Genetic screen

A genetic screen or mutagenesis screen is an experimental technique used to identify and select for individuals who possess a phenotype of interest in a mutagenized population.[1] Hence a genetic screen is a type of phenotypic screen. Genetic screens can provide important information on gene function as well as the molecular events that underlie a biological process or pathway. While genome projects have identified an extensive inventory of genes in many different organisms, genetic screens can provide valuable insight as to how those genes function.[2][3][4][5][6]

This article is about a method to identify the functions of genes. For screening or testing for genetic diseases, see genetic testing.

Basic screening

Forward genetics (or a forward genetic screen) is an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism. Reverse genetics (or a reverse genetic screen), on the other hand, analyzes the phenotype of an organism following the disruption of a known gene. In short, forward genetics starts with a phenotype and moves towards identifying the gene(s) responsible, whereas reverse genetics starts with a known gene and assays the effect of its disruption by analyzing the resultant phenotypes. Both forward and reverse genetic screens aim to determine gene function.[1]

Successful forward genetic screens often have two key components. The first is a defined genetic background of the organism being used and the second is a simple yet constant experimental procedure to identify mutants of interest. Defined genetic backgrounds allow researchers to identify and locate affected genes in mutant individuals with greater efficiency. A simplified screening method is beneficial because it allows for a larger number of individuals to be screened, thereby increasing the probability of generating and identifying mutants of interest.[3]

Since natural allelic mutations are rare, prior to screening geneticists often mutagenize a population of individuals by exposing them to a known mutagen, such as a chemical or radiation, thereby generating a much higher frequency of chromosomal mutations.[1] In some organisms mutagens can be useful for performing saturation screens. Saturation screens are used to uncover all genes involved in a particular phenotype of an organism or species. The screen is carried out by mapping mutants of a biological process until no new genes/gene mutations can be found. Christiane Nüsslein-Volhard and Eric Wieschaus were the first individuals to perform this type of screening procedure.[7]

Screening variations

Many screening variations have been devised to elucidate a gene that leads to a mutant phenotype of interest.

Enhancer

An enhancer screen begins with a mutant individual that has an affected process of interest with a known gene mutation. The screen can then be used to identify additional genes or gene mutations that play a role in that biological or physiological process. A genetic enhancer screen identifies mutations which enhance a phenotype of interest in an already mutant individual. The phenotype of the double mutant (individual with both the enhancer and original background mutation) is more prominent than either of the single mutant phenotypes. The enhancement must surpass the expected phenotypes of the two mutations on their own, and therefore each mutation may be considered an enhancer of the other. Isolating enhancer mutants can lead to the identification of interacting genes or genes which act redundantly with respect to one another.[8]

Suppressor

A suppressor screen is used to identify suppressor mutations which alleviate or revert the phenotype of the original mutation, in a process defined as synthetic viability.[9] Suppressor mutations can be described as second mutations at a site on the chromosome distinct from the mutation under study, which suppress the phenotype of the original mutation.[10] If the mutation is in the same gene as the original mutation it is known as intragenic suppression, whereas a mutation located in a different gene is known as extragenic suppression or intergenic suppression.[1] Suppressor mutations are extremely useful to define the functions of biochemical pathways within a cell and the relationships between different biochemical pathways.

Temperature sensitive

A temperature sensitive screen involves performing temperature shifts to enhance a mutant phenotype. A population grown at low temperature would have a normal phenotype; however, the mutation in the particular gene would make it unstable at a higher temperature. A screen for temperature sensitivity in fruit flies, for example, might involve raising the temperature in the cage until some flies faint, then opening a portal to let the others escape. Individuals selected in a screen are liable to carry an unusual version of a gene involved in the phenotype of interest. An advantage of alleles found in this type of screen is that the mutant phenotype is conditional and can be activated by simply raising the temperature. A null mutation in such a gene may be lethal to the embryo and such mutants would be missed in a basic screen. A famous temperature sensitive screen was carried out independently by Lee Hartwell and Paul Nurse to identify mutants defective in cell cycle in S. cerevisiae and S. pombe, respectively.

Mapping mutants

By the classical genetics approach, a researcher would then locate (map) the gene on its chromosome by crossbreeding with individuals that carry other unusual traits and collecting statistics on how frequently the two traits are inherited together. Classical geneticists would have used phenotypic traits to map the new mutant alleles. With the advent of genomic sequences for model systems such as Drosophila melanogaster, Arabidopsis thaliana and C. elegans many single nucleotide polymorphisms (SNPs) have now been identified that can be used as traits for mapping. In fact, the Heidelberg screen, which was developed in 1980 by Nüsslein-Volhard and Wieschaus cleared the way for future scientists in this field.[11] SNPs are the preferred traits for mapping since they are very frequent, on the order of one difference per 1000 base pairs, between different varieties of organism. Mutagens such as random DNA insertions by transformation or active transposons can also be used to generate new mutants. These techniques have the advantage of tagging the new alleles with a known molecular (DNA) marker that can facilitate the rapid identification of the gene.[7]

Positional cloning

Positional cloning is a method of gene identification in which a gene for a specific phenotype is identified only by its approximate chromosomal location (but not the function); this is known as the candidate region. Initially, the candidate region can be defined using techniques such as linkage analysis, and positional cloning is then used to narrow the candidate region until the gene and its mutations are found. Positional cloning typically involves the isolation of partially overlapping DNA segments from genomic libraries to progress along the chromosome toward a specific gene. During the course of positional cloning, one needs to determine whether the DNA segment currently under consideration is part of the gene.

Tests used for this purpose include cross-species hybridization, identification of unmethylated CpG islands, exon trapping, direct cDNA selection, computer analysis of DNA sequence, mutation screening in affected individuals, and tests of gene expression. For genomes in which the regions of genetic polymorphisms are known, positional cloning involves identifying polymorphisms that flank the mutation. This process requires that DNA fragments from the closest known genetic marker are progressively cloned and sequenced, getting closer to the mutant allele with each new clone. This process produces a contig map of the locus and is known as chromosome walking. With the completion of genome sequencing projects such as the Human Genome Project, modern positional cloning can use ready-made contigs from the genome sequence databases directly.

For each new DNA clone a polymorphism is identified and tested in the mapping population for its recombination frequency compared to the mutant phenotype. When the DNA clone is at or close to the mutant allele, the recombination frequency should be close to zero. If the chromosome walk proceeds through the mutant allele, the new polymorphisms will start to show increase in recombination frequency compared to the mutant phenotype. Depending on the size of the mapping population, the mutant allele can be narrowed down to a small region (<30 Kb). Sequence comparison between wild type and mutant DNA in that region is then required to locate the DNA mutation that causes the phenotypic difference.

Modern positional cloning can more directly extract information from genomic sequencing projects and existing data by analyzing the genes in the candidate region. Potential disease genes from the candidate region can then be prioritized, potentially reducing the amount of work involved. Genes with expression patterns consistent with the disease phenotype, showing a (putative) function related to the phenotype, or homologous to another gene linked to the phenotype are all priority candidates. Generalization of positional cloning techniques in this manner is also known as positional gene discovery.

Positional cloning is an effective method to isolate disease genes in an unbiased manner, and it has been used to identify disease genes for Duchenne muscular dystrophy, Huntington's disease, and cystic fibrosis. However, complications in the analysis arise if the disease exhibits locus heterogeneity.

References
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  2. Patton EE, Zon LI (December 2001). "The art and design of genetic screens: zebrafish". Nat. Rev. Genet. 2 (12): 956–66. doi:10.1038/35103567. PMID 11733748.
  3. Page DR, Grossniklaus U (February 2002). "The art and design of genetic screens: Arabidopsis thaliana". Nat. Rev. Genet. 3 (2): 124–36. doi:10.1038/nrg730. PMID 11836506.
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  5. Jorgensen EM, Mango SE (May 2002). "The art and design of genetic screens: caenorhabditis elegans". Nat. Rev. Genet. 3 (5): 356–69. doi:10.1038/nrg794. PMID 11988761.
  6. Casselton L, Zolan M (September 2002). "The art and design of genetic screens: filamentous fungi". Nat. Rev. Genet. 3 (9): 683–97. doi:10.1038/nrg889. PMID 12209143.
  7. "Genetic Screen". Stem Cells Research. Archived from the original on 2012-04-01. Retrieved 2012-05-03.
  8. Herman RK, Yochem J (2005). "Genetic enhancers". WormBook: 1–11. doi:10.1895/wormbook.1.27.1. PMC 4780930. PMID 18023119.
  9. Puddu, F.; Oelschlaegel, T; Guerini, I; Geisler, NJ; Niu, H; Herzog, M; Salguero, I; Ochoa-Montaño, B; Viré, E; Sung, P; Adams, DJ; Keane, TM; Jackson, SP (2015). "Synthetic viability genomic screening defines Sae2 function in DNA repair". EMBO Journal. 34 (11): 1509–1522. doi:10.15252/embj.201590973. PMC 4474527. PMID 25899817.
  10. Hodgkin J (2005). "Genetic suppression". WormBook: 1–13. doi:10.1895/wormbook.1.59.1. PMC 4781008. PMID 18023120.
  11. St Johnston, D. (2002). "The art and design of genetic screens: Drosophila melanogaster". Nature Reviews. Genetics. 3 (3): 176–88. doi:10.1038/nrg751. PMID 11972155.
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