Advancing Epigenetics Towards Systems Biology

Glossary

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Term Definition
Embryo
A term used to describe the early life stage of a developing organism after fertilization. In humans, the embryo begins after fertilization of an oocyte by a sperm cell and persists up until week 14 of pregnancy.
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Embryonic lethality
Death of an embryo/foetus in the womb. Embryonic lethal genes were first systematically characterized in Drosophila by Eric Wieschaus and Christiane Nüsslein-Volhard. They received a Nobel-Prize in Physiology or Medicine, 1995 for the discovery of the genes involved in the developmental program of the fruit fly.
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Embryonic stem (ES) cells
ES cells are self-renewing cells isolated from the vertebrate inner cell mass of a developing embryo. As ES cells are totipotent they are capable of differentiating into any somatic cell or tissue but they also preserve their capability to remain within the developmental pathway of germ cells. Thus, they are part of the germline.
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Endosperm
Triploid tissue (containing three sets of homologous chromosomes) found in the seeds of flowering plants. It provides nutrition to the developing embryo. It is mostly composed of starch, though it can also contain oils and protein. The cells are formed from a double-fertilization event involving two female nuclei and one male nucleus.
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Enzyme
A protein that facilitates a specific biochemical reaction. Many enzymes work together to build-up and break down biomolecules within the cell. The most central and probably most ancient biochemical pathway driven by enzymes is the citric-acid-cycle. Enzymes also drive transcription, translation, and DNA maintenance.
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Epigenesis
The theory that development of an organism, and in particular the development of a plant or animal from an egg or spore through a sequence of gradual steps in which cells differentiate and organs form - a process of increasing complexity. Counter-argument to preformationism, which holds that the whole organism is already present in the sex cells, and merely gets bigger over time.
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Epigenetic code
Both DNA methylation and histone modifications specifically modify the way that genes are expressed. This has led to the theory that there is an epigenetic code which serves to fine-tune the genetic code engraved in the DNA sequence.
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Epigenetic inheritance
The transmission of information from a cell or multicellular organism to its descendants without that information being encoded in the nucleotide sequence of the gene.
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Epigenetic landscape
Conrad Waddington’s visual analogy for the way cells make decisions during development; the cell can take one of several permitted pathways leading to different cell fates (or cell types)
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).