Pathology of Genetically Engineered and Other Mutant Mice

Figure 3.2 Finding the gene and allele symbol on Mouse Genome Informatics.One of the chapter authors inquired about how to find the correct allele symbol to use relative to a specific reference

(Source: Tamai Y, Nakajima R, Ishikawa T, Takaku K, Seldin MF, Taketo MM. Colonic hamartoma development by anomalous duplication in Cdx2 knockout mice. Cancer Res. 1999 Jun 15;59(12):2965‐70).

Go to the Mouse Genome Informatics home page ( http://www.informatics.jax.org/) and select “Gene.” The link goes to “Genes, Genome Features & Maps.” Then select “Genes and Marker Query.” In the Gene/Marker query box, enter the gene symbol or mutant mouse name, in this case Cdx2 was entered. Note, while gene symbols should be in italics no italics are given on this website or many other websites. This will give you all the genes for which this is part of the symbol or where Cdx2 was used as a synonym at some point in time. Selecting Cdx2 will yield the “Gene Detail” page. In the lower right area is the link to find all 14 of the currently reported allelic mutations (as of 1 May 2020) or the number of specific types of mutations. By selecting “All Mutations and Alleles” a summary field will appear. But which one is correct? By looking at the last author on the referenceit is obvious from the summary. This is confirmed by selecting “ Cdx2 tm1Mmt” to reveal the data sheet on this specific allelic mutation. At the bottom of the field is the reference that is the original reference provided.

Source: The Jackson Laboratory.

Figure 3.3 Current symbols assigned to a variety of unrelated genes originally published as p38.If one searches for the gene symbol p38 the results indicate numerous genes on different chromosomes that at one time were all called p38 . The new names not only separate out the different genes but also reflect to a degree what is currently known about the gene function. By following the links you can obtain much more detail on each gene, the number and details on allelic mutations, and links to the original and many subsequent publications on the topic (MGI accessed 22 April 2020).

Table 3.3 Inbred strains of mice.

Table 3.4 Inbred strain nomenclature.

An inbred strain is designated in capital letters.

A substrain is identified using a forward slash (/) after the strain name followed by a lab code of the strain breeder.

Further substrains derived from the founder add to the end of the lab code of subsequent breeders without another forward slash.

Note that C3H/HeJ has a mutation in the Tlr4 gene making it highly susceptible to gram negative bacterial infection while the C3H/HeN substrain is wildtype for Tlr4 .

Figure 3.4 Nomenclature for hybrid stocks.

Table 3.5 Examples of inbred strain abbreviations.

Table 3.6 F1 and F2 hybrid mice.

Sibling breeding F1 hybrid mice for one generation produces an F2 hybrid population ( Figure 3.4), and continued inbreeding after that eventually leads to the creation of recombinant inbred strains (see below). The F2 hybrid population also has hybrid vigor, but is distinct from the F1 hybrid population because meiosis has resulted in recombinations between the parental chromosomes such that there may be some homozygosity in a minority of the segregating alleles. This makes an F2 hybrid population a tremendous tool for mapping, especially for mapping recessive mutations. For example, if an interesting phenotype is observed in an inbred strain, such as an abnormal hair coat, hair interior defect ( hid ) in all AKR/J mice, these animals can be crossed with another inbred strain, such as BALB/cByJ, that has normal hair ( Figure 3.5). As hid in this example is an autosomal recessive mutation, the obligate heterozygous F1 progeny of this cross will all have a normal hair coat. When these heterozygous progeny are intercrossed to create F2 hybrids, 25% of these mice are expected to have the abnormal hair phenotype. The genetic interval carrying the mutant sequence derives from AKR/J so by screening the DNA from the mutant and unaffected mice in the population with molecular markers distributed evenly across all chromosomes, a pattern emerges in which markers specific to AKR/J and not BALB/cByJ skew to increased homozygosity in the region of the genome specific to the mutation. Usually this works relatively quickly to identify the region in which the mutated gene is located. However, in this particular case, less than 15% of the F2 mice were affected ( Table 3.7) due to modifier genes in BALB/cByJ. Similar crosses with other strains resulted in the expected 25% distribution. This illustrates two points, the deviation from Mendelian expectation due to modifiers and the value of doing mapping crosses with different inbred strains, which in this instance identified different genetic intervals that together reduced the interval and the number of candidate genes ( Figure 3.6) [9, 10].