´,3´OH groups is much higher than for 3´OH hydroxyls of deoxyribose increasing reactive flexibility. 3. RNA chains are chemically more stable than DNA as their basepair interactions are stronger. Therefore, RNA is capable of forming an enormous spectrum of secondary structures with the potential to evolve catalytic function. 4. DNA replication starts with RNA synthesis in all organisms. 5. Ribonucleotides are the universal precursors in cellular biosynthesis of deoxyribonucleotides (DNA). On the early earth, the transition from an RNA- to a DNA-world did not affect the nucleotide sequence. Therefore, this transition likely represents the first epigenetic modification in early evolution. If peptides, such as chaperones, accompanied early replication is not known, but sophisticated proteins may not have been obligatory as RNA is self-catalytic. Thus, epigenetic modification of nucleotide chains may have been an intrinsic property of life right at the very beginning of organismic evolution.
DNA frequently becomes methylated by an enzyme called DNA methyltransferase. DNA methylation is a type of chemical modification which involves the addition of a methyl group to the carbon-5 of the cytosine pyrimidine ring. This methyl group can be sensed by proteins which then themselves modify other proteins posttranslationally. The pattern of posttranslational change creates changes in electric charge within chromatin and this leads to different degrees of chromatin condensation. It also determines whether genes can be transcribed or become silent within highly compacted chromatin. Silence of genes means, that their encoded genetic information is not transribed into mRNA and subsequently it will not be translated into protein molecules. There are many ways of how electric charges between nucleotide molecules and proteins can be altered. These variances of charge are identical with what people call epigenetic tags.
In addition to DNA methylation (i.e. a form of alkylation), proteins can become posttranslationally modified through: methylation (histone methyltransferase), phosphorylation (kinases), acetylation, isoprenylation, glycosylation, ubiquitination, SUMOylation, poly(ADP)ribosylation (PARP).
Chromatin is the molecular substance of a chromosome. It consists of a complex of DNA, RNA and protein in eukaryotic cells. Frequently, people encounter pictures of chromosomes which have a striped pattern of stronger and lighter staining. What are these chromosome bands? Do they represent genes? No, they do not necessarily represent genes nor do they automatically correspond to stretches lacking genes. Chromosomes often presented to the public are most highly compacted metaphase chromosomes or the giant chromosomes (i.e. polytene chromosome) of Drosophila larvae from salivary gland cells. The latter are made up of about 2000 DNA double strands arranged parallel to each other. A single band of a Drosophila giant chromosome can contain about 50.000 nucleotides in a row. But what makes its staining different to an adjacent band? What we see as dark bands is a consequence of an increased concentration of DNA within variably, compacted chromatin that differs in staining on average every 50 kb. But there is also a gradient of diverse higher order degrees of compaction. Further, in the life of a chromosome it alters its appearance. During the so-called interphase it is relaxed with a lot of open chromatin (see FAQ 7). During this phase, some entire chromosomes but mostly only parts thereof retain a strong staining. These subnuclear features are known since the early days of cytology. In 1928, Heitz introducd for them the term 'heterochromatin'. Euchromatin, on the other hand, is highly decondensed chromatin. Chromosomal regions in the genome which lack high numbers of genes are normally compacted in heterochromatin while chromosomal regions with high concentrations of transcribed genes are part of relaxed euchromatin. But these patterns change during development depending on the pattern of particular epigenetic tags present in the chromatin (see FAQ 8).
The discovery of the chromosome was descriptive from the beginning and inseparably interwoven with the discoveries of the cell and the nucleus. All findings became possible only after Leeuwenhoek´s invention of the microscope in 1674. In 1831 Robert Brown described the 'areola' in orchids being constantly detectable in all cells. He called this areola'the nucleus of the cel'.1838 M. J. Schleiden´s incorrect epigenetic theory claimed that a cell-nucleus is created de novo from the fluid of the cell. This served as a classical antithesis to Edouard van Beneden´s 1883 discovery that chromosomes are individual entities. In 1842 Karl Wilhelm von Nägeli discovered subcellular structures that would later became known as chromosomes. He had observed the 'idioplasma', a network of string like bodies which he falsely assumed to form an interlinked network throughout the entire organism. In 1873 Schneider had described the indirect division of the nucleus with a 'Kernfigur'(nuclear figure) and an 'achromatic spindle'. In 1883, Edouard van Beneden found that after fertilization of the germ cells of the nematode Ascaris megalocephala the chromosomes of the male nucleus do not fuse with those of the oocyte nucleus. Therefore, they are distinct entities.This was the empirical foundation of Mendel´s rules, but their connection was found only several years later. Van Beneden did not yet use the word chromsome, which was later coined by Waldyer in 1888. The term reflected the staining behavior of chromosomes after using specific dyes.
Epigenetics is studied in different organisms. They represent all kingdoms of life, i.e. eubacteria, archaea, fungi, animals and plants. It frequently includes comparative analysis from an evolutionary perspective. Examples of some well understood research model organisms are: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Hydra hydra, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Xenopus laevis, Mus musculus. Analysis of some human diseases also help to advance an understanding of epigenetic mechanisms and the underlying causes of certain diseases.
While different models are discussed, the question is best provisionally explained by a classical, simplified example(1,2): The phosphate groups connecting the nucleotides of a DNA chain are negatively charged. In naked dsDNA they would repel each other, and the DNA would represent an 'open chromatin' conformation. However, the extruding N termini of nucleosomes are positively charged. Thus, in chromatin consisting only of DNA and nucleosomes the positive histone N-termini would interact with the negative phosphate groups such that the chromatin is highly compacted ('closed chromatin'). There are high levels of H1 linker histones in this chromatin. In a closed chromatin environment genes cannot be transcribed as the transcription factors are sterically hindered to trigger mRNA synthesis - the genes are 'silenced'. The condensed chromatin however can be relaxed by covalently linking acetylgroups (CH3COO-) especially to the amino groups of Lys of the core histones H3 and H4. Acetylation brings in a negative charge and neutralizes the interaction of the N termini with the phosphate groups. As a consequence, the condensed chromatin is transformed into a transiently relaxed structure (see Fig.1) which allows genes to be transcribed. The enzyme catalyzing acetylation is called histone acetyltransferase. Naively one might assume that starting from a zygote, an organism should successively activate all available genes during development in order to live. Thus, at adult age, all genes should be active. However, the simultaneous activity of all genes would produce an uncontrolable chaos of gene expression patterns not allowing coordinated cell- and organ-differentiation. Therefore, many genes need to be more or less permanently inactivated after they have done their job. Such a status can be triggered and maintained by an epigenetic tag. In our example the tag is the methylation of cytosine. Genes which are methylated by a DNA methyltransferase are recognized by the protein MeCP2 which binds to the methylated nucleotides. This protein is complexed with histone deacetylase. Once MeCP2 binds to methylated DNA, histone deacetylase removes the acetyl groups, and the chromatin becomes condensed and inaccessable again for transcription factors. The silenced chromatin can be maintained over most of an organisms lifespan. An example for a protein mediating such a task is encoded by the polycomb gene.
1. Jones, P. L., G. J. Veenstra, P. A. Wade, D. Vermaak, S. U. Kass, N. Landsberger, J. Strouboulis, and A. P. Wolffe. 1998. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19:187-91.
2. Nan, X., H. H. Ng, C. A. Johnson, C. D. Laherty, B. M. Turner, R. N. Eisenman, and A. Bird. 1998. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386-9.
Figure.1. Bestor, T. H. 1998. Gene silencing. Methylation meets acetylation. Nature 393:311-2. The effects of cytosine methylation and histone deacetylation on transcription. Transcriptional silencing in vertebrates is usually associated with the presence of 5-methylcytosine (m5C) in the DNA. Nan et al.1 and Jones et al.2 have now discovered a link between methylation and histone deacetylation — MeCP2 (a protein that binds methylated DNA) exists in a complex with histone deacetylase
The term 'Genetics' was coined by William Bateson in 1905. However, the term 'gene' is based on ideas of Charles Darwin and Hugo de Vries: In 1878 Hugo de Vries visited Darwin, who directly stimulated de Vries to shift from physiological to evolutionary and genetic studies. The source of de Vries‘ inspiration was Darwin‘s speculation on heredity, i.e. the provisional hypothesis of pangenesis. According to pangenesis, hereditary characters are part of tiny cellular particles called gemmules. All cells produce gemmules during develoment, growth and later life. Gemmules then migrate from somatic to germ cells, where they collect to pass inherited characters to the next generation. This, actually was Darwin‘s famous lamarckist statement! Hugo de Vries suggested a fundamental (and correct) modification: he abandoned Darwin‘s key notion of the migration of gemmules across cell boundaries, and rechristened gemmulae as 'pangenes'. Wilhelm Ludvig Johannsen in 1909 finally coined the term 'gene' (for further reeding see 1). Only later Hermann Muller's discovery in 1927, that genes can be altered by gamma radiation and are therefore real physical entities, and Watson's and Crick's discovery of the DNA structure in 1953 led to genes as the major focus of understanding the morphology of phenotypes, life histories and physiology. In 1942, Waddington defined epigenetics as 'the branch of biology which studies the causal interactions between genes and their products which bring the phenotype into being.' Because this objective was always the driving force of biology since Darwin and before, we now understand from a traditional, historical perspective that there is a tight, inseparable kinship between genetics and epigenetics. Today, epigenetics can be best envisaged as the causal, logical and consequential modern successor of genetics.
1. Gould, S. J. 2002. The structure of evolutionary theory. Belknap Press of Harvard University Press, Cambridge, Mass
The DNA molecules of eukaryotes are linear chains of nucleotides with lengths in the centimeter range. The size of the nuclei in which this DNA resides is on average only 7 micrometer in diameter. The evolution of such long molecules was possible only because the DNA strings were tightly folded around proteins leading to the compaction of a chromosome. The major protein complex with DNA wrapped around itself is called a nucleosome. Each nucleosome consists of four proteins called histones. Nucleosomes are positively charged at the N-termini of their histones. There are two copies of each histone molecule for every 200 bp of DNA. The histones are called H2A, H2B, H3 and H4. Another, larger single histone molecule, H1 is called a linker histone. It binds to DNA molecules which cross over each other and seals the complex at the exterior of the nucleosome such that the DNA does not unfold. The DNA of a typical eukaryotic genome is about 1m long. The compaction of DNA into nucleosomal chains would reduce this length to about 15 to 20 cm. In a 7 micrometer nucleus this still requires further condensation. Therefore, nucleosomes cross-link to each other and additional proteins such as HMG14 and HMG1. Like H1, HMG proteins have a preference for binding crossed DNA molecules. They are also major linker DNA-binding proteins and help in conjunction with the nucleosomes to form higher order chromsome structures.
In 1942 Conrad Hal Waddington defined epigenetics as 'the branch of biology which studies the causal interactions between genes and their products which bring the phenotype into being'. In modern sense the term 'epigenetics' describes heritable changes in genome function that occur without a change in nucleotide sequence within the DNA. For example, when a cell established a particular pattern of 'active' and 'non-active' genes this same pattern will be passed on to a daughter cell even though during cell division all genes are 'shut off' and chromosomes have become tightly wrapped up or condensed. This process allows development of different structures and organs during development. The nucleotides within DNA sometimes become chemically modified. A number of combined, nearby modifications may represent a particular pattern. Such a pattern may serve as a template for passing on its informative message in the form of specific chemical modifications to other molecules. Particular aminoacid groups (e.g. lysines) within proteins such as histones may be modified through acetylation or methylation and serve as transmitters of such information. Such chemical modification patterns are called epigenetic tags.
A chromosome is a large macromolecule which contains part of the genetic information stored in the genome. The core of the chromosome-molecule is a double stranded DNA string which is interacting non-covalently with a large number of proteins (chromatin proteins) and shorter chains of ribonucleic acid (RNA). The DNA of a chromosome within a human cell spans several centimeters and has to be compacted in order to fit into an average cell’s nucleus of 7 micrometer diameter. This compaction is mediated by the proteins associated with the DNA. Each chromosome must contain at least one origin of replication. While prokaryotic microorganisms usually contain a circular chromosome, the ends of linear chromosomes of eurkaryotes must be protected against degradation by special proteins. The ends of linear chromosomes are called telomeres.
The genome represents the entire genetic information stored in the chromosomes of an organism. It enables the fertilized egg (i.e. the zygote) or an embryonic stem cell to complete development into an adult organism containing all organs, physiological functions and structures necessary for living and reproduction. This genetic information is maintained in the nucleotide sequence of DNA, where DNA is an integrated part of the chromosomes. Molecular DNA duplication-processes guarantee the genome to be present in nearly all cells of a respective organism. The genome also serves as a sanctuary for long term storage of the genetic information established over millions of years of evolution. To this end, replica copies of each DNA strand are produced by duplication, which, if damaged through mutation, serve as blueprints for each other to correct occurring errors.