LS4 final exam. Problem based, similar in style and length to the midterm. Articles: just the information covered in class

Transcription

1 LS4 final exam Problem based, similar in style and length to the midterm Articles: just the information covered in class Complementation and recombination rii and others Neurospora haploid spores, heterokaryon, biosynthetic pathways Genetic code reading frame, mutation Hardy-Weinberg allele and genotype frequencies, equilibrium, Chi square Hardy-Weinberg and selection Positional cloning polymorphism, linkage, genotype, gene expression Polymorphism and individual identification Genomics high-throughput sequencing, variant filtering Transgenics, knockouts and knockins vector structure, when to use which Model organisms how to do a mutagenesis screen, haploid vs. diploid Human genetics summary phenotype, genotype, mechanism and treatment Homework problems, practice problems from lecture, section problems, quizzes Additional practice problems will be on the website next week

2 Model organisms To carry out experiments that can t be done in humans To take advantage of the particular genetics of the organism To use genetic tools uniquely available in particular organisms

3 Model organisms Bacteria (E. coli etc.) Yeast (S. cerevisiae) Fungi (N. crassa) Worm (C. elegans) Fly (D. melanogaster) Plant (A. thaliana) Zebrafish (D. rerio) Mouse (M. musculus)

4 Model organisms Why mouse? Mammalian, vertebrate model: close to humans Forward and reverse genetics Transgenic, knock-in and knock-out tools

5 Making a transgenic mouse The transgene integrates randomly into the mouse genome usually in 1 place The mouse is hemizygous for the transgene Multiple copies are present in a tandem array Expression level varies due to copy number and where the transgene integrates

6 Example: Growth hormone Transgenesis can (quickly) check the effect of a overexpression of particular gene

7 Building a transgenic mouse construct The minimal transgene start ATG STOP stop polya promoter transgene (cdna for YFG) terminator Problems with minimal transgenes: lack of expression/silencing overexpression lack of proper regulation

8 Building a better transgenic construct Add one or more intron(s) start ATG STOP stop polya promoter transgene terminator couples and splicing leads to higher mature mrna level

9 Building a better transgenic construct Add enhancer(s) start ATG STOP stop polya promoter transgene terminator position/orientation independent regulators of gene expression can confer tissue-selectivity of gene expression can increase/stabilize gene expression

10 Building a better transgenic construct Add insulators start ATG STOP stop polya promoter transgene terminator protect the transgene from surrounding sequences can avoid cross-interaction with neighboring genes can prevent silencing by chromatin remodeling

11 Building a better transgenic construct Use the native gene start Splice Splice donor acceptor ATG GTaagt C/TAG STOP 5 UTR 3 UTR stop promoter CAP ATG coding region STOP terminator AAAAA Normal promoter, splicing, polya and termination sequences Proper gene regulation Fewer copies will integrate because the construct will be larger May have appropriate surrounding sequences in the vector Still will not be in the normal genomic locus

12 What a transgenic organism can do for you Overexpression of a normal gene Can disrupt a normal pathway or process Too much of a gene product altering a process Altering the stoichiometry of multimeric proteins Can model genetic disorders due to increased expression (Over)expression of a mutant gene Can model dominant disorders Prove that a mutation causes a phenotype Dominant-negative effect in multimeric proteins

13 Transgenics can also be used to explore gene expression Fuse a promoter to a reporter gene start ATG STOP stop polya promoter (YFG) Reporter gene (GFP, βgal) terminator Allows determination of when and where a gene is expressed e.g. early in development e.g. in specific tissues or cells within a tissue Buchberger A et al. Development 130: , 2003

14 Transgenesis in many organisms

15 What a transgenic organism cannot do for you Direct gene expression of a gene in its native location Timing of expression Level of expression Proportional to the other alleles Model reduced expression or allele loss Model recessive disorders The solution.knockout animals!

16 Making a knockout mouse Strachan and Read, Human Molecular Genetics The transgene replaces the wt gene at its normal locus A single copy of the transgene is integrated Normal pattern of expression

17 Building a knockout mouse construct The minimal construct Construct Target gene X Neo R recombination in ES cells X select for neomycin resistant ES cells Targeted gene ES cells heterozygous for the construct But..cells that integrated the construct in other locations will also be Neo resistant

18 Building a knockout mouse construct Add negative selection outside the region of homology Construct Target gene Thymidine kinase (TK) X Neo R recombination in ES cells X select for neomycin + ganciclovir resistant ES cells Targeted gene Thymidine kinase (TK) Neo R ES cells with TK will be killed by ganciclovir so only recombinants will survive

19 Summary of selection strategy

20 Personal (DTC) DNA Testing Ancestry Genetic testing Carrier status (48 disorders) - CF, Tay-Sachs, Sickle cell etc. Drug response (20 drugs) - post-operative nausea Traits - lactose intolerance Disease risk - asthma, cancer Genome (exome) sequencing In your near future!