A problem with root grafts is that they allow transmission of certain  pathogens , such as  Dutch elm disease . Inosculation also sometimes occurs where two stems on the same tree, shrub or vine make contact with each other. This is common in plants such as  strawberries  and  potato .


Natural grafting is rarely seen in herbaceous plants as those types of plants generally have short-lived roots with little to no  secondary growth  in the vascular cambium. [ 15 ]


Occasionally, a so-called " graft hybrid " or more accurately graft chimera can occur where the tissues of the stock continue to grow within the scion. Such a plant can produce flowers and  foliage  typical of both plants as well as shoots intermediate between the two. The best-known example this is probably  + Laburnocytisus  'Adamii' , a graft hybrid between  Laburnum  and  Cytisus , which originated in a  nursery  near  Paris, France , in 1825. This small tree bears yellow flowers typical of  Laburnum anagyroides , purple flowers typical of  Cytisus purpureus  and curious coppery-pink flowers that show characteristics of both "parents". Many species of cactus can also produce graft chimeras under the right conditions although they are often created unintentionally and such results are often hard to replicate.


Grafting has been important in  flowering  research.  Leaves  or shoots from plants induced to flower can be grafted onto uninduced plants and transmit a floral stimulus that induces them to flower. [ 16 ]


The transmission of  plant viruses  has been studied using grafting. Virus indexing involves grafting a symptomless plant that is suspected of carrying a virus onto an indicator plant that is very susceptible to the virus.


Grafting can transfer  chloroplasts  (plant  organelles  that can conduct  photosynthesis ),  mitochondrial DNA  and the entire  cell nucleus  containing the  genome  to potentially make a new species making grafting a form of natural  genetic engineering . [ 17 ]


White spruce  can be grafted with consistent success by using 8–10 cm (3–4 in) scions of current growth on thrifty 4- to 5-year-old  rootstock  (Nienstaedt and Teich 1972). [ 18 ]  Before greenhouse grafting, rootstocks should be potted in late spring, allowed to make seasonal growth, then subjected to a period of chilling outdoors, or for about 8 weeks in a cool room at 2 °C (Nienstaedt 1966). [ 19 ]


A method of grafting white spruce of seed-bearing age during the time of seed harvest in the fall was developed by Nienstaedt et al. (1958). [ 20 ]  Scions of white spruce of 2 ages of wood from 30- to 60-year-old trees were collected in the fall and grafted by 3 methods on potted stock to which different day-length treatments had been applied prior to grafting. The grafted stock were given long-day and natural-day treatments. Survival was 70% to 100% and showed effects of rootstock and post-grafting treatments in only a few cases.  Photoperiod  and temperature treatments after grafting, however, had considerable effect on scion activity and total growth. The best post-grafting treatment was 4 weeks of long-day treatment followed by 2 weeks of short-day treatment, then 8 weeks of chilling, and finally long-day treatment.


Since grafts of white spruce put on relatively little growth in the 2 years after grafting, techniques for accelerating the early growth were studied by Greenwood (1988) [ 21 ]  and others. The cultural regimes used to promote one additional growth cycle in one year involve manipulation of day length and the use of cold storage to satisfy chilling requirements. Greenwood took dormant potted grafts into the greenhouse in early January then gradually raised the temperature during the course of a week until the minimum temperature rose to 15 °C. Photoperiod was increased to 18 hours using  incandescent  lighting. In this technique, grafts are grown until elongation has been completed, normally by mid-March. Soluble 10-52-10 fertilizer is applied at both ends of the growth cycle and 20-20-20 during the cycle, with irrigation as needed. When growth elongation is complete, day length is reduced to 8 hours using a blackout curtain. Budset follows, and the grafts are held in the greenhouse until mid-May. Grafts are then moved into a cooler at 4 °C for 1000 hours, after which they are moved to a shade frame where they grow normally, with applications of fertilizer and  irrigation  as in the first cycle. Grafts are moved into cold frames or unheated greenhouse in September until January. Flower induction treatments are begun on grafts that have reached a minimum length of 1.0 m. Repotting from an initial pot size of 4.5 litre to 16 litre containers with a 2:1:1 soil mix of peat moss, loam, and aggregate.


In one of the first accelerated growth experiments, white spruce grafts made in January and February that would normally elongate shortly after grafting, set bud, and remain in that condition until the following spring, were refrigerated for 500, 1000, or 1500 hours beginning in mid-July, and a non-refrigerated control was held in the nursery. [ 21 ]  After completion of the cold treatment, the grafts were moved into the greenhouse with an 18-hour photoperiod until late October. Height increment was significantly (P 0.01) influenced by cold treatment. Best results were given by the 1000-hour treatment. [ 21 ]


The refrigeration (cold treatment) phase was subsequently shown to be effective when applied 2 months earlier with proper handling and use of blackout curtains, which allows the second growth cycle to be completed in time to satisfy dormancy requirements before January (Greenwood et al. 1988). [ 21 ]


Grafting is often done for non- woody  and  vegetable  plants ( tomato ,  cucumber ,  eggplant  and  watermelon ). [ 22 ]   Tomato grafting  is very popular in Asia and Europe, and is gaining popularity in the United States. The main advantage of grafting is for disease-resistant rootstocks. Researchers in  Japan  developed automated processes using grafting  robots  as early as 1987. [ 23 ] [ 24 ] [ 25 ]  Plastic tubing can be used to prevent desiccation and support the healing at the graft/scion interface. [ 26 ]


As humans began to domesticate plants and animals, horticultural techniques that could reliably propagate the desired qualities of long-lived woody plants needed to be developed. Although grafting is not specifically mentioned in the  Hebrew Bible , it is claimed that ancient Biblical text hints at the practice of grafting. For example,  Leviticus  19:19 states "[the Hebrew people] shalt not sow their field with mingled seed..." ( King James Bible ). Some scholars believe the phrase mingled seeds includes grafting, [ citation needed ]  although this interpretation remains contentious among scholars.


Grafting is also mentioned in the  New Testament . In  Romans 11 , starting at verse 17,  there is a discussion about the grafting of wild  olive  trees concerning the relationship between Jews and  Gentiles . [ 27 ] [ 28 ]


By 500 BCE grafting was well established and practiced in the region as the  Mishna  describes grafting as a commonplace technique used to grow grapevines. [ 29 ]


According to recent research: "grafting technology had been practiced in China before 2000 BC". [ 30 ]  Additional evidence for grafting in China is found in  Jia Sixie's 6th century CE agricultural treatise  Qimin Yaoshu  (Essential Skills for the Common People) . [ 31 ]  It discusses grafting pear twigs onto crab apple, jujube and pomegranate stock (domesticated apples had not yet arrived in China), as well as grafting persimmons. The  Qimin yaoshu  refers to older texts that referred to grafting, but those works are missing. Nonetheless, given the sophistication of the methods discussed, and the long history of arboriculture in the region, grafting must have already been practiced for centuries by this time.


In Greece, a medical record written in 424 BCE contains the first direct reference to grafting. The title of the work is  On the Nature of the Child  and is thought to be written by a follower of  Hippocrates . The language of the author suggests that grafting appeared centuries before this period.


In Rome, Marcus Porcius Cato wrote the oldest surviving Latin text in 160 BCE. The book is called  De Agri Cultura (On Farming Agriculture)  and outlines several grafting methods. Other authors in the region would write about grafting in the following years, however, the publications often featured fallacious scion-stock combinations.


Creating lavishly flourished gardens would be a common form of competition among medieval Islamic leaders at the time. Because the region would receive an influx of foreign ornamentals to decorate these gardens, grafting was used much during this period. [ 29 ]


After the fall of the  Roman Empire , grafting kept being practiced in Christian monasteries and regained popular appeal among lay people during the  Renaissance . The invention of the  printing press  inspired a number of authors to publish books on gardening that included information on grafting. One example,  A New Orchard and Garden: Or, the Best Way for Planting, Graffing, and to Make Any Ground Good for a Rich Orchard, Particularly in the North , was written by William Lawson in 1618. While the book contains practical grafting techniques, some even still used today, it suffers from exaggerated claims of scion-stock compatibility typical of this period.


While grafting continued to grow in Europe during the eighteenth century, it was considered unnecessary in the United States as the produce from fruit trees was largely used either to make cider or feed hogs. [ 29 ]


Beginning in 1864, and without warning, grapevines across France began to sharply decline. Thanks to the efforts of scientists such as  C. V. Riley  and  J. E. Planchon , the culprit was identified to be  phylloxera , an insect that infests the roots of vines and causes fungal infections. Initially, farmers unsuccessfully attempted to contain the pest by removing and burning affected vines. When it was discovered that phylloxera was an invasive species introduced from North America, some suggested importing rootstock from the region as the North American vines were resistant to the pest. Others, opposed to the idea, argued that American rootstocks would imbue the French grapes with an undesirable taste; they instead preferred to inject the soil with expensive pesticides. Ultimately, grafting French vines onto American rootstocks became prevalent throughout the region, creating new grafting techniques and machines. American rootstocks had trouble adapting to the high soil pH value of some regions in France so the final solution to the pandemic was to  hybridize  the American and French variants. [ 29 ]


A  half-sider budgerigar  is an unusual congenital condition that causes a  budgerigar  to display one color on one side of its body and a different color on the other.


This is not a simple genetic mutation, as can be observed in other  color and pattern variations in this species . It is a rare example of a  tetragametic chimera , which originates when two fertilized embryos merge during a very early stage of development — between the 2-cell and the 64-cell stage. Each half has different DNA, with genetically distinct cells and the resultant bird is in effect two budgerigars fused together to form a single autonomous individual. [ 1 ]


The half-sider's coloring is usually divided bilaterally down the center, although, it can differ depending on which stage the twin embryos merged during development. Twin embryos that merged later in development will result in a budgerigar that has a splotchier distribution of the different cell populations.  [ 1 ]


In the case of the half-sider budgerigar, both embryos must possess different genetic phenotypes (one yellow-based and one white-based) [ 2 ]  in order for a visible half-sider to be produced. If both "halves" were the same base, it would still be a tetragametic chimera, but not a half-sider. It is also possible for the half-sider to be male on one side and female on the other (evidenced by a half blue, half brown  cere ) – an example of a  bilateral gynandromorph . [ 1 ]


Breeding a half-sider is unlikely to produce more half-siders, even when breeding two half-siders together, as the genetic makeup of the half that contributed the cells that make up the reproductive system is that which would then be perpetuated, assuming that the bird is even fertile in the first place. The chance of producing another half-sider would be the same as for any other budgerigar pairing. [ 3 ]


Heterogonesis  describes the segregation of parental genomes into distinct cell lineages in the dividing  zygote . [ 1 ] [ 2 ]


Fertilisation  occurs when an  ovum  fuses with a  sperm , forming a  zygote . Normally, the  genomes  of the two parents assort into two  diploid  bi-parental daughter cells. In a heterogoneic cell division, the genome of only one parent assorts into a single daughter cell following the formation of a tripolar (rather than the normal bipolar)  spindle apparatus . [ 3 ]  Heterogonesis allows for chromosomal segregation to occur in a dispermic fertilisation which may subsequently result in  chimerism  or  sesquizygosis .


The term  heterogonesis  was coined in 2016 by Destouni and Vermeesch who observed the phenomenon in  bovine  zygotes. [ 1 ]  The word is derived from the Greek meaning "different parental origin".


Microchimerism  is the presence of a small number of cells in an individual that have originated from another individual and are therefore genetically distinct. This phenomenon may be related to certain types of  autoimmune diseases  although the responsible mechanisms are unclear. The term comes from the prefix "micro" + "chimerism" based on the  hybrid   Chimera  of Greek mythology. The concept was first discovered in the 1960s with the term gaining usage in the 1970s. [ 1 ]


In humans (and perhaps in all  placental mammals ), the most common form is  fetomaternal microchimerism  (also known as  fetal cell microchimerism  or  fetal chimerism ) whereby cells from a  fetus  pass through the  placenta  and establish cell lineages within the mother. Fetal cells have been documented to persist and multiply in the mother for several decades. [ 2 ] [ 3 ]  The exact  phenotype  of these cells is unknown, although several different cell types have been identified, such as various immune lineages,  mesenchymal stem cells , and placental-derived cells. [ 4 ]  A 2012 study at the  Fred Hutchinson Cancer Research Center , Seattle, has detected cells with the  Y chromosome  in multiple areas of the brains of deceased women. [ 5 ]


Fetomaternal microchimerism occurs during pregnancy and shortly after giving birth for most women. However, not all women who have had children contain fetal cells. Studies suggest that fetomaternal microchimerism could be influenced by  killer-cell immunoglobulin-like  (KIR)  ligands . [ 6 ]   Lymphocytes  also influence the development of persisting fetomaternal microchimerism since  natural killer cells  compose about 70% of lymphocytes in the first trimester of pregnancy. KIR patterns on maternal natural killer cells of the mother and KIR ligands on the fetal cells could have an effect on fetomaternal microchimerism. In one study, mothers with  KIR2DS1  exhibited higher levels of fetomaternal microchimerism compared to mothers who were negative for this activating KIR. [ 6 ]


The potential health consequences of these cells are unknown. One hypothesis is that these fetal cells might trigger a  graft-versus-host reaction  leading to  autoimmune disease . This offers a potential explanation for why many autoimmune diseases are more prevalent in middle-aged women. [ 7 ]  Another hypothesis is that fetal cells home to injured or diseased maternal tissue where they act as  stem cells  and participate in repair. [ 8 ] [ 9 ]   It is also possible that the fetal cells are merely innocent bystanders and have no effect on maternal health. [ 10 ]


After giving birth, about 50–75% of women carry fetal immune cell lines. Maternal immune cells are also found in the offspring yielding in  maternal→fetal microchimerism , though this phenomenon is about half as frequent as the former. [ 11 ]


Microchimerism had also been shown to exist after  blood transfusions  to a severely  immunocompromised  population of patients who suffered  trauma . [ 12 ]


Other possible sources of microchimerism include  gestation , [ 13 ]  an individual's older sibling, twin sibling, or vanished twin, with the cells being received in utero. Fetal-maternal microchimerism is especially prevalent after abortion or miscarriage. [ 14 ]


Microchimerism occurs in most pairs of twins in  cattle . In cattle (and other  bovines ), the  placentas  of fraternal twins usually fuse and the twins share blood circulation, resulting in exchange of cell lines.  If the twins are a male–female pair, then XX/XY microchimerism results, and male hormones partially masculinize the heifer (female), creating a  martin heifer  or  freemartin .  Freemartins appear female, but are infertile and so cannot be used for breeding or  dairy production .  Microchimerism provides a method of diagnosing the condition, because male genetic material can be detected in a blood sample. [ 15 ]


Several studies have identified male DNA in the brains of both humans and mice who have previously been pregnant with a male fetus. [ 16 ] [ 17 ]  It has been suggested that the fetal-derived cells can differentiate into those capable of presenting neurotypical immunomarkers on their surface. [ 16 ]  There has been no strong evidence to say microchimerism of the maternal brain leads to disease; however, Parkinson's disease correlates with a higher incidence of brain microchimeras. [ 16 ]  Alzheimer's disease studies support nearly the opposite correlation: the more fetal-derived cells present, the lower the chance of the patient having had Alzheimer's. [ 17 ]


There are many mechanisms at the maternal-fetal interface to prevent immune rejection of fetal cells. Nevertheless, systemic immunological changes occur in pregnant women. For example, condition of women suffering from autoimmune disorders (e.g. rheumatoid arthritis, multiple sclerosis) improves during pregnancy. [ 18 ] [ 19 ]  These changes in immune responses during pregnancy extend to maternal components specific to fetal antigens, because of feto-maternal cell transfer and their retention in mother tissues.
During pregnancy, numbers of fetal cells in maternal tissues increase and correlate with expansion of CD4+  regulatory T cells  (Tregs). [ 20 ]  Decreased expansion and decidual accumulation of Treg cause pregnancy complications (preeclampsia, abortions). [ 20 ]
In mice models, most mother's fetal-specific CD8+ T cells undergo clonal deletion [ 21 ]
and express low levels of chemokine receptors and ligands – this prevents remaining fetal-specific CD8+ T cells from entering the maternal-fetal interface. [ 22 ] [ 23 ]  Mother's fetal-specific CD4+ T cells proliferate, and due to FOXP3 expression, differentiate into Treg cells. [ 24 ]  Mice models show that fetal-specific Treg cells are necessary for successful pregnancy. [ 25 ]


Fetal T cells accumulate during in utero development. Even though the fetus is exposed to noninherited maternal antigens (NIMAs), fetal CD4 +  T cells are capable of alloantigen-induced proliferation, preferentially differentiating to Treg cells and preventing a fetal immune response to maternal antigens. [ 26 ]  This expanded immune tolerance persists in both mother and offspring after birth and allows microchimeric cells to be retained in tissues.


NIMA-specific tolerance causes some interesting immunological phenotypes: sensitization to erythrocyte Rhesus factor (Rh) antigens is reduced among Rh- women born to Rh+ women, [ 27 ]  long-term kidney allograft survival is improved in NIMA-matched donor-recipient sibling pairs, [ 28 ]  or acuteness of bone marrow transplantation graft-versus-host disease is reduced, when recipients of donor stem cells are NIMA-matched. [ 29 ]
Cross-fostering animal studies show that when postnatal NIMA exposure though breastfeeding is eliminated, survival of NIMA-matched allografts is reduced. This suggests that to maintain NIMA-specific tolerance in offspring, breastfeeding is essential, but ingestion of mother's cells alone does not prime NIMA-specific tolerance. Both prenatal and postnatal exposure to mother's cells is required to maintain NIMA-specific tolerance. [ 30 ]


The severity of preexisting autoimmune disorders is reduced during pregnancy and it is most apparent when fetal microchimeric cells levels are highest - during the last trimester. [ 31 ] [ 19 ]  These cells can also replace injured maternal cells and recover tissue function (type I diabetes mouse model showed replacement of defective maternal islet cells by fetal-derived pancreatic cells [ 32 ] ). Fetal microchimeric cells can differentiate into cell types that infiltrate and replace injured cells in models of Parkinson's disease or myocardial infarction. They also help in wound healing by neoangiogenesis. Seeding of fetal microchimeric cells into maternal tissues has been proposed to promote care of offspring after birth (seeding of maternal breast tissue may promote lactation, and seeding of brain may enhance maternal attention). [ 30 ]


Microchimerism has been implicated in autoimmune diseases. Independent studies repeatedly suggested that microchimeric cells of fetal origin may be involved in the  pathogenesis  of  systemic sclerosis . [ 3 ] [ 33 ]  Moreover, microchimeric cells of maternal origin may be involved in the pathogenesis of a group of autoimmune diseases found in children, i.e. juvenile idiopathic inflammatory myopathies (one example would be  juvenile dermatomyositis ). [ 34 ]  Microchimerism has now been further implicated in other autoimmune diseases, including  systemic lupus erythematosus . [ 35 ]  Contrarily, an alternative hypothesis on the role of microchimeric cells in lesions is that they may be facilitating tissue repair of the damaged organ. [ 36 ]


Moreover, fetal immune cells have also been frequently found in breast cancer stroma as compared to samples taken from healthy women. It is not clear, however, whether fetal cell lines promote the development of tumors or, contrarily, protect women from developing breast carcinoma. [ 37 ] [ 38 ]


The presence of fetal cells in mothers can be associated with benefits when it comes to certain autoimmune diseases. In particular, male fetal cells are related to helping mothers with  systemic lupus erythematosus . When kidney biopsies were taken from patients with lupus nephritis, DNA was extracted and run with  PCR . The male fetal DNA was quantified and the presence of specific Y chromosome sequences were found. Women with lupus nephritis containing male fetal cells in their kidney biopsies exhibited better  renal system  functioning. Levels of  serum creatinine , which is related to kidney failure, were low in mothers with high levels of male fetal cells. [ 39 ]  In contrast, women without male fetal cells who had lupus nephritis showed a more serious form of  glomerulonephritis  and higher levels of serum creatinine. [ 39 ]


The specific role that fetal cells play in microchimerism related to certain autoimmune diseases is not fully understood. However, one hypothesis states that these cells supply  antigens , causing inflammation and triggering the release of different foreign antigens. [ 39 ]  This would trigger autoimmune disease instead of serving as a therapeutic. A different hypothesis states that fetal microchimeric cells are involved in repairing tissues. When tissues get inflamed, fetal microchimeric cells go to the damaged site and aid in repair and regeneration of the tissue. [ 39 ]


Fetal maternal microchimerism may be related to autoimmune thyroid diseases. There have been reports of fetal cells in the lining of the blood and thyroid glands of patients with autoimmune thyroid disease. These cells could become activated after delivery of the baby after immune suppression in the mother is lost, suggesting a role of fetal cells in the pathogenesis of such diseases. [ 40 ]  Two types of thyroid disease,  Hashimoto's thyroiditis  (HT) and  Graves' disease  (GD), show similarities to  graft vs host disease  which occurs after  hematopoietic stem cell  transplants. Fetal cells colonize maternal tissues like the thyroid gland and are able to survive many years postpartum. These fetal microchimeric cells in the thyroid show up in the blood of women affected by thyroid diseases. [ 40 ]


Sjögren syndrome  (SS) is an autoimmune rheumatic disease of the exocrine glands. Increased incidence of SS after childbirth suggests a relationship between SS and pregnancy, and this led to the hypothesis that fetal microchimerism may be involved in SS pathogenesis. Studies showed the presence of Y-chromosome-positive fetal cells in minor salivary glands in 11 of 20 women with SS but in only one of eight normal controls. Fetal cells in salivary glands suggest that they may be involved in the development of SS. [ 41 ]


Lichen planus (LP) is a T-cell-mediated autoimmune chronic disease of unknown etiology. Females have a three times higher prevalence than men. LP is characterized by T lymphocytes infiltration of the lower levels of epithelium, where they damage basal cells and cause apoptosis. The fetal microchimerism may trigger a fetus versus host reaction and therefore may play a role in the pathogenesis of autoimmune diseases including LP. [ 42 ]


Pregnancy has a positive effect on the prognosis of  breast cancer  according to several studies  [ 43 ] [ 44 ] [ 45 ]  and it apparently increases the chance of survival after diagnosis of breast cancer. [ 46 ]  Possible positive effects of pregnancy could be explained by the persistence of fetal cells in the blood and maternal tissues. [ 2 ]


Fetal cells are probably actively migrating from  peripheral blood  into the tumor tissue  [ 47 ]  where they are preferentially settled in the tumor stroma [ 38 ]  and one their concentration decreases as they get closer to the healthy breast tissue. [ 48 ]  There are two suggested mechanisms by which the fetal cells could have the positive effect on the breast cancer prognosis. The first mechanism suggests that fetal cells only oversee cancer cells and they attract components of the immune system if needed. The second option is that the down-regulation of the immune system induced by the presence of fetal cells could ultimately lead to cancer prevention, because women in whom FMC is present produce lower concentrations of inflammatory mediators, which may lead to the development of neoplastic tissue. [ 49 ]


The effect also depends on the level of microchimerism: Hyperchimerism (a high rate of microchimerism) and hypochimerism (a low rate of microchimerism) can be related to the negative effect of FMC and thus can promote a worse prognosis of breast cancer. [ 50 ] [ 51 ]  Apparently, women with breast cancer may fail in the process of obtaining and maintaining allogeneic fetal cells. Low concentration and / or complete absence of fetal cells could indicate a predisposition to development of the malignant process.


Study of S. Hallum shows association between male origin fetal cells and ovarian cancer risk. Presence of Y chromosome was used to detect foreign cells in women's blood. Microchimerism is a result of pregnancy, possibility that foreign cells were of transfusion or transplantation origin was rejected due to women's health. Women testing positive for male origin microchimerism cells had reduced hazard rates of ovarian cancer than women testing negative. [ 52 ]
Pregnancy at older ages can reduce risk of ovarian cancer. Numbers of microchimeric cells declines after pregnancy, and ovarian cancer is most frequent in postmenopausal women. This suggests that fetal microchimerism may play a protective role in ovarian cancer as well.
Microchimeric cells also cluster several times more in lung tumors than in surrounding healthy lung tissue. Fetal cells from the bone marrow go to the tumor sites where they may have tissue repair functions. [ 53 ]
Microchimerism of fetomaternal cell trafficking origin might be associated with the pathogenesis or progression of cervical cancer. Male cells were observed in patients with cervical cancer but not in positive controls. Microchimeric cells might induce the alteration of the woman's immune system and make the cervical tissue more susceptible to HPV infection or provide a suitable environment for tumor growth. [ 54 ]


Microchimeric fetal cells expressed collagen I, III and TGF-β3, and they were identified in healed maternal cesarean section scars. This suggests that these cells migrate to the site of damage due to  maternal skin injury signals, and help repair tissue. [ 55 ]


Fetomaternal microchimerism has been shown in experimental investigations of whether fetal cells can cross the blood brain barrier in mice. The properties of these cells allow them to cross the blood brain barrier and target injured brain tissue. [ 56 ]  This mechanism is possible because  umbilical cord  blood cells express some proteins similar to  neurons . When these umbilical cord blood cells are injected in rats with brain injury or stroke, they enter the brain and express certain nerve cell markers. Due to this process, fetal cells could enter the brain during pregnancy and become differentiated into neural cells. Fetal microchimerism can occur in the maternal  mouse brain , responding to certain cues in the maternal body. [ 56 ]


Fetal microchimerism could have an implication on maternal health. Isolating cells in cultures can alter the properties of the stem cells, but in pregnancy the effects of fetal stem cells can be investigated without in vitro cultures. Once characterized and isolated, fetal cells that are able to cross the blood brain barrier could impact certain procedures. [ 56 ]  For example, isolating stem cells can be accomplished through taking them from sources like the umbilical cord. These fetal stem cells can be used in intravenous infusion to repair the brain tissue. Hormonal changes in pregnancy alter neurogenesis, which could create favorable environments for fetal cells to respond to injury. [ 56 ]


The true function on fetal cells in mothers is not fully known, however, there have been reports of positive and negative health effects. The sharing of genes between the fetus and mother may lead to benefits. Due to not all genes being shared, health complications may arise as a result of resource allocation. [ 57 ]  During pregnancy, fetal cells are able to manipulate the maternal system to draw resources from the placenta, while the maternal system tries to limit it. [ 57 ]


Nurse grafting  is a method of  plant propagation  that is used for hard-to-root plant material. If a desirable selection cannot be grown from  seed  (because a seed-grown plant will be genetically different from the parent), it must be propagated asexually ( cloned ) in order to be genetically identical to the parent. Nurse grafting allows a scion to develop its own roots instead of being grafted to a  rootstock .


A large-seeded woody species, e.g. the  chestnut , retains the  cotyledons  inside the seed coat below ground while the  radicle  grows downward and the shoot appears aboveground. To make a nurse seed graft, a germinating seed is needed. A knife is used to cut an opening between the  petioles  of the cotyledons. The scion, taken from dormant wood of the previous season's growth, is cut to a wedge shape at the end and inserted into the cut between the cotyledons, so that the  cambium  surfaces of each can join. The grafted plant is then set in a rooting medium with the union about 1.5 inch below the surface. [ 1 ]


This graft allows the scion to live on the seed's roots long enough to form adventitious roots of its own. This technique is used for  camellias ,  avocados , and chestnuts. [ 1 ]


In this technique, a scion is grafted to a piece of root to keep it alive long enough for it to form its own roots. The graft union is planted below the surface of the growing medium, as with the nurse seed method. Once the scion has formed roots of its own, the rootstock can be removed, or it will die off, as will happen in situations when the scion and rootstock are not closely related. [ 2 ]


This method works well with  apple cultivars ,  cherries ,  plums ,  nectarines , and  pears . It is also useful for propagating rare isolated plants that may be unique and should not be moved from the wild. Such a plant can be propagated by taking a small amount of material that will not harm the parent plant by its removal. [ 3 ]


Nurse root grafting is the best method for propagating tree  peonies . [ 4 ]  Unlike herbaceous peonies with fleshy roots, which are propagated by division, tree peonies have woody stems and extensive root systems that are impractical for division. Their woody stems have few stored reserves and stem cuttings fail before roots are produced. The problem of keeping the scion alive long enough to produce roots (generally a year) is solved by grafting a tree peony shoot on an herbaceous peony root section; the section of root sustains the scion with its ample stored energy. (In contrast, Itoh peony hybrids, which are crosses between herbaceous and tree peonies, are best propagated by stem cuttings, which root easily.)


The basic process for nurse-root grafting of peonies is as follows:


Random  chimeragenesis  on transient templates (RACHITT) is a method to perform molecular  mutagenesis  at a high recombination rate. [ 1 ]  For example, RACHITT can be used to generate increased rate and extent of biodesulfurization of diesel by modification of dibenzothiophene mono-oxygenase.  DNA shuffling  is a similar but less powerful method used in  directed evolution  experiments.


This  biochemistry  article is a  stub . You can help Wikipedia by  expanding it .


This  molecular biology  article is a  stub . You can help Wikipedia by  expanding it .


Tomato grafting  is a horticulture technique that has been utilized in Asia and Europe for  greenhouse  and  high tunnel  production and is gaining popularity in the United States. [ 1 ]  Typically, stock or  rootstock  are selected for their ability to resist infection by certain soilborne pathogens or their ability to increase vigor and fruit yield. The  scion  of the grafted  tomato  represents the upper portion of the plant and is selected for its fruit quality characteristics. There are several methods for grafting tomatoes and they have certain advantages and disadvantages. Once the grafts are made, the plants are moved into a chamber or environment with high  relative humidity  (>90%) and low light levels to reduce water stress in the scion while the graft union forms.


Grafting  of  woody plants  has been common for centuries, but herbaceous grafting has only become popular recently [ when? ]  in agricultural systems. The cultivation of grafted  vegetable  plants began in  Korea  and  Japan  at the end of the 1920s when  watermelon  plants were grafted onto  squash  rootstock [1] .  Since this time, this technique has spread throughout Asia and Europe.  Currently, 81% of Korean and 54% of Japanese vegetable cultivation uses grafting. [ 2 ]   The use of this cultural technique is mainly carried out for intensive cropping systems like greenhouse and tunnel production.  This method is especially popular for vegetable production in the orient, and the number of vegetables in 1998 was estimated to be 540 million transplants in Korea and 750 million in Japan. [ 3 ]   This technique has moved to the  Mediterranean  region as well, where the use of grafting has been proposed as a major component of an integrated management strategy for managing soilborne disease and increasing crop productivity.  Grafted tomato transplant production has increased in  Spain  from less than one million plants in 1999–2000 to over 45 million plants in 2003–2004.  Grafted tomato is also cultivated in  France  and  Italy , and over 20 million tomato plants were grafted in  Morocco  in 2004 as a way to reduce soilborne disease and increase crop production. [ 4 ]


Grafting can take place on a number of crops.  However, because of the added expense, it is typically associated with melons,  cucurbits , and members of the family  Solanaceae  such as  eggplant  and tomato. Tomato grafting became popular in the 1960s as a way to reduce certain diseases caused by soilborne plant pathogens such as  Raletonia solanacearum   [1] . Currently, however, grafting is used to offer not only protection from certain diseases, but also tolerance to abiotic stress like flooding, drought, and salinity  [2] .


The first grafts in the early 20th century were made in order to diminish attacks by infectious organisms, such as  Fusarium oxysporum  on watermelons.  [2]   However, research has shown that this technique can be effective against a variety of  fungal ,  bacterial ,  viral , and  nematode  diseases. [ 5 ]   Furthermore, many researchers are looking to utilize specific rootstocks as an alternative to  methyl bromide -a soil fumigant that has been widely used until recently. [ when? ] [4]  Grafting has been highly effective at overcoming abiotic sources of stress, such as  soil salinity , temperature extremes, and excessive soil moisture. [2]   Grafting has also been utilized to reduce the effects of flooding in areas where a wet season may occur. [ 6 ]


Grafting tomatoes with tolerant rootstocks has been highly effective at producing a saline-tolerant plants. Research indicates that several rootstocks prevent the translocation of  sodium  and  chloride  into the shoot. [ 7 ]   Many of the most economically important vegetable crops like tomato, squash, cucumber, and watermelon are highly sensitive to  thermal stress  in the roots throughout vegetative development and reproduction.  Whether using rootstock tolerant of hot or cold temperatures, the use of temperature tolerant rootstocks often leads to the extension of the growing season in either direction, resulting in better yield and economic stability through the year. [2]   Although the vegetable grafting is typically associated with reduction of disease or abiotic stress, yield is often increased without the presence of these identified sources of stress.


In tomatoes, increases in fruit yield are typically the results of increased fruit size. [ 8 ]   Research has shown that possible mechanisms for increased yield are likely due to increased water and nutrient uptake among vigorous rootstock genotypes. Conductance through the  stoma  was improved in tomato plants when grafted onto vigorous rootstock. [7]   Nutrient uptake for the  macronutrients , such as  phosphorus  and  nitrogen , were enhanced by grafting. [ 9 ] [ 10 ]


There are a variety of methods for grafting vegetable crops.  Cleft grafting occurs when a V-shape is cut into the rootstock and a complementing wedge-shaped scion is inserted.  The graft is then held with a small clip until healing occurs. [ 11 ]   Approach grafting involves notching opposing sides of the stems of the rootstock and scion, and then using a clip to hold the stems together while they fuse.  Once the graft has healed, the original scion is then cut off of the desired rootstock and the unused rootstock is detached from the scion. [ 12 ]   Micrografting is a new technique that has been recently [ when? ]  integrated into micropropagation production for hybrid tomato.  This method uses micropropagated scion shoots that grafted onto 3 week-old rootstock seedlings. [ 13 ]  The most common commercial technique for grafting tomato is tube grafting.  Tube grafting takes place when the scion and rootstock are severed as seedlings and reattached with a small,  silicone  tube or clip. [ 14 ] [ 15 ]   This technique has been highly effective as it can be carried out when plants are very small, thereby eliminating the need for large healing chambers while increasing the output.  Tube grafting has been adopted as the primary method for vegetable grafting on the farm as it can be easily carried out with small healing chambers with typical success rates ranging from 85 to 90 percent  [14] .


Variegation  is the appearance of differently coloured zones in the  foliage ,  flowers , and sometimes the  stems  and  fruit  of  plants , granting a speckled, striped, or patchy appearance. The colors of the patches themselves vary from a slightly lighter shade of the natural coloration to yellow, to white, or other colors entirely such as red and pink. [ 1 ]  This is caused by varying levels and types of  pigment , such as  chlorophyll  in leaves. [ 2 ]  Variegation can be caused by  genetic mutations  affecting pigment production, or by viral infections such as those resulting from  mosaic viruses . [ 3 ]  Many plants are also naturally variegated, such as  Goeppertia insignis . Most of these are herbaceous or climbing plants, and are most often species native to tropical rainforests. [ 4 ]


Many species which are normally non-variegated are known to display variegation. Their appearance is desirable to enthusiasts, and many such plants are  propagated  and sold as unique  cultivars . [ 1 ]  However, in individuals where the variegation occurs in normally- photosynthetic  cells, the lack of functioning  chloroplasts  can slow growth rate. [ 2 ]  Conversely, naturally-variegated plants derive benefits from their appearance, such as improved photosynthetic efficiency in low-light conditions and herbivore deterrence. [ 5 ] [ 6 ]


The term is also sometimes used to refer to colour zonation in  minerals  and the  integument  of  animals .


Chimeric  plants contain tissues with more than one  genotype . [ further explanation needed ]  A variegated chimera contains some tissues that produce chlorophyll and other tissues which do not. [ 7 ]  Because the variegation is due to the presence of two kinds of plant tissue, propagating the plant must be by a vegetative method of propagation that preserves both types of tissue in relation to each other. Typically, stem  cuttings , bud and stem  grafting , and other propagation methods that results in growth from leaf axil buds will preserve variegation. [ citation needed ]  Cuttings with complete variegation may be difficult, if not impossible, to propagate. [ why? ]  Root cuttings will not usually preserve variegation, since the new stem tissue is derived from a particular [ which? ]  tissue type within the root. [ citation needed ]


Some variegation is caused by  structural color , not pigment; the microscopic structure of the plant itself reflects light to produce varying colors. This can happen when an air layer is located just under the  epidermis  resulting in a white or silvery reflection. [ 8 ]  It is sometimes called blister variegation. [ citation needed ]   Pilea   cadierei  (aluminum plant) shows this effect. Leaves of most  Cyclamen  species show such patterned variegation, varying between plants, but consistent within each plant.


The presence of hairs on leaves, which may be coloured differently from the leaf itself, can also produce variable coloration. This is found in various  Begonia  species and their hybrids.


Sometimes venal variegation occurs – the veins of the leaf are picked out in white or yellow. This is due to lack of green tissue above the veins. It can be seen in some  aroids . The  blessed milk thistle ,  Silybum marianum , is a plant in which another type of venal variegation occurs, but in this case it is due to a blister variegation occurring along the veins.


A common cause of variegation is the masking of green  pigment  by other pigments, such as  anthocyanins . This often extends to the whole leaf, causing it to be reddish or purplish. On some plants however, consistent zonal markings occur; such as on some clovers,  bromeliads , certain  Pelargonium  and  Oxalis  species. On others, such as the commonly grown forms of  Coleus , the variegation can vary widely within a population. In  Nymphaea lotus , the tiger lotus, leaf variegations appear under intense illumination.


Virus  infections may cause patterning to appear on the leaf surface. The patterning is often characteristic of the infection. Examples are the  mosaic viruses , which produce a mosaic-type effect on the leaf surface or the  citrus variegation virus  (CVV). Recently [ when? ]  a virus disease,  Hosta virus X  (HVX) has been identified that causes mottled leaf coloring in  hostas . At first, diseased plants were propagated and grown for their mottled foliage, at the risk of infecting other healthy hostas. [ 9 ]  While these diseases are usually serious enough that the gardener would not grow affected plants, there are a few affected plants that can survive indefinitely, and are attractive enough to be grown for ornament; e.g. some variegated  Abutilon  varieties.  Nutrient  deficiency symptoms may cause a temporary or variable yellowing in specific zones on the leaf.  Iron  and  magnesium  deficiencies are common causes of this.  Transposable elements  can cause colour variegation. [ 10 ]


It has been suggested that some patterns of leaf variegation may be part of a "defensive masquerade strategy." [ 11 ]  In this, leaf variegation may appear to a  leaf mining insect  that the leaf is already infested, and this may reduce parasitization of the leaf by leaf miners. [ 12 ]


By convention, the italicised term  'variegata'  as the second part of the Latin  binomial  name, indicates a  species  found in the wild with variegation ( Aloe variegata ). The much more common, non-italicised, inclusion of 'Variegata' as the third element of a name indicates a variegated  cultivar  of an unvariegated parent ( Aucuba japonica  'Variegata'). However, not all variegated plants have this Latin tag, for instance many cultivars of  Pelargonium  have some zonal variegation in their leaves. Other types of variegation may be indicated, e.g.  Daphne odora  'Aureomarginata' has yellow edging on its leaves.


Variegated plants have long been valued by gardeners, as the usually lighter-coloured variegation can 'lift' what would otherwise be blocks of solid green foliage. Many gardening societies have specialist variegated plants groups, such as the  Hardy Plant Society 's Variegated Plant Special Interest Group in the UK.


In 2020, a variegated  Rhaphidophora tetrasperma  plant sold at auction for US$5,300. [ 13 ]  In June 2021, another variegated  Rhaphidophora tetrasperma  plant sold at auction for US$19,297. [ 14 ]


In  biology , the word  gene  has two meanings. The Mendelian gene is a basic unit of  heredity . The molecular gene is a sequence of  nucleotides  in  DNA  that is transcribed to produce a functional  RNA . There are two types of molecular genes: protein-coding genes and non-coding genes. [ 1 ] [ 2 ] [ 3 ]  During  gene expression  (the synthesis of  RNA or protein  from a gene), DNA is first  copied into RNA . RNA can be  directly functional  or be the intermediate  template  for the synthesis of a protein.


The transmission of genes to an organism's  offspring , is the basis of the inheritance of  phenotypic traits  from one generation to the next. These genes make up different DNA sequences, together called a  genotype , that is specific to every given individual, within the  gene pool  of the  population  of a given  species . The genotype, along with environmental and developmental factors, ultimately determines the  phenotype  of the individual.


Most biological traits occur under the combined influence of  polygenes  (a set of different genes) and  gene–environment interactions . Some genetic traits are instantly visible, such as  eye color  or the number of limbs, others are not, such as  blood type , the risk for specific diseases, or the thousands of basic  biochemical  processes that constitute  life . A gene can acquire  mutations  in its  sequence , leading to different variants, known as  alleles , in the  population . These alleles encode slightly different versions of a gene, which may cause different  phenotypical  traits. [ 4 ]  Genes  evolve  due to  natural selection  or  survival of the fittest  and  genetic drift  of the alleles.


There are many different ways to use the term "gene" based on different aspects of their inheritance, selection, biological function, or molecular structure but most of these definitions fall into two categories, the Mendelian gene or the molecular gene. [ 1 ] [ 5 ] [ 6 ] [ 7 ] [ 8 ]


The Mendelian gene is the classical gene of genetics and it refers to any heritable trait. This is the gene described in  The Selfish Gene . [ 9 ]  More thorough discussions of this version of a gene can be found in the articles  Genetics  and  Gene-centered view of evolution .


The molecular gene definition is more commonly used across biochemistry, molecular biology, and most of genetics—the gene that is described in terms of DNA sequence. [ 1 ]  There are many different definitions of this gene—some of which are misleading or incorrect. [ 5 ] [ 10 ]


Very early work in the field that became  molecular genetics  suggested the concept that  one gene makes one protein  (originally 'one gene – one enzyme'). [ 11 ] [ 12 ]  However, genes that produce repressor RNAs were proposed in the 1950s [ 13 ]  and by the 1960s, textbooks were using molecular gene definitions that included those that specified functional RNA molecules such as ribosomal RNA and tRNA (noncoding genes) as well as protein-coding genes. [ 14 ]


This idea of two kinds of genes is still part of the definition of a gene in most textbooks. For example,


The primary function of the genome is to produce RNA molecules. Selected portions of the DNA nucleotide sequence are copied into a corresponding RNA nucleotide sequence, which either encodes a protein (if it is an mRNA) or forms a 'structural' RNA, such as a transfer RNA (tRNA) or ribosomal RNA (rRNA) molecule. Each region of the DNA helix that produces a functional RNA molecule constitutes a gene. [ 15 ]


We define a gene as a DNA sequence that is transcribed. This definition includes genes that do not encode proteins (not all transcripts are messenger RNA). The definition normally excludes regions of the genome that control transcription but are not themselves transcribed. We will encounter some exceptions to our definition of a gene - surprisingly, there is no definition that is entirely satisfactory. [ 16 ]


A gene is a DNA sequence that codes for a diffusible product. This product may be protein (as is the case in the majority of genes) or may be RNA (as is the case of genes that code for tRNA and rRNA). The crucial feature is that the product diffuses away from its site of synthesis to act elsewhere. [ 17 ]


The important parts of such definitions are: (1) that a gene corresponds to a transcription unit; (2) that genes produce both mRNA and noncoding RNAs; and (3) regulatory sequences control gene expression but are not part of the gene itself. However, there's one other important part of the definition and it is emphasized in Kostas Kampourakis' book  Making Sense of Genes .


Therefore in this book I will consider genes as DNA sequences encoding information for functional products, be it proteins or RNA molecules. With 'encoding information', I mean that the DNA sequence is used as a template for the production of an RNA molecule or a protein that performs some function. [ 5 ]


The emphasis on function is essential because there are stretches of DNA that produce non-functional transcripts and they do not qualify as genes. These include obvious examples such as transcribed pseudogenes as well as less obvious examples such as junk RNA produced as noise due to transcription errors. In order to qualify as a true gene, by this definition, one has to prove that the transcript has a biological function. [ 5 ]


Early speculations on the size of a typical gene were based on high-resolution genetic mapping and on the size of proteins and RNA molecules. A length of 1500 base pairs seemed reasonable at the time (1965). [ 14 ]  This was based on the idea that the gene was the DNA that was directly responsible for production of the functional product. The discovery of introns in the 1970s meant that many eukaryotic genes were much larger than the size of the functional product would imply. Typical mammalian protein-coding genes, for example, are about 62,000 base pairs in length (transcribed region) and since there are about 20,000 of them they occupy about 35–40% of the mammalian genome (including the human genome). [ 18 ] [ 19 ] [ 20 ]


In spite of the fact that both protein-coding genes and noncoding genes have been known for more than 50 years, there are still a number of textbooks, websites, and scientific publications that define a gene as a DNA sequence that specifies a protein. In other words, the definition is restricted to protein-coding genes. Here is an example from a recent article in American Scientist.


... to truly assess the potential significance of de novo genes, we relied on a strict definition of the word "gene" with which nearly every expert can agree. First, in order for a nucleotide sequence to be considered a true gene, an open reading frame (ORF) must be present. The ORF can be thought of as the "gene itself"; it begins with a starting mark common for every gene and ends with one of three possible finish line signals. One of the key enzymes in this process, the RNA polymerase, zips along the strand of DNA like a train on a monorail, transcribing it into its messenger RNA form. This point brings us to our second important criterion: A true gene is one that is both transcribed and translated. That is, a true gene is first used as a template to make transient messenger RNA, which is then translated into a protein. [ 21 ]


This restricted definition is so common that it has spawned many recent articles that criticize this "standard definition" and call for a new expanded definition that includes noncoding genes. However, some modern writers still do not acknowledge noncoding genes although this so-called "new" definition has been recognised for more than half a century. [ 22 ] [ 23 ] [ 24 ]


Although some definitions can be more broadly applicable than others, the fundamental complexity of biology means that no definition of a gene can capture all aspects perfectly. Not all genomes are DNA (e.g.  RNA viruses ), [ 25 ]  bacterial  operons  are multiple protein-coding regions transcribed into single large mRNAs,  alternative splicing  enables a single genomic region to encode multiple district products and  trans-splicing  concatenates mRNAs from shorter coding sequence across the genome. [ 26 ] [ 27 ] [ 28 ]  Since molecular definitions exclude elements such as introns, promotors, and other  regulatory regions , these are instead thought of as "associated" with the gene and affect its function.


An even broader operational definition is sometimes used to encompass the complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products. [ 29 ]  This definition categorizes genes by their functional products (proteins or RNA) rather than their specific DNA loci, with regulatory elements classified as  gene-associated  regions. [ 29 ]


The existence of discrete inheritable units was first suggested by  Gregor Mendel  (1822–1884). [ 30 ]  From 1857 to 1864, in  Brno ,  Austrian Empire  (today's Czech Republic), he studied inheritance patterns in 8000 common edible  pea plants , tracking distinct traits from parent to offspring. He described these mathematically as 2 n  combinations where n is the number of differing characteristics in the original peas. Although he did not use the term  gene , he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured  Wilhelm Johannsen 's distinction between  genotype  (the genetic material of an organism) and  phenotype  (the observable traits of that organism). Mendel was also the first to demonstrate  independent assortment , the distinction between  dominant  and  recessive  traits, the distinction between a  heterozygote  and  homozygote , and the phenomenon of discontinuous inheritance.


Prior to Mendel's work, the dominant theory of heredity was one of  blending inheritance , [ 31 ]  which suggested that each parent contributed fluids to the fertilization process and that the traits of the parents blended and mixed to produce the offspring.  Charles Darwin  developed a theory of inheritance he termed  pangenesis , from  Greek  pan ("all, whole") and genesis ("birth") / genos ("origin"). [ 32 ] [ 33 ]  Darwin used the term  gemmule  to describe hypothetical particles that would mix during reproduction.


Mendel's work went largely unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by  Hugo de Vries ,  Carl Correns , and  Erich von Tschermak , who (claimed to have) reached similar conclusions in their own research. [ 34 ]  Specifically, in 1889, Hugo de Vries published his book  Intracellular Pangenesis , [ 35 ]  in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. De Vries called these units "pangenes" ( Pangens  in German), after Darwin's 1868 pangenesis theory.


Twenty years later, in 1909,  Wilhelm Johannsen  introduced the term "gene" (inspired by the  ancient Greek : γόνος,  gonos , meaning offspring and procreation) [ 36 ]  and, in 1906,  William Bateson , that of " genetics " [ 37 ] [ 29 ]  while  Eduard Strasburger , among others, still used the term "pangene" for the fundamental physical and functional unit of heredity. [ 35 ] : Translator's preface, viii


Advances in understanding genes and inheritance continued throughout the 20th century.  Deoxyribonucleic acid  (DNA) was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s. [ 38 ] [ 39 ]  The structure of DNA was studied by  Rosalind Franklin  and  Maurice Wilkins  using  X-ray crystallography , which led  James D. Watson  and  Francis Crick  to publish a model of the double-stranded DNA molecule whose paired  nucleotide bases  indicated a compelling hypothesis for the mechanism of genetic replication. [ 40 ] [ 41 ]


In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities arranged like beads on a string. The experiments of  Benzer  using  mutants  defective in the  rII region of bacteriophage T4  (1955–1959) showed that individual genes have a simple linear structure and are likely to be equivalent to a linear section of DNA. [ 42 ] [ 43 ]


Collectively, this body of research established the  central dogma of molecular biology , which states that  proteins  are translated from  RNA , which is transcribed from  DNA . This dogma has since been shown to have exceptions, such as  reverse transcription  in  retroviruses . The modern study of  genetics  at the level of DNA is known as  molecular genetics .


In 1972,  Walter Fiers  and his team were the first to determine the sequence of a gene: that of  bacteriophage MS2  coat protein. [ 44 ]  The subsequent development of  chain-termination   DNA sequencing  in 1977 by  Frederick Sanger  improved the efficiency of sequencing and turned it into a routine laboratory tool. [ 45 ]  An automated version of the Sanger method was used in early phases of the  Human Genome Project . [ 46 ]


The theories developed in the early 20th century to integrate  Mendelian genetics  with  Darwinian evolution  are called the  modern synthesis , a term introduced by  Julian Huxley . [ 47 ]


This view of evolution was emphasized by  George C. Williams '  gene-centric view of evolution . He proposed that the Mendelian gene is a  unit  of  natural selection  with the definition: "that which segregates and recombines with appreciable frequency." [ 48 ] : 24   Related ideas emphasizing the centrality of Mendelian genes and the importance of natural selection in evolution were popularized by  Richard Dawkins . [ 9 ] [ 49 ]


The development of the  neutral theory of evolution  in the late 1960s led to the recognition that random genetic drift is a major player in evolution and that neutral theory should be the null hypothesis of molecular evolution. [ 50 ]  This led to the construction of  phylogenetic trees  and the development of the  molecular clock , which is the basis of all dating techniques using DNA sequences. These techniques are not confined to molecular gene sequences but can be used on all DNA segments in the genome.


The vast majority of organisms encode their genes in long strands of  DNA  (deoxyribonucleic acid). DNA consists of a  chain  made from four types of  nucleotide  subunits, each composed of: a five-carbon sugar ( 2-deoxyribose ), a  phosphate  group, and one of the four  bases   adenine ,  cytosine ,  guanine , and  thymine . [ 51 ] : 2.1


Two chains of DNA twist around each other to form a DNA  double helix  with the phosphate–sugar backbone spiralling around the outside, and the bases pointing inward with adenine  base pairing  to thymine and guanine to cytosine. The specificity of base pairing occurs because adenine and thymine align to form two  hydrogen bonds , whereas cytosine and guanine form three hydrogen bonds. The two strands in a double helix must, therefore, be  complementary , with their sequence of bases matching such that the adenines of one strand are paired with the thymines of the other strand, and so on. [ 51 ] : 4.1


Due to the chemical composition of the  pentose  residues of the bases, DNA strands have directionality. One end of a DNA  polymer  contains an exposed  hydroxyl  group on the  deoxyribose ; this is known as the  3' end  of the molecule. The other end contains an exposed  phosphate  group; this is the  5' end . The two strands of a double-helix run in opposite directions. Nucleic acid synthesis, including  DNA replication  and  transcription  occurs in the 5'→3' direction, because new nucleotides are added via a  dehydration reaction  that uses the exposed 3' hydroxyl as a  nucleophile . [ 52 ] : 27.2


The  expression  of genes encoded in DNA begins by  transcribing  the gene into  RNA , a second type of nucleic acid that is very similar to DNA, but whose monomers contain the sugar  ribose  rather than  deoxyribose . RNA also contains the base  uracil  in place of  thymine . RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three- nucleotide  sequences called  codons , which serve as the "words" in the genetic "language". The  genetic code  specifies the correspondence during  protein translation  between codons and  amino acids . The genetic code is nearly the same for all known organisms. [ 51 ] : 4.1


The total complement of genes in an organism or cell is known as its  genome , which may be stored on one or more  chromosomes . A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded. [ 51 ] : 4.2   The region of the chromosome at which a particular gene is located is called its  locus . Each locus contains one  allele  of a gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence.


The majority of  eukaryotic  genes are stored on a set of large, linear chromosomes. The chromosomes are packed within the  nucleus  in complex with storage proteins called  histones  to form a unit called a  nucleosome . DNA packaged and condensed in this way is called  chromatin . [ 51 ] : 4.2   The manner in which DNA is stored on the histones, as well as chemical modifications of the histone itself, regulate whether a particular region of DNA is accessible for  gene expression . In addition to genes, eukaryotic chromosomes contain sequences involved in ensuring that the DNA is copied without degradation of end regions and sorted into daughter cells during cell division:  replication origins ,  telomeres , and the  centromere . [ 51 ] : 4.2   Replication origins are the sequence regions where  DNA replication  is initiated to make two copies of the chromosome. Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during  DNA replication . The length of the telomeres decreases each time the genome is replicated and has been implicated in the  aging  process. [ 54 ]  The centromere is required for binding  spindle fibres  to separate sister chromatids into daughter cells during  cell division . [ 51 ] : 18.2


Prokaryotes  ( bacteria  and  archaea ) typically store their genomes on a single, large,  circular chromosome . Similarly, some eukaryotic  organelles  contain a remnant circular chromosome with a small number of genes. [ 51 ] : 14.4   Prokaryotes sometimes supplement their chromosome with additional small circles of DNA called  plasmids , which usually encode only a few genes and are transferable between individuals. For example, the genes for  antibiotic resistance  are usually encoded on bacterial plasmids and can be passed between individual cells, even those of different species, via  horizontal gene transfer . [ 55 ]


Whereas the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, whereas the genomes of complex  multicellular organisms , including humans, contain an absolute majority of DNA without an identified function. [ 56 ]  This DNA has often been referred to as " junk DNA ". However, more recent analyses suggest that, although protein-coding DNA makes up barely 2% of the  human genome , about 80% of the bases in the genome may be expressed, so the term "junk DNA" may be a misnomer. [ 26 ]


The  structure of a protein-coding gene  consists of many elements of which the actual  protein coding sequence  is often only a small part. These include introns and untranslated regions of the mature mRNA. Noncoding genes can also contain introns that are removed during processing to produce the mature functional RNA.


All genes are associated with  regulatory sequences  that are required for their expression. First, genes require a  promoter  sequence. The promoter is recognized and bound by  transcription factors  that recruit and help  RNA polymerase  bind to the region to initiate transcription. [ 51 ] : 7.1   The recognition typically occurs as a  consensus sequence  like the  TATA box . A gene can have more than one promoter, resulting in messenger RNAs ( mRNA ) that differ in how far they extend in the 5' end. [ 58 ]  Highly transcribed genes have "strong" promoter sequences that form strong associations with transcription factors, thereby initiating transcription at a high rate. Others genes have "weak" promoters that form weak associations with transcription factors and initiate transcription less frequently. [ 51 ] : 7.2    Eukaryotic   promoter  regions are much more complex and difficult to identify than  prokaryotic  promoters. [ 51 ] : 7.3


Additionally, genes can have regulatory regions many kilobases upstream or downstream of the gene that alter expression. These act by  binding  to transcription factors which then cause the DNA to loop so that the regulatory sequence (and bound transcription factor) become close to the RNA polymerase binding site. [ 59 ]  For example,  enhancers  increase transcription by binding an  activator  protein which then helps to recruit the RNA polymerase to the promoter; conversely  silencers  bind  repressor  proteins and make the DNA less available for RNA polymerase. [ 60 ]


The mature messenger RNA produced from protein-coding genes contains  untranslated regions  at both ends which contain binding sites for  ribosomes ,  RNA-binding proteins ,  miRNA , as well as  terminator , and  start  and  stop codons . [ 61 ]  In addition, most eukaryotic  open reading frames  contain untranslated  introns , which are removed and  exons , which are connected together in a process known as  RNA splicing . Finally, the ends of gene transcripts are defined by  cleavage and polyadenylation (CPA) sites , where newly produced pre-mRNA gets cleaved and a string of ~200 adenosine monophosphates is added at the 3' end. The  poly(A)  tail protects mature mRNA from degradation and has other functions, affecting translation, localization, and transport of the transcript from the nucleus. Splicing, followed by CPA, generate the final  mature mRNA , which encodes the protein or RNA product. [ 62 ]


Many noncoding genes in eukaryotes have different transcription termination mechanisms and they do not have poly(A) tails.


Many prokaryotic genes are organized into  operons , with multiple protein-coding sequences that are transcribed as a unit. [ 63 ] [ 64 ]  The genes in an  operon  are transcribed as a continuous  messenger RNA , referred to as a  polycistronic mRNA . The term  cistron  in this context is equivalent to gene. The transcription of an operon's mRNA is often controlled by a  repressor  that can occur in an active or inactive state depending on the presence of specific metabolites. [ 65 ]  When active, the repressor binds to a DNA sequence at the beginning of the operon, called the  operator region , and represses  transcription  of the  operon ; when the repressor is inactive transcription of the operon can occur (see e.g.  Lac operon ). The products of operon genes typically have related functions and are involved in the same  regulatory network . [ 51 ] : 7.3


Though many genes have simple structures, as with much of biology, others can be quite complex or represent unusual edge-cases. Eukaryotic genes often have introns that are much larger than their exons, [ 66 ] [ 67 ]  and those introns can even have other genes  nested inside them . [ 68 ]  Associated enhancers may be many kilobase away, or even on entirely different chromosomes operating via physical contact between two chromosomes. [ 69 ] [ 70 ]  A single gene can encode multiple different functional products by  alternative splicing , and conversely a gene may be split across chromosomes but those transcripts are concatenated back together into a functional sequence by  trans-splicing . [ 71 ]  It is also possible for  overlapping genes  to share some of their DNA sequence, either on opposite strands or the same strand (in a different reading frame, or even the same reading frame). [ 72 ]


In all organisms, two steps are required to read the information encoded in a gene's DNA and produce the protein it specifies. First, the gene's DNA is  transcribed  to messenger RNA ( mRNA ). [ 51 ] : 6.1   Second, that mRNA is  translated  to protein. [ 51 ] : 6.2   RNA-coding genes must still go through the first step, but are not translated into protein. [ 73 ]  The process of producing a biologically functional molecule of either RNA or protein is called  gene expression , and the resulting molecule is called a  gene product .


The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the  genetic code . Sets of three nucleotides, known as  codons , each correspond to a specific amino acid. [ 51 ] : 6   The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961 using frameshift mutations in the rIIB gene of bacteriophage T4 [ 74 ]  (see  Crick, Brenner et al. experiment ).


Additionally, a " start codon ", and three " stop codons " indicate the beginning and end of the  protein coding region . There are 64 possible codons (four possible nucleotides at each of three positions, hence 4 3  possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms. [ 75 ]


Transcription  produces a single-stranded  RNA  molecule known as  messenger RNA , whose nucleotide sequence is complementary to the DNA from which it was transcribed. [ 51 ] : 6.1   The mRNA acts as an intermediate between the DNA gene and its final protein product. The gene's DNA is used as a template to generate a  complementary  mRNA. The mRNA matches the sequence of the gene's DNA  coding strand  because it is synthesised as the complement of the  template strand . Transcription is performed by an  enzyme  called an  RNA polymerase , which reads the template strand in the  3'  to  5'  direction and synthesizes the RNA from  5'  to  3' . To initiate transcription, the polymerase first recognizes and binds a  promoter  region of the gene. Thus, a major mechanism of  gene regulation  is the blocking or sequestering the promoter region, either by tight binding by  repressor  molecules that physically block the polymerase or by organizing the DNA so that the promoter region is not accessible. [ 51 ] : 7


In  prokaryotes , transcription occurs in the  cytoplasm ; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In  eukaryotes , transcription occurs in the nucleus, where the cell's DNA is stored. The RNA molecule produced by the polymerase is known as the  primary transcript  and undergoes  post-transcriptional modifications  before being exported to the cytoplasm for translation. One of the modifications performed is the  splicing  of  introns  which are sequences in the transcribed region that do not encode a protein.  Alternative splicing  mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells and also occurs in some prokaryotes. [ 51 ] : 7.5  [ 76 ]


Translation  is the process by which a  mature mRNA  molecule is used as a template for synthesizing a new  protein . [ 51 ] : 6.2   Translation is carried out by  ribosomes , large complexes of RNA and protein responsible for carrying out the chemical reactions to add new  amino acids  to a growing  polypeptide chain  by the formation of  peptide bonds . The genetic code is read three nucleotides at a time, in units called  codons , via interactions with specialized RNA molecules called  transfer RNA  (tRNA). Each tRNA has three unpaired bases known as the  anticodon  that are complementary to the codon it reads on the mRNA. The tRNA is also  covalently  attached to the  amino acid  specified by the complementary codon. When the tRNA binds to its complementary codon in an mRNA strand, the ribosome attaches its amino acid cargo to the new polypeptide chain, which is synthesized from  amino terminus  to  carboxyl terminus . During and after synthesis, most new proteins must  fold  to their active  three-dimensional structure  before they can carry out their cellular functions. [ 51 ] : 3


Genes are regulated  so that they are  expressed  only when the product is needed, since expression draws on limited resources. [ 51 ] : 7   A cell regulates its gene expression depending on its  external environment  (e.g.  available nutrients ,  temperature  and other  stresses ), its internal environment (e.g.  cell division cycle ,  metabolism ,  infection status ), and its  specific role  if in a  multicellular  organism. Gene expression can be regulated at any step: from  transcriptional initiation , to  RNA processing , to  post-translational modification  of the protein. The regulation of  lactose  metabolism genes in  E. coli  ( lac  operon ) was the first such mechanism to be described in 1961. [ 77 ]


A typical protein-coding gene is first copied into  RNA  as an intermediate in the manufacture of the final protein product. [ 51 ] : 6.1   In other cases, the RNA molecules are the actual functional products, as in the synthesis of  ribosomal RNA  and  transfer RNA . Some RNAs known as  ribozymes  are capable of  enzymatic function , while others such as  microRNAs  and  riboswitches  have regulatory roles. The  DNA  sequences from which such RNAs are transcribed are known as  non-coding RNA genes . [ 73 ]


Some  viruses  store their entire genomes in the form of  RNA , and contain no DNA at all. [ 78 ] [ 79 ]  Because they use RNA to store genes, their  cellular   hosts  may synthesize their proteins as soon as they are  infected  and without the delay in waiting for transcription. [ 80 ]  On the other hand, RNA  retroviruses , such as  HIV , require the  reverse transcription  of their  genome  from RNA into DNA before their proteins can be synthesized.


Organisms inherit their genes from their parents.  Asexual  organisms simply inherit a complete copy of their parent's genome.  Sexual  organisms have two copies of each chromosome because they inherit one complete set from each parent. [ 51 ] : 1


According to  Mendelian inheritance , variations in an organism's  phenotype  (observable physical and behavioral characteristics) are due in part to variations in its  genotype  (particular set of genes). Each gene specifies a particular trait with a different sequence of a gene ( alleles ) giving rise to different phenotypes. Most eukaryotic organisms (such as the pea plants Mendel worked on) have two alleles for each trait, one inherited from each parent. [ 51 ] : 20


Alleles at a locus may be  dominant  or  recessive ; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, whereas recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. If you know the genotypes of the organisms, you can determine which alleles are dominant and which are recessive. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems. Mendel's work demonstrated that alleles assort independently in the production of  gametes , or  germ cells , ensuring variation in the next generation. Although Mendelian inheritance remains a good model for many traits determined by single genes (including a number of well-known  genetic disorders ) it does not include the physical processes of DNA replication and cell division. [ 81 ] [ 82 ]


The growth, development, and reproduction of organisms relies on  cell division ; the process by which a single  cell  divides into two usually identical  daughter cells . This requires first making a duplicate copy of every gene in the  genome  in a process called  DNA replication . [ 51 ] : 5.2   The copies are made by specialized  enzymes  known as  DNA polymerases , which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by  base pairing , the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is  semiconservative ; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA. [ 51 ] : 5.2


The rate of DNA replication in living cells was first measured as the rate of phage T4 DNA elongation in phage-infected  E. coli  and found to be impressively rapid. [ 83 ]  During the period of exponential DNA increase at 37 °C, the rate of elongation was 749 nucleotides per second.


After DNA replication, the cell must physically separate the two genome copies and divide into two distinct membrane-bound cells. [ 51 ] : 18.2   In  prokaryotes  ( bacteria  and  archaea ) this usually occurs via a relatively simple process called  binary fission , in which each circular genome attaches to the  cell membrane  and is separated into the daughter cells as the membrane  invaginates  to split the  cytoplasm  into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in  eukaryotes . Eukaryotic cell division is a more complex process known as the  cell cycle ; DNA replication occurs during a phase of this cycle known as  S phase , whereas the process of segregating  chromosomes  and splitting the  cytoplasm  occurs during  M phase . [ 51 ] : 18.1


The duplication and transmission of genetic material from one generation of cells to the next is the basis for molecular inheritance and the link between the classical and molecular pictures of genes. Organisms inherit the characteristics of their parents because the cells of the offspring contain copies of the genes in their parents' cells. In  asexually reproducing  organisms, the offspring will be a genetic copy or  clone  of the parent organism. In  sexually reproducing  organisms, a specialized form of cell division called  meiosis  produces cells called  gametes  or  germ cells  that are  haploid , or contain only one copy of each gene. [ 51 ] : 20.2   The gametes produced by females are called  eggs  or ova, and those produced by males are called  sperm . Two gametes fuse to form a  diploid   fertilized egg , a single cell that has two sets of genes, with one copy of each gene from the mother and one from the father. [ 51 ] : 20


During the process of meiotic cell division, an event called  genetic recombination  or  crossing-over  can sometimes occur, in which a length of DNA on one  chromatid  is swapped with a length of DNA on the corresponding homologous non-sister chromatid. This can result in reassortment of otherwise linked alleles. [ 51 ] : 5.5   The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together (known as  genetic linkage ). [ 84 ]  Genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. [ 84 ]


The  genome  is the total genetic material of an organism and includes both the genes and  non-coding sequences . [ 85 ]  Eukaryotic genes can be annotated using FINDER. [ 86 ]


The  genome size , and the number of genes it encodes varies widely between organisms. The smallest genomes occur in  viruses , [ 95 ]  and  viroids  (which act as a single non-coding RNA gene). [ 96 ]  Conversely, plants can have extremely large genomes, [ 97 ]  with  rice  containing >46,000 protein-coding genes. [ 91 ]  The total number of protein-coding genes (the Earth's  proteome ) is estimated to be 5 million sequences. [ 98 ]


Although the number of base-pairs of DNA in the human genome has been known since the 1950s, the estimated number of genes has changed over time as definitions of genes, and methods of detecting them have been refined. Initial theoretical predictions of the number of human genes in the 1960s and 1970s were based on mutation load estimates and the numbers of mRNAs and these estimates tended to be about 30,000 protein-coding genes. [ 99 ] [ 100 ] [ 101 ]  During the 1990s there were guesstimates of up to 100,000 genes and early data on detection of mRNAs ( expressed sequence tags ) suggested more than the traditional value of 30,000 genes that had been reported in the textbooks during the 1980s. [ 102 ]


The initial draft sequences of the human genome confirmed the earlier predictions of about 30,000 protein-coding genes however that estimate has fallen to about 19,000 with the ongoing  GENCODE  annotation project. [ 103 ]  The number of noncoding genes is not known with certainty but the latest estimates from Ensembl suggest 26,000 noncoding genes. [ 104 ]


Essential genes are the set of genes thought to be critical for an organism's survival. [ 106 ]  This definition assumes the abundant availability of all relevant  nutrients  and the absence of environmental stress. Only a small portion of an organism's genes are essential. In bacteria, an estimated 250–400 genes are essential for  Escherichia coli  and  Bacillus subtilis , which is less than 10% of their genes. [ 107 ] [ 108 ] [ 109 ]  Half of these genes are  orthologs  in both organisms and are largely involved in  protein synthesis . [ 109 ]  In the budding yeast  Saccharomyces cerevisiae  the number of essential genes is slightly higher, at 1000 genes (~20% of their genes). [ 110 ]  Although the number is more difficult to measure in higher eukaryotes, mice and humans are estimated to have around 2000 essential genes (~10% of their genes). [ 111 ]  The synthetic organism,  Syn 3 , has a minimal genome of 473 essential genes and quasi-essential genes (necessary for fast growth), although 149 have unknown function. [ 105 ]


Essential genes include  housekeeping genes  (critical for basic cell functions) [ 112 ]  as well as genes that are expressed at different times in the organisms  development  or  life cycle . [ 113 ]  Housekeeping genes are used as  experimental controls  when  analysing gene expression , since they are  constitutively expressed  at a relatively constant level.


Gene nomenclature  was established by the  HUGO Gene Nomenclature Committee  (HGNC), a committee of the  Human Genome Organisation , for each known human gene in the form of an approved gene name and  symbol  (short-form  abbreviation ), which can be accessed through a database maintained by HGNC. Symbols are chosen to be unique, and each gene has only one symbol (although approved symbols sometimes change). Symbols are preferably kept consistent with other members of a  gene family  and with homologs in other species, particularly the  mouse  due to its role as a common  model organism . [ 114 ]


Genetic engineering is the modification of an organism's  genome  through  biotechnology . Since the 1970s, a  variety of techniques  have been developed to specifically add, remove and edit genes in an organism. [ 115 ]  Recently developed  genome engineering  techniques use engineered  nuclease   enzymes  to create targeted  DNA repair  in a  chromosome  to either disrupt or edit a gene when the break is repaired. [ 116 ] [ 117 ] [ 118 ] [ 119 ]  The related term  synthetic biology  is sometimes used to refer to extensive genetic engineering of an organism. [ 120 ]


Genetic engineering is now a routine research tool with  model organisms . For example, genes are easily added to  bacteria [ 121 ]  and lineages of  knockout mice  with a specific gene's function disrupted are used to investigate that gene's function. [ 122 ] [ 123 ]  Many organisms have been genetically modified for applications in  agriculture , industrial biotechnology, and  medicine .


For multicellular organisms, typically the  embryo  is engineered which grows into the adult  genetically modified organism . [ 124 ]  However, the genomes of cells in an adult organism can be edited using  gene therapy  techniques to treat genetic diseases.


The  Gene Wiki  is a project within  Wikipedia  that aims to describe the relationships and functions of all human  genes . It was established to transfer information from  scientific resources  to Wikipedia stub articles. [ 1 ] [ 2 ] [ 3 ]


The Gene Wiki project also initiated publication of gene-specific  review articles  in the journal  Gene , together with the editing of the gene-specific pages in Wikipedia. [ 4 ]


The Gene Wiki project in collaboration with the journal  Gene  was terminated in May 2022, ten years after the project's initiation. A report by the  project's leaders  summarizes the project's achievements. [ 5 ]


The  human genome  contains an estimated 20,000–25,000  protein-coding genes . [ 6 ]   The goal of the Gene Wiki project is to create seed articles for every  notable  human gene, that is, every gene whose function has been assigned in the  peer-reviewed   scientific literature . Approximately half of human genes have assigned function, therefore the total number of articles seeded by the Gene Wiki project would be expected to be in the range of 10,000–15,000. To date, [ as of? ]  approximately 11,000 articles have been created or augmented to include Gene Wiki project content. [ citation needed ]


Once seed articles have been established, the hope and expectation is that these will be  annotated  and expanded by editors ranging in experience from the lay audience to students to professionals and academics. [ 1 ]


Only a small portion of the genome actually encodes  protein  in the human genome. Understanding the function of a gene that codes for a protein generally requires understanding of the function of the corresponding protein. In addition to including basic information about the gene, the project therefore also includes information about the protein encoded by the gene. The function of other portions of the genome,  non-coding DNA , also called "junk" DNA in the past because they had no apparent function, actually are thought to have regulatory functions.


Stubs for the Gene Wiki project are created by a  bot  and contain links to the following primary gene/protein databases:


A  report  found that between 2013 and 2017, the content which Gene Wiki contributed to Wikipedia got  crowdsourced  development over time. [ 8 ]


An  internal control region  is a sequence of  DNA  located with the  coding region  of  eukaryotic   genes  that binds  regulatory elements  such as  activators  or  repressors . This region can recruit  RNA Polymerase  or contribute to  splicing .


A  minigene  is a minimal gene fragment that includes an  exon  and the control regions necessary for the gene to express itself in the same way as a  wild type  gene fragment. This is a minigene in its most basic sense. More complex minigenes can be constructed containing multiple exons and  intron(s) . Minigenes provide a valuable tool for researchers evaluating  splicing  patterns both  in vivo  and  in vitro  biochemically assessed experiments. [ 1 ] [ 2 ]  Specifically, minigenes are used as splice reporter  vectors  (also called  exon-trapping  vectors) and act as a probe to determine which factors are important in splicing outcomes. They can be constructed to test the way both  cis-regulatory elements  (RNA effects) and  trans-regulatory elements  (associated  proteins / splicing factors ) affect gene expression. [ 3 ]


Minigenes were first described as the somatic assembly of DNA segments and consisted of DNA regions known to encode the protein and the flanking regions required to express the protein. The term was first used in a paper in 1977 to describe the cloning of two minigenes that were designed to express a peptide. [ 4 ]


RNA splicing was discovered in the late 1970s through the study of adenoviruses that invade mammals and replicate inside them. Researchers identified RNA molecules that contained sequences from noncontiguous parts of the virus’s genome. This discovery led to the conclusion that regulatory mechanisms existed which affected mature RNA and the genes it expresses. [ 5 ]  Using minigenes as a splice reporting vector to explore the effects of RNA splicing regulation naturally followed and remains the major use of minigenes to date.


In order to provide a good minigene model, the gene fragment should have all of the necessary elements to ensure it exhibits the same  alternative splicing (AS)  patterns as the  wild type  gene, i.e., the length of the fragment must include all upstream and downstream sequences which can affect its splicing. [ 1 ] [ 2 ]  Therefore, most minigene designs begin with a thorough  in silico  analysis of the requirements of the experiment before any "wet" lab work is conducted. [ 6 ]  With the advent of  Bioinformatics  and widespread use of computers, several good programs now exist for the identification of cis-acting control regions that affect the splicing outcomes of a gene [ 7 ] [ 8 ]   and advanced programs can even consider splicing outcomes in various tissue types. [ 9 ]  Differences in minigenes are usually reflected in the final size of the fragment, which is in turn a reflection of the complexity of the minigene itself. The number of foreign DNA elements (exon and introns) inserted into the constitutive exons and introns of a given fragment varies with the type of experiment and the information being sought. A typical experiment might involve  wild type  minigenes which are expected to express genes normally in a comparison run against genetically engineered  allelic variations  which replace the wild-type gene and have been cloned into the same flanking sequences as the original fragment. These types of experiments help to determine the effect of various mutations on  pre-mRNA  splicing. [ 3 ]


Once a suitable genomic fragment is chosen (Step 1), the exons and introns of the fragment can be inserted and amplified, along with the flanking constitutive exons and introns of the original gene, by  PCR . The primers for PCR can be chosen so that they leave " sticky ends " at 3' sense and anti-sense strands (Step 2). These "sticky-ends" can be easily incorporated into a TOPO Vector by ligation into a commercially available source which has ligase already attached to it at the sight of incorporation [ 10 ]   (Step 3). The subsequent TOPO Vectors can be transfected into E.coli cells (Step 4). After incubation, total RNA can be extracted from the bacterial colonies and analyzed using  RT-PCR  to quantify ratios of exon inclusion/exclusion (step 5). The minigene can be transfected into different cell types with various splicing factors to test trans-acting elements (Step 6). The expressed genes or the proteins they encode can be analyzed to evaluate splicing components and their effects via a variety of methods including  hybridization  or  size-exclusion chromatography . [ 1 ] [ 2 ]


RNA splicing  errors have been estimated to occur in a third of genetic diseases. [ citation needed ]  To understand  pathogenesis  and identify potential targets of therapeutic intervention in these diseases, explicating the splicing elements involved is essential. [ 11 ]  Determining the complete set of components involved in splicing presents many challenges due to the abundance of alternative splicing, which occurs in most human genes, and the specificity in which splicing is carried out  in vivo . [ 2 ]   Splicing is distinctly conducted from cell type to cell type and across different stages of cellular development. Therefore, it is critical that any  in vitro  or bioinformatic assumptions about splicing regulation are confirmed  in vivo . [ 12 ]    Minigenes are used to elucidate  cis -regulatory elements,  trans -regulatory elements and other regulators of pre-mature RNA splicing  in vivo . [ 2 ]  Minigenes have been applied to the study of a diverse array of genetic diseases due to the aforementioned abundance of alternatively spliced genes and the specificity and variation observed in splicing regulation. [ 1 ] [ 2 ] [ 12 ]  The following are examples of minigene use in various diseases. While it is not an exhaustive list, it does provide a better understanding of how minigenes are utilized.


RNA splicing errors can have drastic effects on how proteins function, including the hormones secreted by the  endocrine system . These effects on hormones have been identified as the cause of many endocrine disorders including thyroid-related pathological conditions,  rickets ,  hyperinsulinemic hypoglycemia  and  congenital adrenal hyperplasia . [ 13 ]   One specific example of a splicing error causing an endocrine disease that has been studied using minigenes is a type of  growth hormone deficiency  called isolated growth hormone deficiency (IGHD), a disease that results in growth failure. IGHD type II is an autosomal dominant form caused by a mutation in the intervening sequence (IVS) adjacent to exon 3 of the gene encoding growth hormone 1, the GH-1 gene. This mutated form of IVS3 causes exon 3 to be skipped in the mRNA product. The mRNA (-E3) encodes a truncated form of hGH that then inhibits normal hGH secretion.  Minigenes were used to determine that a  point mutation  within an intron splice enhancer (ISE) embedded in IVS3 was to blame for the skipping of E3.  Moreover, it was determined that the function of the ISE is influenced by a nearby  transposable AC element , revealing that this particular splicing error is caused by a trans-acting factor. [ 14 ]


Accumulation of  tau protein  is associated with  neurodegenerative diseases  including  Alzheimer's  and  Parkinson's  diseases as well as other  tauopathies . [ 15 ]   Tau protein isoforms are created by alternative splicing of exons 2, 3 and 10. The regulation of tau splicing is specific to stage of development, physiology and location. Errors in tau splicing can occur in both exons and introns and, depending on the error, result in changes to protein structure or loss of function. [ 16 ]   Aggregation of these abnormal tau proteins correlates directly with pathogenesis and disease progression. Minigenes have been used by several researchers to help understand the regulatory components responsible for mRNA splicing of the TAU gene. [ 15 ] [ 16 ] [ 17 ]


Cancer is a complex, heterogeneous disease that can be hereditary or the result of environmental stimuli. [ 18 ]    Minigenes are used to help oncologists understand the roles  pre-mRNA  splicing plays in different cancer types. Of particular interest are cancer specific genetic mutations that disrupt normal splicing events, including those affecting  spliceosome  components and  RNA-binding proteins  such as  heterogeneous nuclear ribonucleoparticules (hnRNP) ,  serine/arginine-rich (SR) proteins  and  small ribonucleoproteins (snRNP) . [ 19 ] [ 20 ]  Proteins encoded by aberrantly spliced pre-mRNAs are functionally different and contribute to the characteristic anomalies exhibited by cancer cells, including their ability to proliferate, invade and undergo angiogenesis, and metastasis. [ 20 ]  Minigenes help researchers identify genetic mutations in cancer that result in splicing errors and determine the downstream effects those splicing errors have on gene expression. [ 21 ]  Using knowledge obtained from studies employing minigenes, oncologists have proposed tests designed to detect products of abnormal gene expression for diagnostic purposes. [ 22 ]   Additionally, the prospect of using minigenes as a  cancer immunotherapy  is being explored. [ 23 ] [ 24 ]


NM_023928 NM_001319839 NM_001319840


NP_001306768 NP_001306769 NP_076417