Advancing Epigenetics Towards Systems Biology

Glossary

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Term Definition
Epigenetic marks
(tags) Features not directly governed by the genetic code, which include methylation of DNA and covalent modification of histone proteins. The latter may also be tagged with methyl, acetyl, ubiquitin, phosphate, poly(ADP)ribose and other biochemical groups. These groups and their particular pattern of protein modification (e.g. mono-, bi-, tri-methylated at different amino acids and combinations of amino acids) modify the function of the tagged proteins and influence the way genes are expressed.
Epigenetic reprogramming
Resetting epigenetic tags so they resemble those of other cells from earlier developmental stages. This is of particular relevance for germline cells after the fusion of gametes when the genome is brought back into a kind of "zero-state" of gene expression.
Epigenetics
The studies of heritable changes in gene function that occur without a change in the sequence of nuclear DNA and the processes involved in the unfolding development of an organism.
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Epigenome
the epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it, and when to do it. Different cells have different marks. These marks, which are not part of the DNA itself, can be passed on from cell to cell as cells divide, and from one generation to the next. Thus, these marks may constitute heritable epigenetic marks—but not necessarily—some of them may be lost during the cell cycle but they nevertheless provide a signature or flavor of chromatin that can correspond to its functional state.
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Epigenomic map
Diagramatic representation of the gene expression, DNA methylation and histone modification status of a particular genomic region.
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Epigenotype
Encompasses the specific set of epigenetic marks peculiar to different cells, which determines their fate (i.e. wether they remain germline or will be brain or bone).
Epimutations
Alterations to normal epigenetic marks that can be passed down from parents to offspring via their germline.
Euchromatin
A type of chromatin that is rich in gene concentration.
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Expression
Production of observable/detectable characteristics of an organism, usually due to the synthesis of protein.
Extra-embryonic tissues
Vertebrate embryos have four extra-embryonic tissues: amnion, chorion, yolk sac and the allantois. In placental animals these tissues form the placenta.
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Facio-scapulo-humeral dystrophy
(FSHD) One of the most common types of muscular dystrophy caused most frequently by an autosomal dominant mutation in an as yet unidentified gene. Initial weakness is seen in facial muscles.
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Fission yeast
A type of fungus that reproduces exclusively by medial fission to produce two daughter cells of equal sizes. Saccharomyces pombe is the best-known species and was isolated in 1893 by Lindner from East African millet beer. It is an important eukaryotic microorganisms serving as model organism for molecular biological research, i.e. especially cell cycle research. See also budding yeast.
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Friendly bacteria
A common reference to those bacteria that offer some benefit to human hosts, such as Lactobacillus species, which convert milk protein to lactic acid in the gut. The presence of such bacterial colonies also inhibits the growth of potentially pathogenic bacteria.
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Gene
1. Most widely used definition: A gene is a basic unit of DNA. It is transcribed into RNA molecules which either serve as a template to generate a polypeptide chain or fullfill regulatory, structural or catalytic functions. 2. More basic definition used by Richard Dawkins: A gene is defined as any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection.
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Gene expression
Genes that are expressed are made into RNA (transcribed by RNA polymerase). The RNA transcript may subsequently be converted to protein (translated). Not all genes (e.g. rRNA, tRNA genes) are translated into protein.
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