Epigenetics

epigeneticepigeneticallyepigenetic regulationepigenetic alterationsEpigenetic modificationsepigenetic changesepigenetic landscapeepigenetic factorsepigenetic markerepigenetic mechanisms
In biology, epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence.wikipedia
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Phenotypic trait

traittraitscharacters
Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal development.
The phenotype is dependent on the genetic make-up of the organism, and also influenced by the environmental conditions to which the organism is subjected across its ontogenetic development, including various epigenetic processes.

Epigenomics

epigenomicepigenomic profilinggenome-wide DNA methylation patterns
The "epigenome" is a parallel to the word "genome", referring to the overall epigenetic state of a cell, and epigenomics refers to global analyses of epigenetic changes across the entire genome.
Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome.

C. H. Waddington

Conrad Hal WaddingtonConrad WaddingtonC.H. Waddington
From the generic meaning, and the associated adjective epigenetic, British embryologist C. H. Waddington coined the term epigenetics in 1942 as pertaining to epigenesis, in parallel to Valentin Haecker's 'phenogenetics' (Phänogenetik).
Conrad Hal Waddington CBE FRS FRSE (8 November 1905 – 26 September 1975) was a British developmental biologist, paleontologist, geneticist, embryologist and philosopher who laid the foundations for systems biology, epigenetics, and evolutionary developmental biology.

Paramutation

Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, DNA methylation reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.
In epigenetics, a paramutation is an interaction between two alleles at a single locus, whereby one allele induces a heritable change in the other allele.

Transgenerational epigenetic inheritance

epigenetic inheritancetransgenerationaltransgenerational epigenetic
Most epigenetic changes only occur within the course of one individual organism's lifetime; however, these epigenetic changes can be transmitted to the organism's offspring through a process called transgenerational epigenetic inheritance.
Transgenerational epigenetic inheritance is the transmission of epigenetic markers from one organism to the next (i.e., parent–child transmission) that affects the traits of offspring without alteration of the primary structure of DNA (i.e. the sequence of nucleotides) —in other words, epigenetically.

Cold Spring Harbor Laboratory

Cold Spring HarborCold Spring Harbor SymposiumCold Springs Harbor Laboratory
A consensus definition of the concept of epigenetic trait as a "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence" was formulated at a Cold Spring Harbor meeting in 2008, although alternate definitions that include non-heritable traits are still being used.
Plant genome sequencing; epigenetics and stem cell fate; stem cell signaling; plant-environment interactions; using genetic insights to increase yield of staple crops, e.g., maize, rice, wheat; increase fruit yield in flowering plants, e.g., tomato.

Reprogramming

Yamanaka factorsreprogrammedDNA methylation reprogramming
Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, DNA methylation reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.
In biology, reprogramming refers to erasure and remodeling of epigenetic marks, such as DNA methylation, during mammalian development or in cell culture.

Carcinogenesis

tumorigenesisoncogenesisoncogenic
Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, DNA methylation reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.
The process is characterized by changes at the cellular, genetic, and epigenetic levels and abnormal cell division.

Cell potency

pluripotentpluripotencymultipotent
During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells.
In mouse primordial germ cells, genome-wide reprogramming leading to totipotency involves erasure of epigenetic imprints.

Transvection (genetics)

transvectiontransvection in genetics
Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, DNA methylation reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.
Transvection is an epigenetic phenomenon that results from an interaction between an allele on one chromosome and the corresponding allele on the homologous chromosome.

DNA damage (naturally occurring)

DNA damageDNA damagesdamage
DNA damage is very frequent, occurring on average about 60,000 times a day per cell of the human body (see DNA damage (naturally occurring)).
These errors can give rise to mutations or epigenetic alterations.

Epigenome

epigenomesChromatin domains
The "epigenome" is a parallel to the word "genome", referring to the overall epigenetic state of a cell, and epigenomics refers to global analyses of epigenetic changes across the entire genome.
Epigenetics is a currently active topic in cancer research.

Canalisation (genetics)

canalizationcanalisationcanalised
Waddington held that cell fates were established during development in a process he called canalisation much as a marble rolls down to the point of lowest local elevation.
Waddington introduced the concept of the epigenetic landscape, in which the state of an organism rolls "downhill" during development.

Gene expression

expressionexpressedexpress
Epigenetics most often involves changes that affect gene activity and expression, but the term can also be used to describe any heritable phenotypic change.
These effects are referred to as epigenetic and involve the higher order structure of DNA, non-sequence specific DNA binding proteins and chemical modification of DNA.

Developmental psychology

developmental psychologistchild psychologychild psychologist
In a sense somewhat unrelated to its use in biological disciplines, the term "epigenetic" has also been used in developmental psychology to describe psychological development as the result of an ongoing, bi-directional interchange between heredity and the environment.
It involves the study of both the genetic and environmental mechanisms that underlie the development of social and cognitive competencies, as well as the epigenetic (gene-environment interactions) processes that adapt these competencies to local conditions.

Chromatin

chromatin structuresex chromatinnuclear chromatin
The microstructure (not code) of DNA itself or the associated chromatin proteins may be modified, causing activation or silencing.
Epigenetic modification of the structural proteins in chromatin via methylation and acetylation also alters local chromatin structure and therefore gene expression.

Computational epigenetics

computational epigenomics
Furthermore, the use of bioinformatics methods has a role in (computational epigenetics).
uses bioinformatic methods to complement experimental research in epigenetics.

Bisulfite sequencing

Methylation-specific PCRbisulfite conversionbisulfite
Epigenetic research uses a wide range of molecular biological techniques to further understanding of epigenetic phenomena, including chromatin immunoprecipitation (together with its large-scale variants ChIP-on-chip and ChIP-Seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes, DNA adenine methyltransferase identification (DamID) and bisulfite sequencing.
DNA methylation was the first discovered epigenetic mark, and remains the most studied.

Gene

genesnumber of genesgene sequence
The Greek prefix epi- ( "over, outside of, around") in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic basis for inheritance.
RNA-mediated epigenetic inheritance has also been observed in plants and very rarely in animals.

Stem cell

stem cellsstem cell researchstem-cell research
During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells.
They share many similar properties, such as pluripotency and differentiation potential, the expression of pluripotency genes, epigenetic patterns, embryoid body and teratoma formation, and viable chimera formation, but there are many differences within these properties.

Structural inheritance

structural
Furthermore, in addition to the maintenance and transmission of methylated DNA states, the same principle could work in the maintenance and transmission of histone modifications and even cytoplasmic (structural) heritable states.
Structural inheritance or cortical inheritance is the transmission of an epigenetic trait in a living organism by a self-perpetuating spatial structures.

ChIP-sequencing

ChIP-seq(ChIP-Seq)
Epigenetic research uses a wide range of molecular biological techniques to further understanding of epigenetic phenomena, including chromatin immunoprecipitation (together with its large-scale variants ChIP-on-chip and ChIP-Seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes, DNA adenine methyltransferase identification (DamID) and bisulfite sequencing.
This epigenetic information is complementary to genotype and expression analysis.

Proliferating cell nuclear antigen

PCNA
DNMT1 is the most abundant methyltransferase in somatic cells, localizes to replication foci, has a 10–40-fold preference for hemimethylated DNA and interacts with the proliferating cell nuclear antigen (PCNA).
PCNA is a homotrimer and achieves its processivity by encircling the DNA, where it acts as a scaffold to recruit proteins involved in DNA replication, DNA repair, chromatin remodeling and epigenetics.

Methylation

methylatedhypermethylationmethylate
These modifications include acetylation, methylation, ubiquitylation, phosphorylation, sumoylation, ribosylation and citrullination.
It has been recognized as a key process underlying epigenetics.

Epigenetic code

The phrase "genetic code" has also been adapted – the "epigenetic code" has been used to describe the set of epigenetic features that create different phenotypes in different cells from the same underlying DNA sequence.
The epigenetic code is hypothesised to be a defining code in every eukaryotic cell consisting of the specific epigenetic modification in each cell.