1. 2 March, 2005 Chapter 12 Mutational dissection Normal gene Altered gene with altered phenotype mutagenesis

2. Overview Mutational analysis is a way to discover genes involved in a biological process. Process usually involves application of a mutagen followed by screening or selection for mutants with variant phenotypes. Mutations that reduce or eliminate gene function are called loss-of-function. Mutations that increase gene activity or create novel activity are called gain-of- function.

3. Mutational analysis Powerful tool for studying biological processes –forward genetics: identification of mutants and descriptions of their heritable phenotypes precedes molecular analysis of products –reverse genetics: based on genome sequences, gene of potential interest is mutated and the phenotype of mutated gene is studied In classical genetics, mutagens were widely used In a neo-classical approach, insertional mutagens (e.g., transgenic elements) both disrupt gene and tag it for isolation

5. Components of mutational dissection Not all possible mutations of gene can be recovered for analysis –both mutagen and nature of gene contribute to its target size, the ability to produce useful mutations –goal is to saturate for mutations, identifying all genes that affect the biological process Steps in mutational analysis –selection of mutagen –assay system –genetic and phenotypic characterization of mutations

6. Target Size

7. Selection of mutagen Random vs directed approaches Choice of mutagen depends upon ability of mutagen to give rise to mutations with effect on phenotype, whether in coding region or in regulatory region Mutagenicity depends on many factors –uptake and toxicity to cells –sex and species differences –prokaryote vs eukaryote

10. Targeted gene knockouts Replacement of endogenous gene with ectopic (introduced) genetically engineered DNA that inactivates gene –homologous recombination replaces normal gene with inactive one –heritable change, commonly done in bacteria, yeast, and mice Site-directed mutagenesis –alteration of specific sites in cloned DNA molecule

13. Phenocopy Specifically interfere with mRNA or gene product Antisense RNA –introduce into target cells RNA complementary (antisense) to mRNA –hybridizes to endogenous mRNA, resulting in loss of protein product Double-stranded RNA interference –introduction of dsRNA that leads to destruction of mRNA Chemical compounds (aka, chemical genetics) –small molecules tested for ability to affect protein –can be done in automated systems

16. Mutational assay Somatic mutations –occur in somatic cells –mutant sectors of tissue result from mutated somatic cell clone usually dominant –usually not passed to offspring exception: plants in which reproductive tissue grows from mutant somatic tissue Germinal mutation –in germ-line set aside during development –mutations detected in progeny of mutagenized individual

18. Germ-line mutations Dominant mutations appear in F 1 Autosomal recessive mutations require F 2 or F 3 or special backcrosses Special techniques for autosomal recessive mutations –induction of development in unfertilized eggs (e.g., zebrafish) –induction of mutated sectors produced by mitotic crossover (e.g., Drosophila) –procedure accelerates screening, but still requires crosses to recover mutation

21. Forward and reverse mutations Unrelated to forward and reverse genetics Forward mutation: change away from wild- type allele –a +  a –D +  D Reverse mutation: change back toward wild-type allele (reversion, back mutation) –a  a + –D  D +

22. Genetic selection vs genetic screen Genetic selection –mutagenesis scheme kills off all individuals which do not have trait –especially useful in microbial systems for detecting rare mutations Genetic screen –individuals carrying mutation identified because they or some of their progeny display phenotype of interest –must examine every individual –especially useful in study of development

25. Genetic screens (1) Can be applied to any problem, depending upon ingenuity and resources Biochemical mutations –screening for auxotrophs from mutagenized prototrophs –supply various substrates required for growth Morphological mutations –change in shape or form Lethal mutations –premature death –recessive lethals are more useful than dominant lethals that are difficult to maintain

26. Genetic screens (2) Conditional mutations –display wild-type under permissive (nonrestrictive) conditions –display mutant phenotype under restrictive conditions –e.g., temperature-sensitive mutations Behavioral mutations Secondary screens –search for mutations that alter mutant phenotype modifier mutations application of recombinant DNA technology

27. Analysis of mutations Single genetic differences (dominant, recessive, multiple alleles) can characterized and mapped by standard genetic means Crosses between recessive mutants with the same phenotype reveal whether the mutations are in the same gene (alleles) (complementation test) Genes can be cloned and molecular differences identified Eventually, functional sites and domains can be identified

29. Diagnostics Both gain-of-function and loss-of-function can be dominant or recessive Sometimes extensive analysis is needed to distinguish between gain-of-function and loss-of-function Loss-of-function –partial or complete elimination of activity of gene’s encoded product Gain-of-function –hypermorph: more gene activity –neomorph: novel gene activity

35. Assignment: Concept map, Solved Problem 1, Basic problems except 9, Challenging problems except 20, 21.