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Xenopus gene nomenclature

Working guidelines for naming transgenic constructs, and transgenic and mutant Xenopus lines

Standard nomenclature is critical to make your research accessible to the broad scientific community and to ensure reproducibility, consistency and provenance. These working nomenclature guidelines were developed in consultation with the Xenopus stock centers, the NXR and EXRC, following best practices used by all other model organisms. Brevity and clarity are strongly encouraged when naming the transgenic construct and its subsequent Xenopus lines. Transient lines, i.e., those that are not maintained or supplied, do not need these formal names.
  • Transgenic Constructs: Overview
    • STANDARD Tg CONSTRUCT NAME

      Tg(enhancer or promoter:ORF or gene symbol)
      Example: Tg(cryga:GFP) A transgenic construct with gamma crystallin (cryga) driving enhanced GFP Example: Tg(Rno.elas:DNthra-GFP) Tg construct with Rat elastase promoter driving dominant negative thyroid hormone receptor, fused to GFP.
    • Tg indicates transgene, and the entire construct name is italicized.
    • The most salient features of the transgene should be described within parentheses, no spaces.
    • List regulatory sequences to the left of colon ( : ) and coding sequences to right.
    • Use the official gene symbol and lowercase for Xenopus genes (e.g., tubb2b not NBT).
    • Fluorescent proteins are capitalized or start with a capital letter (e.g., GFP, Katushka, Tomato), and prefixes are generally in lower case (e.g., eGFP, mCherry, dEGFP) - don't underline.
    • Hyphens ( – ) indicate fusion proteins (do not use equals sign = or double colons ::).
    • Modified functionality (e.g., CA = constitutively active, DN = dominant negative) is indicated as prefix to gene symbol, (e.g., DNthra).
    • Responsive elements (REs) are indicated after gene or gene family symbol (e.g., TRE, WntREs).
    • Where gene sequence(s) from another species are used, precede gene symbol with 3-letter species code, and a period, then gene symbol. Species codes are Hsa= human, Rna= rat, Dre= zebrafish, Mmu= mouse. e.g., Tg(Hsa.UBC:Gal4).
    • Where one promoter drives two or more coding sequence, separate coding sequences with a comma ( , ) e.g, Tg(CMV:eGFP,RFP)).
    • Multiple cassettes are separated by a semicolon ( ; ) not a comma** (e.g, Tg(tubb2b:GFP;NBTtau:GFP). (**Note: this is a change from previous version of guidelines).
    • Omit spaces to keep the name as a single computer-readable 'word'.

    • What not to include in a Tg construct or line name (but do include these details in a full description):
    • Engineered sequences (e.g., GFP, Cre, rtTA, tetO) do not need foreign/bacterial species prefixes, as these are widely understood.
    • Omit construct multipliers (e.g., 7x), names of modified clones (e.g., BAC, PAC), or targeting vector (e.g., FLP or LOX sites).
    • Omit method used for transgenesis (e.g., sperm-mediated, pTransgenesis, REMI).
    • Do not include the size of the promoter, enhancer, or cis-regulatory sequence (e.g., 1.5kb), rather report this in the full description of the transgene, or add as superscript number to distinguish similar lines.
    • Do not include RRID (i.e., stable research identification numbers).
  • Transgenic Xenopus Lines: Overview
    • STANDARD Tg XENOPUS LINE NAME

      Species.Tg(enhancer or promoter:ORF or gene symbol)Lab code
      Example: Xtr.Tg(cryga:GFP)NXR A X. tropicalis Tg line carrying a gamma crystallin GFP construct, made by the NXR Example: Xla.Tg(Rno.elas:DNthra-GFP;cryga:GFP)Brown A Brown lab X. laevis (Xla.) line with 205bp rat (Rno) elastase (elas) promoter driving dominant negative (DN) thyroid receptor alpha (thra) (also known as TRDN) fused ( - ) to GFP, and carrying a gamma crystallin (cryga) GFP cassette as marker of integration.
      Example: Xla.Tg(Xtr.lmo2:Katushka;cryga:Venous)EXRC This Tg X. laevis line carries a 4755bp X. tropicalis sequence for lmo2 promoter driving the red fluorescent protein, Katushka, and a second cassette as marker for integration, gamma crystallin (cryga) driving Venus expression in lens, and was made by the EXRC.
    • Each maintained/supplied Tg Xenopus line is given an official, stable name that is based on the Tg construct(s) used (outlined above), with the following additions:
      • Species is indicated using a previx, using a 3-letter code, followed by a period ( . ).
      • Xla is the abbreviation for X. laevis
        Xtr is the abbreviation for X. tropicalis
        
      • Each line should be fully described, including background strain, RRID number and generation number, if known.
      • Indicate Lab of origin using a ILAR lab code, in superscript, following parentheses.
      • When a sequence of the alternate Xenopus species is used i.e., a X. laevis line that carries a construct made with X. tropicalis sequence, indicate this within the parentheses using the 3-letter abbreviation, as is done for other foreign species genes.
      • Serial numbers before Lab code are generally unnecessary, but can be used in some circumstances (see notes about serial numbers, below).
  • Mutant Xenopus Lines: Overview
    • STANDARD MUTANT XENOPUS LINE NAME

      Species.gene symbol or phenotypemutation typeLab code
      Example: Xtr.frzb,frzb2tmHorb A doudle CRISPR knockout of frzb and frzb2 by the Horb Lab. Example: Xla.fxr1tmHorb X. laevis line with CRISPR targeted mutation in fxr1 gene, made by the Horb Lab. Example: Xtr.nopmKhok or Xtr.hps6nopKhok or Xtr.hps6mKhok All three of these names are good names. Called ‘no privacy’ (nop) because embryos had a transparent phenotype, this mutant line was originally bred in Lyle Zimmerman’s lab at NIMR/MRC. The colony is now maintained and supplied by the Khokha Lab. The location of the ‘no privacy’ mutation was later found to be a 10bp deletion in the hsp6 gene, so the line can also be named using the gene symbol, with an ‘m’ to indicate a ‘mutation’ in hps6, or with the ‘nop’ in the superscript.
    • Each maintained or supplied mutant Xenopus line is given an official, stable name following these basic rules:
    • Species is indicated using a 3-letter code, Xla or Xtr, followed by a period.
    • The line is named after the location of the mutation, in italics, with no spaces.
      • If location is known, use gene symbol (e.g., Xla.fxr1tmHorb)
      • If location is unknown, use abbreviated phenotype or common name (e.g., Xla.nopmKhok)
    • Indicate double knockouts by separating gene symbols with a comma ( , ).
    • The mutation type is indicated in superscript, followed by ILAR lab code
      • i.e. m=mutation, tm=targeted mutation (e.g. CRISPR), ins=insertion, del=deletion.
    • Serial numbers, in prefix before Lab code, are generally unnecessary, but can be used in some circumstances (e.g., Xtr.Tg(cdknx:GFP)Papal, Xtr.raxtmHorb (see notes below).

    • Note on using serial numbers: Change in rule
    • Serial numbers are generally unnecessary, but can be used in some cases to:
    • distinguish lines with the same Tg but with different phenotypic characteristics (e.g. due to unknown transgene integration event).
    • distinguish lines with the same Tg construct but in different genetic background.
    • identify which non-interbreeding colony of a particular line is supplied/used.
    • distinguish between lines with constructs effecting the same gene, but where the changes within the construct may be too small, incremental, or too complex (e.g., serial deletions, different sized inserts) to fully capture in a name.
    • Example:    Xla.Tg(Dre.noto:GFP)1Amaya, Xla.Tg(Dre.noto:GFP)2Amaya
      These X. laevis lines have GFP expression in the pineal gland and notochord. ‘1Amaya’ was developed in a pigmented J-strain background, and ‘2Amaya’ in albino J-strain frogs.
      
      *Example:    Xla.Tg(foxi1:Katushka)1.5EXRC and Xla.Tg(foxi1:Katushka)6EXRC
      EXRC maintains two Tg X. laevis lines with different upstream promoter sequences for the same gene, called ‘1.5foxi1:Kat’ and ‘6.0foxi1:Kat’. Using the sequence length as a serial number would succinctly identify which lines is being used/discussed. 
      
      *Example:    Xtr.apctm1NXR and  Xtr.apctm2NXR
      The NXR made 2 lines of X. tropicalis apc mutants, using CRISPR, targeting different regions of the gene. Full details of CRISPR target location, guide RNA sequence and potential phenotypic or functional differences will be in description of the line. 
      
      *Example:    Xtr.Tg(mlc3:GFP)1EXRC and  Xtr.Tg(mlc3:GFP)2EXRC
      A stock center needed to re-establish a popular Xtr.Tg line from frozen gametes after the colony died, hypothetically, after water heaters failed in a flood.  Frogs from the original colony were called Xtr.Tg(mlc3:GFP)EXRC which were supplied for 7 years (2010-2017). The newly bred, 2nd colony is now called Xtr.Tg(mlc3:GFP)2EXRC, supplied from 2018-onwards. If another lab bought and maintains the earlier animals, they keep the original name, Xtr.Tg(mlc3:GFP)1EXRC, and the lab can record generation number they use (e.g., F5).
      
      *hypothetical examples
      

Last Updated: 29th August, 2018

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