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Phenotype and Function Reading 222-224 Problem set D Genetics can be used as a tool to study problems in biology and has made important contributions to the fields of development, cell biology and neurobiology. One of the goals in this type of research is to use mutations to reveal the normal function of a gene. However, to infer the function of a gene from mutant phenotypes, we need to know how the mutation perturbs the activity of the gene. Two questions are particularly important to address. (1) Does a recessive mutation reduce or eliminate gene function? (2) Does a dominant mutation reduce or alter gene function? Recessive or dominant? The first goal in understanding the nature of a mutation is to determine if it is dominant or recessive. In most cases mutant alleles are recessive to the wild-type alleles. There are also more complicated cases where two alleles are neither dominant nor recessive. If the heterozygote expresses the phenotype of both alleles, the alleles are called codominant. This is most frequently seen with molecular assays for gene function, for example, in ABO blood types. The phenotype of the heterozygote can also be intermediate between the phenotypes of the homozygotes. In these cases the alleles are referred to as incompletely dominant. Loss-of-function mutations Recessive mutations almost always reduce or eliminate gene activity. Mutations that reduce gene function are called weak or hypomorphic. Mutations that eliminate gene function are called null or amorphic. Whether a mutation is hypomorphic or amorphic can be determined by genetic criteria. Hypomorphic mutations reduce but do not eliminate gene activity. An example is the apricot allele (wa) of the white gene. This mutation is recessive and results in apricot colored eyes. If we compare the phenotypes of wild-type and wa alleles, there are two interpretations of how the white gene functions. One possibility is that white produces eye color and the wa allele reduces that production. Alternatively the white locus could inhibit eye color and the wa allele increases the effectiveness of white to inhibit eye color. In 1932 Hermann Muller proposed that one could distinguish between these possibilities by changing the dose of the wa allele. If white produces eye color then increasing the dose of wa should increase eye color. However, if white inhibits eye color, then increasing the dose of wa should lead to less eye color. In fact when Muller conducted the dosage experiments with wa, he found that as the dosage of w a increased the mutant phenotype is less severe. wa/Df(w) > wa/wa > wa/wa/Dp(wa) more mutant (less pigment)-------------------less mutant (more pigment) Amorphic mutations eliminate gene activity and behave similar to a deficiency of the locus. Recessive alleles of white (w) that lead to a white eye phenotype are considered to be amorphic. As w dosage increases, the mutant phenotype remains unchanged. w/Df = w/w = w/w/Dp(w) more mutant (less pigment)-------------------less mutant (more pigment) Hypomorphic alleles can cause a range of mutant phenotypes. The albino gene of mice encodes tyrosinase, which is one of the enzymes that produces the fur pigment melanin from tyrosine. Mutant alleles of various strengths have been isolated. Patches of skin from these mice can be incubated with radioactive tyrosine and the amount of tyrosine incorporated into melanin can be measured. The table below is a comparison of the fur color phenotypes and levels of tyrosinase from mice carrying various albino alleles. C is the wild-type gene, c is the amorphic allele and the remaining alleles are hypomorphic. Genotype C+/C+ C+/c cch/cch ce/ce c/c fur color Black Black grey off white white cpm of C14-tyrosine incorporated 1200 +/- 36 617 +/- 33 442 +/- 15 98 +/- 11 47 +/- 5 From both the phenotypes and biochemical assays we can see that the different alleles have various activities: C+ > cch > ce > c. This kind of graded set of alleles is called an allelic series. When inferring the function of a gene, it is important to know the null phenotype, the phenotype in the absence of gene function. However, null alleles can often result in phenotypes that are difficult to interpret, and in these cases hypomorphic alleles can be more informative. For example, mutations that disrupt signalling through the Ras pathway in C. elegans cause a lethal phenotype that is not understood. However, the Ras pathway is also important for cell signalling during generation of a vulva, which occurs late in development well after the Ras pathway null mutants die. Because hypomorphic mutations in these genes result in no or partial lethality, animals homozygous for hypomorphic mutations can develop into adults with abnormal vulvae, revealing the role of these genes in cell signalling. Dominant mutations: haploinsufficient or gain-of-function? Haploinsufficient mutations Dominant mutations can reduce (haloinsufficient alleles) or alter (Gain-of-function alleles) gene function. Dominant mutations that cause a reduction or elimination of gene function define genes that are required in two doses. These mutations are known as haploinsufficient because the haploid dose of the gene is not sufficient for normal gene function. Thus, unlike the albino gene described above in which reducing gene function 50% does not have a phenotypic consequence, haploinsufficient mutations define genes in which a 50% reduction in gene function does affect phenotype. Animals heterozygous for a haploinsufficient mutation (m/+) have a phenotype similar to animals heterozygous for a deficiency for the locus (Df/+). In Drosophila, there are about 50 Minute genes that are defined by haploinsufficient mutations. These mutations cause the same phenotype: homozygous flies die, and heterozygous flies have thin bristles and develop slowly. One of the Minute genes has been shown to encode a ribosomal protein. Gain-of function mutations There are three types of gain-of-function mutations. These mutations are usually, but not always, dominant to their wild-type alleles. Hypermorphic mutations increase gene activity relative to their wild-type alleles. Adding wild-type gene activity to the hypermorphic gene activity leads to a more severe mutant phenotype. One example of hypermorphic alleles are dominant alleles of the C. elegans gene lin-12 [lin-12(d)]. The lin-12 gene is required for certain cells to determine their fates normally. genotype lin-12(lf) / lin12(lf) lin-12(+) / lin12(+) lin-12(gf) / lin12(gf) Cell A B fate Cell B B fate A fate B fate A fate A fate One copy of lin-12(gf) transforms some B cells to the A fate. As the dosage of wild-type alleles is increased more B cells are transformed to the A fate. lin-12(gf)/+/Dp lin-12(+) > lin-12(gf)/+ > lin-12(gf)/Df more mutant more B cells transformed to A cells less mutant fewer B cells transformed to A cells Thus lin-12(gf) alleles increase lin-12 gene activity, resulting in the transformation of B cells to the A fate. lin-12 amorphic and hypomorphic alleles [lin-12(lf)] lead to cell fate transformations in the opposite direction, transforming cell A to a B fate. The two types of lin-12 alleles that cause opposite transformations in cell fate have led to a model in which the lin-12 gene functions as a binary switch in cell fate determination: if lin-12 is active cells adopt fate A, if lin-12 is inactive cells adopt fate B. 2. Antimorphic mutations, which are also called dominant negative mutations, alter gene activity to antagonize the activity of the wildtype allele. Wild-type gene function depends on the ratio of mutant gene dosage to wild-type dosage: the higher the ratio, the more severe the mutant phenotype. mutant (m)/wild type (+) ratio genotype phenotype 2:1 1:1 1:2 m/m/Dp(+ ) more mutant m/+ m/+/Dp( +) less mutant Examples of antimorphic mutations are certain missense mutations in the DNA binding domain of the lac repressor. Because the lac repressor is a tetramer, mutant repressors can complex with wildtype repressors and poison the complex. In this case as the ratio of mutant:wild-type alleles increases, more defective tetramers are formed, and the phenotype becomes more mutant. 3. Neomorphic mutations lead to novel gene activity. These alleles differ from hypermorphic and antimorphic alleles in that they are insensitive to dosage. Dominant mutations in the Drosophila Antennapedia (Antp) gene can have a dramatic neomorphic phenotype. Flies with one copy of the dominant AntpNs mutation have legs growing out of there heads in place of antennae. AntpNs mutations are neomorphic because they are insensitive to changes in the dosage of the wild-type gene AntpNs / Df = AntpNs / + = AntpNs / + /Dp(+) The Antp gene is normally transcribed in the thorax where it promotes leg development. The AntpNs mutation is caused by the insertion of a transposable element upstream of the Antp gene which leads to Antp expression in the head. This ectopic expression of the Antp gene promotes leg formation in the wrong place. In the next series of lectures, we will discuss how genetics has been used as a tool to understand a developmental signaling pathway. What you have learned in this lecture will be used again later on to determine how mutations disrupt gene function in specific cases. Problem set D 1. You find a mouse with no tail. In order to determine whether this mouse carries a new mutation, you cross it to a normal mouse. All the F1 progeny of this cross are wild type. What does this mean? You then mate all the F1 males to their sisters and observe that three out of 42 F2 animals have no tail and two have short tails. What could explain this pattern of inheritance? You map the no tail mutation by recombination and realize that there is a stock available that is heterozygous for a deletion that removes the region where the no tail mutation maps. You cross animals without tails to animals that are heterozygous for the deletion. All the progeny for this cross are wild type. Assuming that the deletion really removes the gene mutated by your mutation, explain this result. 2. You are studying the regulation of the lac operon in E. coli and perform a merodiploid (partial diploids) analysis with various regulatory and structural gene variants that you isolated. Your first results are shown below (in units of ß-galactosidase activity). Experiment Genotype 1. 2. 3. 4. lacI+O+Z+ lacI-OcZ+ lacI-OcZlacI-O+Z+/lacI+O+Z+ ß-galactosidase activity + Inducer - Inducer 100 100 1 200 0.1 100 0.1 0.1 lacI encodes the lac repressor and is active in the absence of inducer (i.e., lac repressor binds to the lac operator and inhibits transcription from the lac promoter). Addition of inducer inhibits the repressor and stimulates transcription from the lac promoter. lacO is the operator, the region to which lac repressor binds, and lacOc mutations are constitutive operator mutations, causing lacZ expression in the presence of repressor and absence of inducer. lacZ encodes ß-galactosidase, an enzyme that functions as a tetramer. a) Why is the induced activity in experiment 4 twice that of 1. You generate additional merodiploids and get the surprising results shown below. Experiment Genotype 5. 6. 7. 8. lacI-OcZ-/lacI+O+Z+ lacI+OcZ-/lacI-O+Z+ lacI-O+Z-/lacI+OcZ+ lacI+OcZ+/lacI-O+Z- Induced Uninduced 10 10 10 10 0.1 0.1 100 100 b) Describe a hypothesis to explain the results of experiments 5-8. 3. Drosophila homozygous for an allele of the thick veins gene, tkvSz2, are normal-appearing adults except that the veins on the wings are much thicker than the wild-type wing veins. Flies hemizygous for that allele and a deficiency of the gene (tkvSz2/Df) die as embryos. a. What is the nature of the tkvSz2 allele (amorph, hypomorph, haploinsufficient, hypermorph, antimorph, neomorph)? b. Based on the mutant phenotypes, what are the functions of the wild type thick veins gene? It plays an essential role during development of flies and also functions in regulating the morphology of wing veins. 4. You compare the phenotype of animals that are homozygous for a mutation (m/m), that are heterozygous for the mutation (m/+), that are hemizygous for the mutation (m/Df), that contain an extra copy of the wild-type gene (m/m/+), and that are hemizygous for the locus (Df/+). Which of these animals will exhibit a wild-type phenotype, and of the animals that exhibit a mutant phenotype, which will exhibit the more severe phenotype (order the mutants based on strength of phenotype) when the mutation is: a. Hypomorphic (Explain your reasoning for each example.) b. haploinsufficient c. antimorphic 5. The C. elegans lin-14 gene controls the timing of development in C. elegans. LIN-14 protein is high early in development and gradually decreases as development proceeds. lin-14 is defined by both dominant and recessive mutant alleles. Animals that are homozygous for recessive alleles develop precociously (developmental events occur much earlier than normal) because LIN14 protein levels are lowered or eliminated, similar to the levels seen later in development. Animals that contain dominant alleles are retarded in development (developmental events occur much earlier than normal) because LIN-14 levels are higher than they should be late in development. You are given three lin-14 mutants. a) Animals that are homozygous for mutation A develops precociously and development is even more precocious when the mutation is placed over a deficiency of the locus. What type of a mutation is this? b) Animals that are homozygous for mutation B develops precociously and development is similar when the mutation is placed over a deficiency of the locus. What type of a mutation is this? c) Animals that are heterozygous for mutation C are retarded. Development is less retarded when the C mutation is placed over a deficiency and more retarded when the animals contain one C mutant gene and two wild-type genes. What type of a mutation is this?