Mendelian inheritance

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https://en.wikipedia.org/wiki/Mendelian_inheritance

Gregor Mendel, the Moravian Augustinian friar who founded the modern science of genetics

Mendelian inheritance (also known as Mendelism) is a type of biological inheritance following the principles originally proposed by Gregor Mendel in 1865 and 1866, re-discovered in 1900 by Hugo de Vries and Carl Correns, and later popularized by William Bateson. These principles were initially controversial. When Mendel's theories were integrated with the Boveri–Sutton chromosome theory of inheritance by Thomas Hunt Morgan in 1915, they became the core of classical genetics. Ronald Fisher combined these ideas with the theory of natural selection in his 1930 book The Genetical Theory of Natural Selection, putting evolution onto a mathematical footing and forming the basis for population genetics within the modern evolutionary synthesis.

History

Main article: History of genetics

The principles of Mendelian inheritance were named for and first derived by Gregor Johann Mendel, a nineteenth-century Moravian monk who formulated his ideas after conducting simple hybridization experiments with pea plants (Pisum sativum) he had planted in the garden of his monastery. Between 1856 and 1863, Mendel cultivated and tested some 5,000 pea plants. From these experiments, he induced two generalizations which later became known as Mendel's Principles of Heredity or Mendelian inheritance. He described his experiments in a two-part paper, Versuche über Pflanzen-Hybriden (Experiments on Plant Hybridization), that he presented to the Natural History Society of Brno on 8 February and 8 March 1865, and which was published in 1866.

Mendel's results were at first largely ignored. Although they were not completely unknown to biologists of the time, they were not seen as generally applicable, even by Mendel himself, who thought they only applied to certain categories of species or traits. A major roadblock to understanding their significance was the importance attached by 19th-century biologists to the apparent blending of many inherited traits in the overall appearance of the progeny, now known to be due to multi-gene interactions, in contrast to the organ-specific binary characters studied by Mendel. In 1900, however, his work was "re-discovered" by three European scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak. The exact nature of the "re-discovery" has been debated: De Vries published first on the subject, mentioning Mendel in a footnote, while Correns pointed out Mendel's priority after having read De Vries' paper and realizing that he himself did not have priority. De Vries may not have acknowledged truthfully how much of his knowledge of the laws came from his own work and how much came only after reading Mendel's paper. Later scholars have accused Von Tschermak of not truly understanding the results at all.

Regardless, the "re-discovery" made Mendelism an important but controversial theory. Its most vigorous promoter in Europe was William Bateson, who coined the terms "genetics" and "allele" to describe many of its tenets. The model of heredity was contested by other biologists because it implied that heredity was discontinuous, in opposition to the apparently continuous variation observable for many traits. Many biologists also dismissed the theory because they were not sure it would apply to all species. However, later work by biologists and statisticians such as Ronald Fisher showed that if multiple Mendelian factors were involved in the expression of an individual trait, they could produce the diverse results observed, thus demonstrating that Mendelian genetics is compatible with natural selection. Thomas Hunt Morgan and his assistants later integrated Mendel's theoretical model with the chromosome theory of inheritance, in which the chromosomes of cells were thought to hold the actual hereditary material, and created what is now known as classical genetics, a highly successful foundation which eventually cemented Mendel's place in history.

Mendel's findings allowed scientists such as Fisher and J.B.S. Haldane to predict the expression of traits on the basis of mathematical probabilities. An important aspect of Mendel's success can be traced to his decision to start his crosses only with plants he demonstrated were true-breeding. He only measured discrete (binary) characteristics, such as color, shape, and position of the seeds, rather than quantitatively variable characteristics. He expressed his results numerically and subjected them to statistical analysis. His method of data analysis and his large sample size gave credibility to his data. He had the foresight to follow several successive generations (P, F₁, F₂, F₃) of pea plants and record their variations. Finally, he performed "test crosses" (backcrossing descendants of the initial hybridization to the initial true-breeding lines) to reveal the presence and proportions of recessive characters.

Inheritance tools

Punnett Squares

Punnett Squares are a well known genetics tool that was created by an English geneticist, Reginald Punnett, which can visually demonstrate all the possible genotypes that an offspring can receive, given the genotypes of their parents. Each parent carries two alleles, which can be shown on the top and the side of the chart, and each contribute one of them towards reproduction at a time. Each of the squares in the middle demonstrates the number of times each pairing of parental alleles could combine to make potential offspring. Using probabilities, one can then determine which genotypes the parents can create, and at what frequencies they can be created.

For example, if two parents both have a heterozygous genotype, then there would be a 50% chance for their offspring to have the same genotype, and a 50% chance they would have a homozygous genotype. Since they could possible contribute two identical alleles, the 50% would be chopped in half at 25% to account for each type of homozygote, whether this was a homozygous dominant genotype, or a homozygous recessive genotype.

Pedigrees

Pedigrees are visual tree like representations that demonstrate exactly how alleles are being passed from past generations to future ones. They also provide a diagram displaying each individual that carries a desired allele, and exactly which side of inheritance it was received from, whether it was from their mother's side or their father's side. Pedigrees can also be used to aid researchers in determining the inheritance pattern for the desired allele, because they share information such as the gender of all individuals, the phenotype, a predicted genotype, the potential sources for the alleles, and also based its history, how it could continue to spread in the future generations to come. By using pedigrees, scientists have been able to find ways to control the flow of alleles over time, so that alleles that act problematic can be resolved upon discovery.

Mendel's genetic discoveries

Five parts of Mendel's discoveries were an important divergence from the common theories at the time and were the prerequisite for the establishment of his rules.

1. Characters are unitary, that is, they are discrete e.g.: purple vs. white, tall vs. dwarf. There is no medium-sized plant or light purple flower.
2. Genetic characteristics have alternate forms, each inherited from one of two parents. Today these are called alleles.
3. One allele is dominant over the other. The phenotype reflects the dominant allele.
4. Gametes are created by random segregation. Heterozygotic individuals produce gametes with an equal frequency of the two alleles.
5. Different traits have independent assortment. In modern terms, genes are unlinked.

According to customary terminology, the principles of inheritance discovered by Gregor Mendel are here referred to as Mendelian laws, although today's geneticists also speak of Mendelian rules or Mendelian principles, as there are many exceptions summarized under the collective term Non-Mendelian inheritance. The laws were initially formulated by the geneticist Thomas Hunt Morgan in 1916.

Characteristics Mendel used in his experiments

P-Generation and F₁-Generation: The dominant allele for purple-red flower hides the phenotypic effect of the recessive allele for white flowers. F₂-Generation: The recessive trait from the P-Generation phenotypically reappears in the individuals that are homozygous with the recessive genetic trait.

Myosotis: Colour and distribution of colours are inherited independently.

Mendel selected for the experiment the following characters of pea plants:

• Form of the ripe seeds (round or roundish, surface shallow or wrinkled)
• Colour of the seed–coat (white, gray, or brown, with or without violet spotting)
• Colour of the seeds and cotyledons (yellow or green)
• Flower colour (white or violet-red)
• Form of the ripe pods (simply inflated, not contracted, or constricted between the seeds and wrinkled)
• Colour of the unripe pods (yellow or green)
• Position of the flowers (axial or terminal)
• Length of the stem 

When he crossed purebred white flower and purple flower pea plants (the parental or P generation) by artificial pollination, the resulting flower colour was not a blend. Rather than being a mix of the two, the offspring in the first generation (F₁-generation) were all purple-flowered. Therefore, he called this biological trait dominant. When he allowed self-fertilization in the uniform looking F₁-generation, he obtained both colours in the F₂ generation with a purple flower to white flower ratio of 3 : 1. In some of the other characters also one of the traits was dominant.

He then conceived the idea of heredity units, which he called hereditary "factors". Mendel found that there are alternative forms of factors—now called genes—that account for variations in inherited characteristics. For example, the gene for flower color in pea plants exists in two forms, one for purple and the other for white. The alternative "forms" are now called alleles. For each trait, an organism inherits two alleles, one from each parent. These alleles may be the same or different. An organism that has two identical alleles for a gene is said to be homozygous for that gene (and is called a homozygote). An organism that has two different alleles for a gene is said to be heterozygous for that gene (and is called a heterozygote).

Mendel hypothesized that allele pairs separate randomly, or segregate, from each other during the production of the gametes in the seed plant (egg cell) and the pollen plant (sperm). Because allele pairs separate during gamete production, a sperm or egg carries only one allele for each inherited trait. When sperm and egg unite at fertilization, each contributes its allele, restoring the paired condition in the offspring. Mendel also found that each pair of alleles segregates independently of the other pairs of alleles during gamete formation.

The genotype of an individual is made up of the many alleles it possesses. The phenotype is the result of the expression of all characteristics that are genetically determined by its alleles as well as by its environment. The presence of an allele does not mean that the trait will be expressed in the individual that possesses it. If the two alleles of an inherited pair differ (the heterozygous condition), then one determines the organism's appearance and is called the dominant allele; the other has no noticeable effect on the organism's appearance and is called the recessive allele.

Mendel's laws of inheritance

Law	Definition
Law of dominance and uniformity	Some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the effect of the dominant allele.
Law of segregation	During gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene.
Law of independent assortment	Genes of different traits can segregate independently during the formation of gametes.

Law of Dominance and Uniformity

F₁ generation: All individuals have the same genotype and same phenotype expressing the dominant trait (red).
F₂ generation: The phenotypes in the second generation show a 3 : 1 ratio.
In the genotype 25 % are homozygous with the dominant trait, 50 % are heterozygous genetic carriers of the recessive trait, 25 % are homozygous with the recessive genetic trait and expressing the recessive character.

In Mirabilis jalapa and Antirrhinum majus are examples for intermediate inheritance. As seen in the F₁-generation, heterozygous plants have "light pink" flowers—a mix of "red" and "white". The F₂-generation shows a 1:2:1 ratio of red: light pink: white.

If two parents are mated with each other who differ in one genetic characteristic for which they are both homozygous (each pure-bred), all offspring in the first generation (F₁) are equal to the examined characteristic in genotype and phenotype showing the dominant trait. This uniformity rule or reciprocity rule applies to all individuals of the F₁-generation.

The principle of dominant inheritance discovered by Mendel states that in a heterozygote the dominant allele will cause the recessive allele to be "masked": that is, not expressed in the phenotype. Only if an individual is homozygous with respect to the recessive allele will the recessive trait be expressed. Therefore, a cross between a homozygous dominant and a homozygous recessive organism yields a heterozygous organism whose phenotype displays only the dominant trait.

The F₁ offspring of Mendel's pea crosses always looked like one of the two parental varieties. In this situation of "complete dominance", the dominant allele had the same phenotypic effect whether present in one or two copies.

But for some characteristics, the F₁ hybrids have an appearance in between the phenotypes of the two parental varieties. A cross between two four o'clock (Mirabilis jalapa) plants shows an exception to Mendel's principle, called incomplete dominance. Flowers of heterozygous plants have a phenotype somewhere between the two homozygous genotypes. In cases of intermediate inheritance (incomplete dominance) in the F₁-generation Mendel's principle of uniformity in genotype and phenotype applies as well. Research about intermediate inheritance was done by other scientists. The first was Carl Correns with his studies about Mirabilis jalapa.

Law of Segregation of genes

A Punnett square for one of Mendel's pea plant experiments – self-fertilization of the F1 generation

The Law of Segregation of genes applies when two individuals, both heterozygous for a certain trait are crossed, for example, hybrids of the F₁-generation. The offspring in the F₂-generation differ in genotype and phenotype so that the characteristics of the grandparents (P-generation) regularly occur again. In a dominant-recessive inheritance, an average of 25% are homozygous with the dominant trait, 50% are heterozygous showing the dominant trait in the phenotype (genetic carriers), 25% are homozygous with the recessive trait and therefore express the recessive trait in the phenotype. The genotypic ratio is 1: 2 : 1, and the phenotypic ratio is 3: 1.

In the pea plant example, the capital "B" represents the dominant allele for purple blossom and lowercase "b" represents the recessive allele for white blossom. The pistil plant and the pollen plant are both F₁-hybrids with genotype "B b". Each has one allele for purple and one allele for white. In the offspring, in the F₂-plants in the Punnett-square, three combinations are possible. The genotypic ratio is 1 BB : 2 Bb : 1 bb. But the phenotypic ratio of plants with purple blossoms to those with white blossoms is 3 : 1 due to the dominance of the allele for purple. Plants with homozygous "b b" are white flowered like one of the grandparents in the P-generation.

In cases of incomplete dominance the same segregation of alleles takes place in the F₂-generation, but here also the phenotypes show a ratio of 1 : 2 : 1, as the heterozygous are different in phenotype from the homozygous because the genetic expression of one allele compensates the missing expression of the other allele only partially. This results in an intermediate inheritance which was later described by other scientists.

In some literature sources, the principle of segregation is cited as the "first law". Nevertheless, Mendel did his crossing experiments with heterozygous plants after obtaining these hybrids by crossing two purebred plants, discovering the principle of dominance and uniformity first.

Molecular proof of segregation of genes was subsequently found through observation of meiosis by two scientists independently, the German botanist Oscar Hertwig in 1876, and the Belgian zoologist Edouard Van Beneden in 1883. Most alleles are located in chromosomes in the cell nucleus. Paternal and maternal chromosomes get separated in meiosis because during spermatogenesis the chromosomes are segregated on the four sperm cells that arise from one mother sperm cell, and during oogenesis the chromosomes are distributed between the polar bodies and the egg cell. Every individual organism contains two alleles for each trait. They segregate (separate) during meiosis such that each gamete contains only one of the alleles. When the gametes unite in the zygote the alleles—one from the mother one from the father—get passed on to the offspring. An offspring thus receives a pair of alleles for a trait by inheriting homologous chromosomes from the parent organisms: one allele for each trait from each parent. Heterozygous individuals with the dominant trait in the phenotype are genetic carriers of the recessive trait.

Law of Independent Assortment

Segregation and independent assortment are consistent with the chromosome theory of inheritance.

When the parents are homozygous for two different genetic traits (llSS and LL s_P s_P), their children in the F₁ generation are heterozygous at both loci and only show the dominant phenotypes (Ll S s_P). P-Generation: Each parent possesses one dominant and one recessive trait purebred (homozygous). In this example, solid coat color is indicated by S (dominant), Piebald spotting by s_P (recessive), while fur length is indicated by L (short, dominant) or l (long, recessive). All individuals are equal in genotype and phenotype. In the F₂ generation all combinations of coat color and fur length occur: 9 are short haired with solid colour, 3 are short haired with spotting, 3 are long haired with solid colour and 1 is long haired with spotting. The traits are inherited independently, so that new combinations can occur. Average number ratio of phenotypes 9:3:3:1

For example 3 pairs of homologous chromosomes allow 8 possible combinations, all equally likely to move into the gamete during meiosis. This is the main reason for independent assortment. The equation to determine the number of possible combinations given the number of homologous pairs = 2^x (x = number of homologous pairs)

The Law of Independent Assortment proposes alleles for separate traits are passed independently of one another. That is, the biological selection of an allele for one trait has nothing to do with the selection of an allele for any other trait. Mendel found support for this law in his dihybrid cross experiments. In his monohybrid crosses, an idealized 3:1 ratio between dominant and recessive phenotypes resulted. In dihybrid crosses, however, he found a 9:3:3:1 ratios. This shows that each of the two alleles is inherited independently from the other, with a 3:1 phenotypic ratio for each.

Independent assortment occurs in eukaryotic organisms during meiotic metaphase I, and produces a gamete with a mixture of the organism's chromosomes. The physical basis of the independent assortment of chromosomes is the random orientation of each bivalent chromosome along the metaphase plate with respect to the other bivalent chromosomes. Along with crossing over, independent assortment increases genetic diversity by producing novel genetic combinations.

There are many deviations from the principle of independent assortment due to genetic linkage.

Of the 46 chromosomes in a normal diploid human cell, half are maternally derived (from the mother's egg) and half are paternally derived (from the father's sperm). This occurs as sexual reproduction involves the fusion of two haploid gametes (the egg and sperm) to produce a zygote and a new organism, in which every cell has two sets of chromosomes (diploid). During gametogenesis the normal complement of 46 chromosomes needs to be halved to 23 to ensure that the resulting haploid gamete can join with another haploid gamete to produce a diploid organism.

In independent assortment, the chromosomes that result are randomly sorted from all possible maternal and paternal chromosomes. Because zygotes end up with a mix instead of a pre-defined "set" from either parent, chromosomes are therefore considered assorted independently. As such, the zygote can end up with any combination of paternal or maternal chromosomes. For human gametes, with 23 chromosomes, the number of possibilities is 2²³ or 8,388,608 possible combinations. This contributes to the genetic variability of progeny. Generally, the recombination of genes has important implications for many evolutionary processes.

Mendelian trait

A Mendelian trait is one whose inheritance follows Mendel's principles—namely, the trait depends only on a single locus, whose alleles are either dominant or recessive.

Many traits are inherited in a non-Mendelian fashion.

Non-Mendelian inheritance

Main article: Non-Mendelian inheritance

Mendel himself warned that care was needed in extrapolating his patterns to other organisms or traits. Indeed, many organisms have traits whose inheritance works differently from the principles he described; these traits are called non-Mendelian.

For example, Mendel focused on traits whose genes have only two alleles, such as "A" and "a". However, many genes have more than two alleles. He also focused on traits determined by a single gene. But some traits, such as height, depend on many genes rather than just one. Traits dependent on multiple genes are called polygenic traits.

Chromosomal crossover

From Wikipedia, the free encyclopedia

Crossing over occurs between prophase I and metaphase I and is the process where two homologous non-sister chromatids pair up with each other and exchange different segments of genetic material to form two recombinant chromosome sister chromatids. It can also happen during mitotic division, which may result in loss of heterozygosity. Crossing over is important for the normal segregation of chromosomes during meiosis. Crossing over also accounts for genetic variation, because due to the swapping of genetic material during crossing over, the chromatids held together by the centromere are no longer identical. So, when the chromosomes go on to meiosis II and separate, some of the daughter cells receive daughter chromosomes with recombined alleles. Due to this genetic recombination, the offspring have a different set of alleles and genes than their parents do. In the diagram, genes B and b are crossed over with each other, making the resulting recombinants after meiosis Ab, AB, ab, and aB.

Thomas Hunt Morgan's illustration of crossing over (1916)

A double crossing over

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

Crossing over was described, in theory, by Thomas Hunt Morgan; the term crossover was coined by Morgan and Eleth Cattell. Hunt relied on the discovery of Frans Alfons Janssens who described the phenomenon in 1909 and had called it "chiasmatypie". The term chiasma is linked, if not identical, to chromosomal crossover. Morgan immediately saw the great importance of Janssens' cytological interpretation of chiasmata to the experimental results of his research on the heredity of Drosophila. The physical basis of crossing over was first demonstrated by Harriet Creighton and Barbara McClintock in 1931.

The linked frequency of crossing over between two gene loci (markers) is the crossing-over value. For fixed set of genetic and environmental conditions, recombination in a particular region of a linkage structure (chromosome) tends to be constant and the same is then true for the crossing-over value which is used in the production of genetic maps.

When Hotta et al. in 1977 compared meiotic crossing-over (recombination) in lily and mouse they concluded that diverse eukaryotes share a common pattern. This finding suggested that chromosomal crossing over is a general characteristic of eukaryotic meiosis.

Origins

There are two popular and overlapping theories that explain the origins of crossing-over, coming from the different theories on the origin of meiosis. The first theory rests upon the idea that meiosis evolved as another method of DNA repair, and thus crossing-over is a novel way to replace possibly damaged sections of DNA. The second theory comes from the idea that meiosis evolved from bacterial transformation, with the function of propagating diversity.

In 1931, Barbara McClintock discovered a triploid maize plant. She made key findings regarding corn's karyotype, including the size and shape of the chromosomes. McClintock used the prophase and metaphase stages of mitosis to describe the morphology of corn's chromosomes, and later showed the first ever cytological demonstration of crossing over in meiosis. Working with student Harriet Creighton, McClintock also made significant contributions to the early understanding of codependency of linked genes.

DNA repair theory

Crossing over and DNA repair are very similar processes, which utilize many of the same protein complexes. In her report, "The Significance of Responses of the Genome to Challenge", McClintock studied corn to show how corn's genome would change itself to overcome threats to its survival. She used 450 self-pollinated plants that received from each parent a chromosome with a ruptured end. She used modified patterns of gene expression on different sectors of leaves of her corn plants to show that transposable elements ("controlling elements") hide in the genome, and their mobility allows them to alter the action of genes at different loci. These elements can also restructure the genome, anywhere from a few nucleotides to whole segments of chromosome. Recombinases and primases lay a foundation of nucleotides along the DNA sequence. One such particular protein complex that is conserved between processes is RAD51, a well conserved recombinase protein that has been shown to be crucial in DNA repair as well as cross over. Several other genes in D. melanogaster have been linked as well to both processes, by showing that mutants at these specific loci cannot undergo DNA repair or crossing over. Such genes include mei-41, mei-9, hdm, spnA, and brca2. This large group of conserved genes between processes supports the theory of a close evolutionary relationship. Furthermore, DNA repair and crossover have been found to favor similar regions on chromosomes. In an experiment using radiation hybrid mapping on wheat's (Triticum aestivum L.) 3B chromosome, crossing over and DNA repair were found to occur predominantly in the same regions. Furthermore, crossing over has been correlated to occur in response to stressful, and likely DNA damaging, conditions. 

Links to bacterial transformation

The process of bacterial transformation also shares many similarities with chromosomal cross over, particularly in the formation of overhangs on the sides of the broken DNA strand, allowing for the annealing of a new strand. Bacterial transformation itself has been linked to DNA repair many times. The second theory comes from the idea that meiosis evolved from bacterial transformation, with the function of propagating genetic diversity. Thus, this evidence suggests that it is a question of whether cross over is linked to DNA repair or bacterial transformation, as the two do not appear to be mutually exclusive. It is likely that crossing over may have evolved from bacterial transformation, which in turn developed from DNA repair, thus explaining the links between all three processes.

Chemistry

A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with a homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.

Meiotic recombination may be initiated by double-stranded breaks that are introduced into the DNA by exposure to DNA damaging agents, or the Spo11 protein. One or more exonucleases then digest the 5' ends generated by the double-stranded breaks to produce 3' single-stranded DNA tails (see diagram). The meiosis-specific recombinase Dmc1 and the general recombinase Rad51 coat the single-stranded DNA to form nucleoprotein filaments. The recombinases catalyze invasion of the opposite chromatid by the single-stranded DNA from one end of the break. Next, the 3' end of the invading DNA primes DNA synthesis, causing displacement of the complementary strand, which subsequently anneals to the single-stranded DNA generated from the other end of the initial double-stranded break. The structure that results is a cross-strand exchange, also known as a Holliday junction. The contact between two chromatids that will soon undergo crossing-over is known as a chiasma. The Holliday junction is a tetrahedral structure which can be 'pulled' by other recombinases, moving it along the four-stranded structure.

• 
  Holliday Junction
   
• 
  Molecular structure of a Holliday junction.
   
• 
  Molecular structure of a Holliday junction. From PDB: 3CRX​.

MSH4 and MSH5

The MSH4 and MSH5 proteins form a hetero-oligomeric structure (heterodimer) in yeast and humans. In the yeast Saccharomyces cerevisiae MSH4 and MSH5 act specifically to facilitate crossovers between homologous chromosomes during meiosis. The MSH4/MSH5 complex binds and stabilizes double Holliday junctions and promotes their resolution into crossover products. An MSH4 hypomorphic (partially functional) mutant of S. cerevisiae showed a 30% genome wide reduction in crossover numbers, and a large number of meioses with non exchange chromosomes. Nevertheless, this mutant gave rise to spore viability patterns suggesting that segregation of non-exchange chromosomes occurred efficiently. Thus in S. cerevisiae proper segregation apparently does not entirely depend on crossovers between homologous pairs.

Chiasma

The grasshopper Melanoplus femur-rubrum was exposed to an acute dose of X-rays during each individual stage of meiosis, and chiasma frequency was measured. Irradiation during the leptotene-zygotene stages of meiosis (that is, prior to the pachytene period in which crossover recombination occurs) was found to increase subsequent chiasma frequency. Similarly, in the grasshopper Chorthippus brunneus, exposure to X-irradiation during the zygotene-early pachytene stages caused a significant increase in mean cell chiasma frequency. Chiasma frequency was scored at the later diplotene-diakinesis stages of meiosis. These results suggest that X-rays induce DNA damages that are repaired by a crossover pathway leading to chiasma formation.

Class I and class II crossovers

Double strand breaks (DSBs) are repaired by two pathways to generate crossovers in eukaryotes. The majority of them are repaired by MutL homologs MLH1 and MLH3, which defines the class I crossovers. The remaining are the result of the class II pathway, which is regulated by MUS81 endonuclease and FANCM translocase. There are interconnections between these two pathways—class I crossovers can compensate for the loss of class II pathway. In MUS81 knockout mice, class I crossovers are elevated, while total crossover counts at chiasmata are normal. However, the mechanisms underlining this crosstalk are not well understood. A recent study suggests that a scaffold protein called SLX4 may participate in this regulation. Specifically, SLX4 knockout mice largely phenocopies the MUS81 knockout—once again, an elevated class I crossovers while normal chiasmata count. In FANCM knockout mice, the class II pathway is hyperactivated, resulting in increased numbers of crossovers that are independent of the MLH1/MLH3 pathway.

Consequences

The difference between gene conversion and chromosomal crossover.

In most eukaryotes, a cell carries two versions of each gene, each referred to as an allele. Each parent passes on one allele to each offspring. An individual gamete inherits a complete haploid complement of alleles on chromosomes that are independently selected from each pair of chromatids lined up on the metaphase plate. Without recombination, all alleles for those genes linked together on the same chromosome would be inherited together. Meiotic recombination allows a more independent segregation between the two alleles that occupy the positions of single genes, as recombination shuffles the allele content between homologous chromosomes.

Recombination results in a new arrangement of maternal and paternal alleles on the same chromosome. Although the same genes appear in the same order, some alleles are different. In this way, it is theoretically possible to have any combination of parental alleles in an offspring, and the fact that two alleles appear together in one offspring does not have any influence on the statistical probability that another offspring will have the same combination. This principle of "independent assortment" of genes is fundamental to genetic inheritance. However, the frequency of recombination is actually not the same for all gene combinations. This leads to the notion of "genetic distance", which is a measure of recombination frequency averaged over a (suitably large) sample of pedigrees. Loosely speaking, one may say that this is because recombination is greatly influenced by the proximity of one gene to another. If two genes are located close together on a chromosome, the likelihood that a recombination event will separate these two genes is less than if they were farther apart. Genetic linkage describes the tendency of genes to be inherited together as a result of their location on the same chromosome. Linkage disequilibrium describes a situation in which some combinations of genes or genetic markers occur more or less frequently in a population than would be expected from their distances apart. This concept is applied when searching for a gene that may cause a particular disease. This is done by comparing the occurrence of a specific DNA sequence with the appearance of a disease. When a high correlation between the two is found, it is likely that the appropriate gene sequence is really closer

Non-homologous crossover

See also: Unequal crossing over and Chromosomal translocation

Crossovers typically occur between homologous regions of matching chromosomes, but similarities in sequence and other factors can result in mismatched alignments. Most DNA is composed of base pair sequences repeated very large numbers of times. These repetitious segments, often referred to as satellites, are fairly homogeneous among a species. During DNA replication, each strand of DNA is used as a template for the creation of new strands using a partially-conserved mechanism; proper functioning of this process results in two identical, paired chromosomes, often called sisters. Sister chromatid crossover events are known to occur at a rate of several crossover events per cell per division in eukaryotes. Most of these events involve an exchange of equal amounts of genetic information, but unequal exchanges may occur due to sequence mismatch. These are referred to by a variety of names, including non-homologous crossover, unequal crossover, and unbalanced recombination, and result in an insertion or deletion of genetic information into the chromosome. While rare compared to homologous crossover events, these mutations are drastic, affecting many loci at the same time. They are considered the main driver behind the generation of gene duplications and are a general source of mutation within the genome.

The specific causes of non-homologous crossover events are unknown, but several influential factors are known to increase the likelihood of an unequal crossover. One common vector leading to unbalanced recombination is the repair of double-strand breaks (DSBs). DSBs are often repaired using homology directed repair, a process which involves invasion of a template strand by the DSB strand (see figure below). Nearby homologous regions of the template strand are often used for repair, which can give rise to either insertions or deletions in the genome if a non-homologous but complementary part of the template strand is used. Sequence similarity is a major player in crossover – crossover events are more likely to occur in long regions of close identity on a gene. This means that any section of the genome with long sections of repetitive DNA is prone to crossover events.

The presence of transposable elements is another influential element of non-homologous crossover. Repetitive regions of code characterize transposable elements; complementary but non-homologous regions are ubiquitous within transposons. Because chromosomal regions composed of transposons have large quantities of identical, repetitious code in a condensed space, it is thought that transposon regions undergoing a crossover event are more prone to erroneous complementary match-up; that is to say, a section of a chromosome containing a lot of identical sequences, should it undergo a crossover event, is less certain to match up with a perfectly homologous section of complementary code and more prone to binding with a section of code on a slightly different part of the chromosome. This results in unbalanced recombination, as genetic information may be either inserted or deleted into the new chromosome, depending on where the recombination occurred.

While the motivating factors behind unequal recombination remain obscure, elements of the physical mechanism have been elucidated. Mismatch repair (MMR) proteins, for instance, are a well-known regulatory family of proteins, responsible for regulating mismatched sequences of DNA during replication and escape regulation. The operative goal of MMRs is the restoration of the parental genotype. One class of MMR in particular, MutSβ, is known to initiate the correction of insertion-deletion mismatches of up to 16 nucleotides. Little is known about the excision process in eukaryotes, but E. coli excisions involve the cleaving of a nick on either the 5' or 3' strand, after which DNA helicase and DNA polymerase III bind and generate single-stranded proteins, which are digested by exonucleases and attached to the strand by ligase. Multiple MMR pathways have been implicated in the maintenance of complex organism genome stability, and any of many possible malfunctions in the MMR pathway result in DNA editing and correction errors. Therefore, while it is not certain precisely what mechanisms lead to errors of non-homologous crossover, it is extremely likely that the MMR pathway is involved.

Synapsis

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Synapsis

Synapsis during Meiosis. The circled area is the part where synapsis occurs, where the two chromatids meet before crossing over

Synapsis or Syzygy is the pairing of two chromosomes that occurs during meiosis. It allows matching-up of homologous pairs prior to their segregation, and possible chromosomal crossover between them. Synapsis takes place during prophase I of meiosis. When homologous chromosomes synapse, their ends are first attached to the nuclear envelope. These end-membrane complexes then migrate, assisted by the extranuclear cytoskeleton, until matching ends have been paired. Then the intervening regions of the chromosome are brought together, and may be connected by a protein-DNA complex called the synaptonemal complex. During synapsis, autosomes are held together by the synaptonemal complex along their whole length, whereas for sex chromosomes, this only takes place at one end of each chromosome.

This is not to be confused with mitosis. Mitosis also has prophase, but does not ordinarily do pairing of two homologous chromosomes.

When the non-sister chromatids intertwine, segments of chromatids with similar sequence may break apart and be exchanged in a process known as genetic recombination or "crossing-over". This exchange produces a chiasma, a region that is shaped like an X, where the two chromosomes are physically joined. At least one chiasma per chromosome often appears to be necessary to stabilise bivalents along the metaphase plate during separation. The crossover of genetic material also provides a possible defences against 'chromosome killer' mechanisms, by removing the distinction between 'self' and 'non-self' through which such a mechanism could operate. A further consequence of recombinant synapsis is to increase genetic variability within the offspring. Repeated recombination also has the general effect of allowing genes to move independently of each other through the generations, allowing for the independent concentration of beneficial genes and the purging of the detrimental.

Following synapsis, a type of recombination referred to as synthesis dependent strand annealing (SDSA) occurs frequently. SDSA recombination involves information exchange between paired non-sister homologous chromatids, but not physical exchange. SDSA recombination does not cause crossing-over. Both the non-crossover and crossover types of recombination function as processes for repairing DNA damage, particularly double-strand breaks (see Genetic recombination).

The central function of synapsis is therefore the identification of homologues by pairing, an essential step for a successful meiosis. The processes of DNA repair and chiasma formation that take place following synapsis have consequences at many levels, from cellular survival through to impacts upon evolution itself.

Chromosome silencing

In mammals, surveillance mechanisms remove meiotic cells in which synapsis is defective. One such surveillance mechanism is meiotic silencing that involves the transcriptional silencing of genes on asynapsed chromosomes. Any chromosome region, either in males or females, that is asynapsed is subject to meiotic silencing. ATR, BRCA1 and gammaH2AX localize to unsynapsed chromosomes at the pachytene stage of meiosis in human oocytes and this may lead to chromosome silencing. The DNA damage response protein TOPBP1 has also been identified as a crucial factor in meiotic sex chromosome silencing. DNA double-strand breaks appear to be initiation sites for meiotic silencing.

Recombination

In female Drosophila melanogaster fruit flies, meiotic chromosome synapsis occurs in the absence of recombination. Thus synapsis in Drosophila is independent of meiotic recombination, consistent with the view that synapsis is a precondition required for the initiation of meiotic recombination. Meiotic recombination is also unnecessary for homologous chromosome synapsis in the nematode.

Genetic recombination

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Genetic_recombination

A model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left. Most recombination events appear to be the SDSA type.

Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes (random orientation of pairs of homologous chromosomes in meiosis I); & (2) intrachromosomal recombination, occurring through crossing over.

During meiosis in eukaryotes, genetic recombination involves the pairing of homologous chromosomes. This may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange (a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed) (see SDSA – Synthesis Dependent Strand Annealing pathway in Figure); or by the breaking and rejoining of DNA strands, which forms new molecules of DNA (see DHJ pathway in Figure).

Recombination may also occur during mitosis in eukaryotes where it ordinarily involves the two sister chromosomes formed after chromosomal replication. In this case, new combinations of alleles are not produced since the sister chromosomes are usually identical. In meiosis and mitosis, recombination occurs between similar molecules of DNA (homologous sequences). In meiosis, non-sister homologous chromosomes pair with each other so that recombination characteristically occurs between non-sister homologues. In both meiotic and mitotic cells, recombination between homologous chromosomes is a common mechanism used in DNA repair.

Gene conversion – the process during which homologous sequences are made identical also falls under genetic recombination.

Genetic recombination and recombinational DNA repair also occurs in bacteria and archaea, which use asexual reproduction.

Recombination can be artificially induced in laboratory (in vitro) settings, producing recombinant DNA for purposes including vaccine development.

V(D)J recombination in organisms with an adaptive immune system is a type of site-specific genetic recombination that helps immune cells rapidly diversify to recognize and adapt to new pathogens.

Synapsis

Main article: Synapsis

During meiosis, synapsis (the pairing of homologous chromosomes) ordinarily precedes genetic recombination.

Mechanism

Genetic recombination is catalyzed by many different enzymes. Recombinases are key enzymes that catalyse the strand transfer step during recombination. RecA, the chief recombinase found in Escherichia coli, is responsible for the repair of DNA double strand breaks (DSBs). In yeast and other eukaryotic organisms there are two recombinases required for repairing DSBs. The RAD51 protein is required for mitotic and meiotic recombination, whereas the DNA repair protein, DMC1, is specific to meiotic recombination. In the archaea, the ortholog of the bacterial RecA protein is RadA.

Bacterial recombination

Main article: Bacterial recombination

In bacteria there is regular genetic recombination, as well as ineffective transfer of genetic material, expressed as unsuccessful transfer or abortive transfer, which is any bacterial DNA transfer of the donor cell to recipients which have set the incoming DNA as part of the genetic material of the recipient. Abortive transfer was registered in the following transduction and conjugation. In all cases, the transmitted fragment is diluted by the culture growth.

Chromosomal crossover

Main article: Chromosomal crossover

Thomas Hunt Morgan's illustration of crossing over (1916)

In eukaryotes, recombination during meiosis is facilitated by chromosomal crossover. The crossover process leads to offspring having different combinations of genes from those of their parents, and can occasionally produce new chimeric alleles. The shuffling of genes brought about by genetic recombination produces increased genetic variation. It also allows sexually reproducing organisms to avoid Muller's ratchet, in which the genomes of an asexual population tend to accumulate deleterious mutations over time than beneficial or reversing mutations.

Chromosomal crossover involves recombination between the paired chromosomes inherited from each of one's parents, generally occurring during meiosis. During prophase I (pachytene stage) the four available chromatids are in tight formation with one another. While in this formation, homologous sites on two chromatids can closely pair with one another, and may exchange genetic information.

Because there is a small probability of recombination at any location along a chromosome, the frequency of recombination between two locations depends on the distance separating them. Therefore, for genes sufficiently distant on the same chromosome, the amount of crossover is high enough to destroy the correlation between alleles.

Tracking the movement of genes resulting from crossovers has proven quite useful to geneticists. Because two genes that are close together are less likely to become separated than genes that are farther apart, geneticists can deduce roughly how far apart two genes are on a chromosome if they know the frequency of the crossovers. Geneticists can also use this method to infer the presence of certain genes. Genes that typically stay together during recombination are said to be linked. One gene in a linked pair can sometimes be used as a marker to deduce the presence of the other gene. This is typically used to detect the presence of a disease-causing gene.

The recombination frequency between two loci observed is the crossing-over value. It is the frequency of crossing over between two linked gene loci (markers), and depends on the distance between the genetic loci observed. For any fixed set of genetic and environmental conditions, recombination in a particular region of a linkage structure (chromosome) tends to be constant, and the same is then true for the crossing-over value which is used in the production of genetic maps.

Gene conversion

Main article: Gene conversion

In gene conversion, a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed. Gene conversion occurs at high frequency at the actual site of the recombination event during meiosis. It is a process by which a DNA sequence is copied from one DNA helix (which remains unchanged) to another DNA helix, whose sequence is altered. Gene conversion has often been studied in fungal crosses where the 4 products of individual meioses can be conveniently observed. Gene conversion events can be distinguished as deviations in an individual meiosis from the normal 2:2 segregation pattern (e.g. a 3:1 pattern).

Nonhomologous recombination

Recombination can occur between DNA sequences that contain no sequence homology. This can cause chromosomal translocations, sometimes leading to cancer.

In B cells

Main article: Immunoglobulin class switching

B cells of the immune system perform genetic recombination, called immunoglobulin class switching. It is a biological mechanism that changes an antibody from one class to another, for example, from an isotype called IgM to an isotype called IgG.

Genetic engineering

In genetic engineering, recombination can also refer to artificial and deliberate recombination of disparate pieces of DNA, often from different organisms, creating what is called recombinant DNA. A prime example of such a use of genetic recombination is gene targeting, which can be used to add, delete or otherwise change an organism's genes. This technique is important to biomedical researchers as it allows them to study the effects of specific genes. Techniques based on genetic recombination are also applied in protein engineering to develop new proteins of biological interest.

Examples include Restriction enzyme mediated integration, Gibson assembly and Golden Gate Cloning.

Recombinational repair

DNA damages caused by a variety of exogenous agents (e.g. UV light, X-rays, chemical cross-linking agents) can be repaired by homologous recombinational repair (HRR). These findings suggest that DNA damages arising from natural processes, such as exposure to reactive oxygen species that are byproducts of normal metabolism, are also repaired by HRR. In humans, deficiencies in the gene products necessary for HRR during meiosis likely cause infertility In humans, deficiencies in gene products necessary for HRR, such as BRCA1 and BRCA2, increase the risk of cancer (see DNA repair-deficiency disorder).

In bacteria, transformation is a process of gene transfer that ordinarily occurs between individual cells of the same bacterial species. Transformation involves integration of donor DNA into the recipient chromosome by recombination. This process appears to be an adaptation for repairing DNA damages in the recipient chromosome by HRR. Transformation may provide a benefit to pathogenic bacteria by allowing repair of DNA damage, particularly damages that occur in the inflammatory, oxidizing environment associated with infection of a host.

When two or more viruses, each containing lethal genomic damages, infect the same host cell, the virus genomes can often pair with each other and undergo HRR to produce viable progeny. This process, referred to as multiplicity reactivation, has been studied in lambda and T4 bacteriophages, as well as in several pathogenic viruses. In the case of pathogenic viruses, multiplicity reactivation may be an adaptive benefit to the virus since it allows the repair of DNA damages caused by exposure to the oxidizing environment produced during host infection. See also reassortment.

Meiotic recombination

A molecular model for the mechanism of meiotic recombination presented by Anderson and Sekelsky is outlined in the first figure in this article. Two of the four chromatids present early in meiosis (prophase I) are paired with each other and able to interact. Recombination, in this model, is initiated by a double-strand break (or gap) shown in the DNA molecule (chromatid) at the top of the figure. Other types of DNA damage may also initiate recombination. For instance, an inter-strand cross-link (caused by exposure to a cross-linking agent such as mitomycin C) can be repaired by HRR.

Two types of recombinant product are produced. Indicated on the right side is a "crossover" (CO) type, where the flanking regions of the chromosomes are exchanged, and on the left side, a "non-crossover" (NCO) type where the flanking regions are not exchanged. The CO type of recombination involves the intermediate formation of two "Holliday junctions" indicated in the lower right of the figure by two X-shaped structures in each of which there is an exchange of single strands between the two participating chromatids. This pathway is labeled in the figure as the DHJ (double-Holliday junction) pathway.

The NCO recombinants (illustrated on the left in the figure) are produced by a process referred to as "synthesis dependent strand annealing" (SDSA). Recombination events of the NCO/SDSA type appear to be more common than the CO/DHJ type. The NCO/SDSA pathway contributes little to genetic variation, since the arms of the chromosomes flanking the recombination event remain in the parental configuration. Thus, explanations for the adaptive function of meiosis that focus exclusively on crossing-over are inadequate to explain the majority of recombination events.

Achiasmy and heterochiasmy

Achiasmy is the phenomenon where autosomal recombination is completely absent in one sex of a species. Achiasmatic chromosomal segregation is well documented in male Drosophila melanogaster. Heterochiasmy occurs when recombination rates differ between the sexes of a species. This sexual dimorphic pattern in recombination rate has been observed in many species. In mammals, females most often have higher rates of recombination. The "Haldane-Huxley rule" states that achiasmy usually occurs in the heterogametic sex.

RNA virus recombination

Numerous RNA viruses are capable of genetic recombination when at least two viral genomes are present in the same host cell. Recombination is largely responsible for RNA virus diversity and immune evasion. RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among picornaviridae ((+)ssRNA) (e.g. poliovirus). In the retroviridae ((+)ssRNA)(e.g. HIV), damage in the RNA genome appears to be avoided during reverse transcription by strand switching, a form of recombination.

Recombination also occurs in the reoviridae (dsRNA)(e.g. reovirus), orthomyxoviridae ((-)ssRNA)(e.g. influenza virus) and coronaviridae ((+)ssRNA) (e.g. SARS).

Recombination in RNA viruses appears to be an adaptation for coping with genome damage. Switching between template strands during genome replication, referred to as copy-choice recombination, was originally proposed to explain the positive correlation of recombination events over short distances in organisms with a DNA genome (see first Figure, SDSA pathway).

Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans.

Especially in coronaviruses, recombination may also occur even among distantly related evolutionary groups (subgenera), due to their characteristic transcription mechanism, that involves subgenomic mRNAs that are formed by template switching.

When replicating its (+)ssRNA genome, the poliovirus RNA-dependent RNA polymerase (RdRp) is able to carry out recombination. Recombination appears to occur by a copy choice mechanism in which the RdRp switches (+)ssRNA templates during negative strand synthesis. Recombination by RdRp strand switching also occurs in the (+)ssRNA plant carmoviruses and tombusviruses.

Recombination appears to be a major driving force in determining genetic variability within coronaviruses, as well as the ability of coronavirus species to jump from one host to another and, infrequently, for the emergence of novel species, although the mechanism of recombination in is unclear.

In early 2020, many genomic sequences of Australian SARS‐CoV‐2 isolates have deletions or mutations (29742G>A or 29742G>U; "G19A" or "G19U") in the s2m, suggesting that RNA recombination may have occurred in this RNA element. 29742G("G19"), 29744G("G21"), and 29751G("G28") were predicted as recombination hotspots. During the first months of the COVID-19 pandemic, such a recombination event was suggested to have been a critical step in the evolution of SARS-CoV-2's ability to infect humans. Linkage disequilibrium analysis confirmed that RNA recombination with the 11083G > T mutation also contributed to the increase of mutations among the viral progeny. The findings indicate that the 11083G > T mutation of SARS-CoV-2 spread during Diamond Princess shipboard quarantine and arose through de novo RNA recombination under positive selection pressure. In three patients on the Diamond Princess cruise, two mutations, 29736G > T and 29751G > T (G13 and G28) were located in Coronavirus 3′ stem-loop II-like motif (s2m) of SARS-CoV-2. Although s2m is considered an RNA motif highly conserved in 3' untranslated region among many coronavirus species, this result also suggests that s2m of SARS-CoV-2 is RNA recombination/mutation hotspot.

Schematic representation of the s2m RNA secondary structure, with tertiary structural interactions indicated as long range contacts.

SARS-CoV-2's entire receptor binding motif appeared, based on preliminary observations, to have been introduced through recombination from coronaviruses of pangolins. However, more comprehensive analyses later refuted this suggestion and showed that SARS-CoV-2 likely evolved solely within bats and with little or no recombination.

Role of recombination in the origin of life

Nowak and Ohtsuki noted that the origin of life (abiogenesis) is also the origin of biological evolution. They pointed out that all known life on earth is based on biopolymers and proposed that any theory for the origin of life must involve biological polymers that act as information carriers and catalysts. Lehman argued that recombination was an evolutionary development as ancient as the origins of life. Smail et al. proposed that in the primordial Earth, recombination played a key role in the expansion of the initially short informational polymers (presumed to be RNA) that were the precursors to life.