Transgenerational epigenetics
Encyclopedia
Epigenetic inheritance is the transmittance of information from one generation to the next that affects the traits of offspring without alteration of the primary structure of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 (i.e., the sequence of nucleotides) or from environmental cues. The term “epigenetic inheritance” is used to describe both cell–cell and organism–organism information transfer, while transgenerational epigenetics typically refers only to the latter. Although these two levels of epigenetic inheritance are equivalent in unicellular organisms, they may have distinct mechanisms and evolutionary distinctions in multicellular organisms.
Four general categories of epigenetic modification are known: 1) self-sustaining metabolic loops, in which a mRNA or protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 product of a gene stimulates transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...

 of the gene (e.g. Wor1 gene in Candida albicans), 2) structural templating in which structures are replicated using a template or scaffold structure on the parent (e.g. prions, proteins that replicate by changing the structure of normal proteins to match their own), 3) chromatin
Chromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...

 marks, in which methyl or acetyl groups bind to DNA nucleotides or histones thereby altering gene expression patterns (e.g. Lcyc gene in Linaria vulgaris described below), and 4) RNA silencing, in which small RNA strands interfere (RNAi) with the transcription of DNA or translation of mRNA (known only from a few studies, mostly in Caenorhabditis elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...

).

For some epigenetically influenced traits, the epigenetic marks can be induced by the environment and some marks are heritable, leading some to view epigenetics as a relaxation of the rejection of soft inheritance
Soft inheritance
Soft inheritance is the term coined by Ernst Mayr to include such ideas as Lamarckism, that an organism can pass on characteristics that it acquired during its lifetime to its offspring. It contrasts with modern ideas of inheritance, which Mayr called hard inheritance...

 of acquired characteristics.

Major Controversies in the History of the Inheritance

Humans have recognized that traits of the parents are often seen in offspring. This insight led to the practical application of selective breeding of plants and animals, eventually leading to domestication, but did not address the central question of inheritance: how are these traits conserved between generations, and what causes variation?

Blending vs. Particulate Inheritance

Addressing these related questions, scientists during the time of the Enlightenment largely argued for the blending hypothesis, in which parental traits were homogenized in the offspring much like buckets of different colored paint being mixed together. Critics of Charles Darwin's On the Origin of Species, pointed out that under this scheme of inheritance, variation would quickly be swamped by the majority phenotype. In the paint bucket analogy, this would be seen by mixing two colors together and then mixing the resulting color with only one of the parent colors 20 times; the rare variant color would quickly fade.

Unknown to most of the European scientific community, a monk by the name of Gregor Mendel
Gregor Mendel
Gregor Johann Mendel was an Austrian scientist and Augustinian friar who gained posthumous fame as the founder of the new science of genetics. Mendel demonstrated that the inheritance of certain traits in pea plants follows particular patterns, now referred to as the laws of Mendelian inheritance...

 had resolved the question of how traits are conserved between generations through breeding experiments with pea plants. Charles Darwin
Charles Darwin
Charles Robert Darwin FRS was an English naturalist. He established that all species of life have descended over time from common ancestry, and proposed the scientific theory that this branching pattern of evolution resulted from a process that he called natural selection.He published his theory...

 thus did not know of Mendel's proposed "particulate inheritance" in which traits were not blended but passed to offspring in discrete units that we now call genes. Darwin came to reject the blending hypothesis even though his ideas and Mendel's were not unified until the 1930s, a period referred to as the Modern Synthesis.

Inheritance of Innate vs. Acquired Characteristics

In his 1809 book, Philosophie Zoologique, Jean-Baptiste Lamarck
Jean-Baptiste Lamarck
Jean-Baptiste Pierre Antoine de Monet, Chevalier de la Marck , often known simply as Lamarck, was a French naturalist...

 recognized that each species experiences a unique set of challenges due to its form and environment. Thus, he proposed that the characters used most often would accumulate a “nervous fluid.” Such acquired accumulations would then be transmitted to the individual’s offspring. In modern terms, a nervous fluid transmitted to offspring would be a form of epigenetic inheritance.

Lamarckism, as this body of thought became known, was the standard explanation for change in species over time when Charles Darwin and Alfred Russel Wallace
Alfred Russel Wallace
Alfred Russel Wallace, OM, FRS was a British naturalist, explorer, geographer, anthropologist and biologist...

 co-proposed a theory of evolution by natural selection in 1859. Responding to Darwin and Wallace's theory, a revised neo-Lamarckism attracted a small following of biologists, though the Lamarckian zeal was quenched in large part due to Weismann’s
August Weismann
Friedrich Leopold August Weismann was a German evolutionary biologist. Ernst Mayr ranked him the second most notable evolutionary theorist of the 19th century, after Charles Darwin...

 famous experiment in which he cut off the tails of mice over several successive generations without having any effect on tail length. Thus the emergent consensus that acquired characteristics could not be inherited became canon.

Origin of epigenetics and revision of the modern synthesis

Non-genetic variation and inheritance, however, proved to be quite common. Concurrent to the Modern Synthesis (unifying Mendelian genetics and natural selection), C. H. Waddington was working to unify developmental biology
Developmental biology
Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and "morphogenesis", which is the process that gives rise to tissues, organs and anatomy.- Related fields of study...

 and genetics. In so doing, he coined the word “epigenetic” to represent the ordered differentiation of embryonic cells into functionally distinct cell types despite having identical primary structure of their DNA. Waddington’s epigenetics was sporadically discussed, becoming more of a catch-all for puzzling non-genetic heritable characters rather than advancing the body of inquiry. Consequently, the definition of Waddington’s word has itself evolved, broadening beyond the subset of developmentally signaled, inherited cell specialization.

Does epigenetic inheritance compromise the foundation of the Modern Synthesis? Outlining the Central Dogma of Molecular Biology
Central dogma of molecular biology
The central dogma of molecular biology was first articulated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970:In other words, the process of producing proteins is irreversible: a protein cannot be used to create DNA....

, Francis Crick
Francis Crick
Francis Harry Compton Crick OM FRS was an English molecular biologist, biophysicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson...

  succinctly stated, “DNA is held in a configuration by histone[s] so that it can act as a passive template for the simultaneous synthesis of RNA and protein[s]. None of the detailed “information” is in the histone (italic added for emphasis). However, he closes the article stating, “this scheme explains the majority of the present experimental results!” (italic added for emphasis). Indeed the emergence of epigenetic inheritance (in addition to advances in the study of evolutionary-development, phenotypic plasticity, evolvability, and systems biology) has strained the current framework of the Modern Synthesis and prompted the re-examination of previously dismissed evolutionary mechanisms.

Origin and inheritance of epigenes

See main article: Epigenetics
Epigenetics
In biology, and specifically genetics, epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence – hence the name epi- -genetics...



Epigenetic variation may take one of four general forms. Others may yet be elucidated, but currently self-sustaining feedback loops, spatial templating, chromatin marking, and RNA-mediated pathways modify epigenes at the level of individual cells. Epigenetic variation within multicellular organisms may be endogenous, generated by cell–cell signaling (e.g. during cell differentiation early in development), or exogenous, a cellular response to environmental cues.

Removal vs. retention of epigenetic marks

In sexually reproducing organisms, much of the epigenetic modification within cells is reset during meiosis (e.g. marks at the FLC locus controlling plant vernalization ), though some epigenetic responses have been shown to be conserved (e.g. transposon methylation in plants ). Differential inheritance of epigenetic marks due to underlying maternal or paternal biases in removal or retention mechanisms may lead to the assignment of epigenetic causation to some parent of origin effects in animals and plants.

Removal of epigenetic marks

In mammals, male and female gametes join during fertilization in different cell cycle states and with different configuration of the genome. The epigenetic marks of the male are rapidly diluted. First, the protamines associated with male DNA are replaced with histones from the female's cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...

, most of which are acetylated due to either higher abundance of acetylated histones in the female's cytoplasm or through preferential binding of the male DNA to acetylated histones. Second, male DNA is systematically demethylated in many organisms, however the mechanism and functional outcome of this process has yet to be elucidated.

Recognition of the importance of epigenetic programming to the establishment and fixation of cell line identity during early embryogenesis has recently stimulated interest in artificial removal of epigenetic programming. Epigenetic manipulations may allow for restoration of totipotency in stem cells or cells more generally, thus generalizing regenerative medicine
Regenerative medicine
Regenerative medicine is the "process of replacing or regenerating human cells, tissues or organs to restore orestablish normal function". This field holds the promise of regenerating damaged tissues and organs in the body by replacing damaged tissue and/or by stimulating the body's own repair...

.

Retention of epigenetic marks

Cellular mechanisms may allow for co-transmission of some epigenetic marks. During replication, DNA polymerases working on the leading and lagging strands are coupled by the DNA processivity factor proliferating cell nuclear antigen (PCNA), which has also been implicated in patterning and strand crosstalk that allows for copy fidelity of epigenetic marks. Work on histone modification copy fidelity has remained in the model phase, but early efforts suggest that modifications of new histones are patterned on those of the old histones and that new and old histones randomly assort between the two daughter DNA strands. With respect to transfer to the next generation, many marks are removed as described above. Emerging studies are finding patterns of epigenetic conservation across generations. For instance, centromeric
Centromere
A centromere is a region of DNA typically found near the middle of a chromosome where two identical sister chromatids come closest in contact. It is involved in cell division as the point of mitotic spindle attachment...

 satellites resist demethylation. The mechanism responsible for this conservation is not known, though some evidence suggests that methylation of histones may contribute.

Decay of epigenetic marks

Whereas the mutation rate
Mutation rate
In genetics, the mutation rate is the chance of a mutation occurring in an organism or gene in each generation...

 in a given 100 base gene may be 10−7 per generation, epigenes may “mutate” several times per generation or may be fixed for many generations. This raises the question: are changes in epigene frequencies is evolution? Rapidly decaying epigenetic effects on phenotypes (i.e. lasting less than three generations) may explain some of the residual variation in phenotypes after genotype and environment are accounted for. However, distinguishing these short-term effects from the effects of the maternal environment on early ontogeny
Ontogeny
Ontogeny is the origin and the development of an organism – for example: from the fertilized egg to mature form. It covers in essence, the study of an organism's lifespan...

 remains a challenge.

Contribution to phenotypes

The relative importance of genetic and epigenetic inheritance is subject to debate. Though hundreds of examples of epigenetic modification of phenotypes have been published, few studies have been conducted outside of the laboratory setting. Therefore, the interactions of genes and epigenes with the environment cannot be inferred despite the central role of environment in natural selection. Experimental methodologies for manipulating epigenetic mechanisms are nascent (e.g.) and will need rigorous demonstration before studies explicitly testing the relative contributions of genotype, environment, and epigenotype are feasible.

A study has shown chilhood abuse (defined in this study as “sexual contact, severe physical abuse and/or severe neglect”) leads to epigenetic modifications of glucocorticoid receptor expression which play a role in HPA activity. Animal experiments have shown that epigenetic changes depend on mother-infant interactions after birth. In a recent study investigating correlations among maternal stress in pregnancy and methylation in teenagers and their mothers, it has been found that children of women who were abused during pregnancy were significantly more likely than others to have methylated glucocorticoid-receptor genes, which in turn change the response to stress, leading to a higher susceptibility to anxiety.

Effects on Fitness

Epigenetic inheritance may only affect fitness
Fitness (biology)
Fitness is a central idea in evolutionary theory. It can be defined either with respect to a genotype or to a phenotype in a given environment...

 if it predictably alters a trait under selection. Evidence has been forwarded that environmental stimuli are important agents in the alteration of epigenes. Ironically, Darwinian evolution may act on these neo-Lamarckian acquired characteristics as well as the cellular mechanisms producing them (e.g. methyltransferase genes).
Epigenetic inheritance may confer a fitness benefit to organisms that deal with environmental changes at intermediate timescales. Short-cycling changes are likely to have DNA-encoded regulatory processes, as the probability of the offspring needing to respond to changes multiple times during their lifespans is high. On the other end, natural selection will act on populations experiencing changes on longer-cycling environmental changes. In these cases, if epigenetic priming of the next generation is deleterious to fitness over most of the interval (e.g. misinformation about the environment), these genotypes and epigenotypes will be lost. For intermediate time cycles, the probability of the offspring encountering a similar environment is sufficiently high without substantial selective pressure on individuals lacking a genetic architecture capable of responding to the environment. Naturally, the absolute lengths of short, intermediate, and long environmental cycles will depend on the trait, the length of epigenetic memory, and the generation time of the organism.
Much of the interpretation of epigenetic fitness effects centers on the hypothesis that epigenes are important contributors to phenotypes, which remains to be resolved.

Deleterious effects

Inherited epigenetic marks may be important for regulating important components of fitness. In plants, for instance, the Lcyc gene in Linaria vulgaris
Linaria vulgaris
Linaria vulgaris is a species of toadflax , native to most of Europe and northern Asia, from the United Kingdom south to Spain in the west, and east to eastern Siberia and western China...

controls the symmetry of the flower. Linnaeus first described radially symmetric mutants, which arises when Lcyc is heavily methylated. Given the importance of floral shape to pollinators, methylation of Lcyc homologues (e.g. CYCLOIDEA) may have deleterious effects on plant fitness. In animals, numerous studies have shown that inherited epigenetic marks can increase susceptibility to disease. Transgenerational epigenetic influences are also suggested to contribute to disease, especially cancer, in humans. Tumor methylation patterns in gene promotors have been shown to correlate positively with familial history of cancer. Furthermore, methylation of the MSH2 gene is correlated with early-onset colorectal and endometrial cancers.

Putatively adaptive effects

Experimentally demethylated seeds of the model organism
Model organism
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...

 Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...

have significantly higher mortality, stunted growth, delayed flowering, and lower fruit set, indicating that epigenes may increase fitness. Furthermore, environmentally induced epigenetic responses to stress have been shown to be inherited and positively correlated with fitness. In animals, communal nesting changes mouse behavior increasing parental care regimes and social abilities that are hypothesized to increase offspring survival and access to resources (such as food and mates), respectively.

Macroevolutionary Patterns

Inherited epigenetic effects on phenotypes have been documented in bacteria, protists, fungi, plants, and animals. Though no systematic study of epigenetic inheritance has been conducted (most focus on model organisms), there is preliminary evidence that this mode of inheritance is more important in plants than in animals. The early differentiation of animal germlines is likely to preclude epigenetic marking occurring later in development, while in plants and fungi somatic
Somatic
The term somatic means 'of the body',, relating to the body. In medicine, somatic illness is bodily, not mental, illness. The term is often used in biology to refer to the cells of the body in contrast to the germ line cells which usually give rise to the gametes...

 cells may be incorporated into the germ line.

Life history
Life history
In sociological and anthropological research, a life history is the overall picture of the informant's or interviewee's life. The purpose of the interview is to be able to describe what it is like to be this particular person, that is, the one being interviewed.-Background:The method was first...

patterns may also contribute to the occurrence of epigenetic inheritance. Sessile organisms, those with low dispersal capability, and those with simple behavior may benefit most from conveying information to their offspring via epigenetic pathways. Geographic patterns may also emerge, where highly variable and highly conserved environments might host fewer species with important epigenetic inheritance.
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