Naming rules for genetically engineered mice
Have you found out that when you are querying or looking at paper, you will often find a few thieves, and also the name of the number, superscript, and symbol, such as: 129- Trp53 tm1Holl /J, FVB-Tg (PomcCre) 5Brn... Looks very complicated. These are actually the full names of genetically engineered mice.
If you deconstruct this long string of characters, common genetically engineered mice can be divided into two ways:
Gene-directed modified mouse naming, such as knockout, knock-in, point mutation, and so on.
Randomly transgenic mouse naming
The name of genetically modified mice
The names of this type of mouse are basically the same:
Below we explain each of these components one by one~
Line background
If the genetic modification is done on a single mouse background and no other lines are introduced during the breeding process, it can be represented by a shorthand line. such as:
If you are on a mixed line background, you can use these lines (<3) abbreviations with a semicolon as an interval. The recipient is indicated before the semicolon and the donor is indicated after the semicolon. For example, a knockout of a gene from a C57BL/6 and 129 hybrid ES cell line can be expressed as B6;129. Until this line is backcrossed to the inbred line with C57BL/6 mice, it can be rewritten as B6.129.
If the donor line is mixed or has an unknown source, then back to the extent of the inbred line of the recipient line, it can be expressed as .Cg, for example: B6.Cg.
If there are more than 3 ancestral lines or a mixed genetic background with unknown sources, then it is represented by STOCK.
Modified gene
The gene name here uses Gene Symbol.
What is the difference between Gene Symbol and Gene Name?
Gene Symbol has the following characteristics :
- The only species in the species
- Short, 3-5 letters, no more than 10 letters
- Use only Roman letters and Arabic numerals
- Beginning with an uppercase letter followed by a lowercase letter or number
- Does not include tissue specificity or molecular weight
- Best to match the first letter of Gene Name
- Italic representation
- Homologous genes of different species use the same Gene Symbol
Gene Name generally has the following characteristics :
- Short, can be a few words, including gene functions or features
- First letter lowercase (except for names or proper nouns)
- Use American spelling
For example, you will understand, for example:
Shh is Gene Symbol, and sonic hedgehog is its Gene Name.
So, if you want to find a knockout strain for a gene, it's best to enter Gene Symbol instead of Gene Name or a previous name.
Here is a special mention of such situations where the point is over-expressed:
Two of the most commonly used site-specific overexpression sites, one Rosa26 site and one H11 site.
Rosa26 is a gene, so you can use its Gene Symbol, which is Gt (ROSA) 26Sor .
H11 is not a specific gene, but a specific chromosomal location between two genes, so there is no Gene Symbol. The currently accepted name is Igs2 , which stands for the abbreviation of intergenic site 2.
Modification method (superscript)
- Tm
For the ES cell targeting pathway to obtain the line, tm is used to indicate the targeted mutation. - Em
For genetically modified strains mediated by nuclease systems such as CRISPR/Cas9 or Talen, em is used to denote endonuclease-mediated mutation.
Number (superscript)
The number here refers to the serial number of the modified gene in the laboratory.
For example: Trp53 tm1Holl represents the first mutation of the Trp53 gene in Holl's laboratory.
Sometimes you will see tm1.1, tm1.2, which refers to the progeny mouse strain obtained from the conditional knockout (CKO) mice after mating with the germline recombinase tool mouse, in order to interact with the parental CKO. The mouse (numbered tm1) was distinguished. The progeny of the parental CKO mouse mated with other tissue-specific recombinase tool mice were not named separately.
Insert structure (superscript)
For gene knockouts and conditional gene knockouts, the part of the inserted structure is generally not included in the naming, ie, the number is followed by the laboratory code.
For example: Trp53 tm1Holl .
If there is a knock-in gene, the inserted foreign gene can be written in parentheses.
For example: Cd19 tm1(cre)Labcode indicates that the Cre gene is knocked into the Cd19 gene.
If you are typing RNAi, write the target for RNAi in parentheses.
For example: Gene tm#(RNAi:Il23a)Labcode .
Laboratory code (superscript)
The general laboratory code is an acronym for the name of the institution.
such as:
J represents The Jackson Laboratory;
Kyo stands for Kyoto University;
Smoc represents Shanghai Southern Model Creature; and so on.
Naming of random transgenic mice
The names of this type of mouse are basically the same:
The name Tg stands for Transgene.
Transfer gene
The parenthesis information of the transferred gene and Gene Symbol are filled in parentheses.
Numbering
Refers to the GM founder number or serial number prepared by the laboratory.
If a transposon system is used to prepare a transgenic mouse, the Tn is followed by a Tn, indicating a transposable element. Subsequent parentheses generally need to include: the abbreviation abbreviations used, and the constructed vector structure, both linked with a "-": TgTn(transposon_class_abbreviation-vector)#Labcode.
For example: B6.Cg-TgTn(sb-lacZ, GFP) IF2Jtak/JtakRbrc, where sb is an abbreviation for sleeping beauty.
Knowing the naming rules of genetically engineered mice, you may have to ask again, the name can not always write the full name every time? Indeed, we usually use abbreviated methods when describing the genetically engineered mice used in the article. How can I write it?
General abbreviations for genetically engineered mice
Gene knockout
Everyone is familiar with it. You can use the plus and minus signs to indicate wildtype allele and mutant allele:
KO homozygous Gene -/-
KO heterozygous Gene +/-
Wild type control Gene +/+ or WT (wildtype)
2. Gene knock-in
Write the typed component in the superscript, for example:
Shh gene E177A point mutation heterozygote: Shh E177A/+
If the Shh gene is knocked into the reporter gene or the Cre recombinase gene, it can be written as Shh EGFP/+ , or it can be directly written as Shh-EGFP and Shh-Cre.
3. Genetic modification
Generally write the expressed gene structure directly, for example:
Villin promoter Transgenic mice that drive the EGFP reporter gene can be expressed as Vil-EGFP.
4. Conditional gene knockout
Use flox as the superscript, for example:
CKO homozygous Gene flox/flox or Gene f/f
CKO heterozygous Gene flox/+ or Gene f/+
If a mouse with systemic knockout is obtained after mating with Cre or a germline-expressing Cre tool mouse, it can be abbreviated according to the rules of KO mice.
If mated with tissue-specific Cre mice, they can be combined to write: Gene flox/flox ; Cre.
If only one tissue-specific Cre tool mouse is used in the article, it can also be abbreviated as KO. Gene -/- can represent flox homozygous and Cre-positive mice.
If there are many different Cres, then you need to express them separately.
For example, homozygous mice in which Tlr5 flox mice are knocked out with progeny of small intestinal epithelial cells (IEC)-specific Cre (Vil-Cre) and DC cell-specific Cre (CD11c-Cre) can be expressed separately. For Tlr5 flox / flox; Vil-Cre and Tlr5 flox / flox; CD11c-Cre. If you think that this is too much trouble, you can also say: Tlr5 ΔIEC and Tlr5 ΔDC .
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