FlyBase:Nontraditional alleles

G.1. Nontraditional alleles

In addition to 'alleles' in the traditional sense, FlyBase now names and curates further classes of allele so that phenotypic or expression pattern data can be captured for in vitro construct alleles and alleles of reporter (e.g., Ecol\lacZ), effector (e.g., Scer\FLP) or toxin (e.g., Rcom\DT-A) genes. Since these alleles have not historically been named by researchers, and have been named by FlyBase, their presentation in FlyBase requires some explanation:

G.1.1. Alleles of reporter genes

Alleles of reporter genes currently fall into two main classes, those resulting from enhancer trap experiments, and those resulting from promoter (or other regulatory region) analysis, where a fragment is used to drive the expression of a reporter gene. Ecol\lacZ will be used for illustration.

Enhancer trap results:

• The enhancer trap construct causes an allele of a gene and is expressed in a pattern consistent with insertion in that gene. The resulting insertion will be described with the format P{A92}hL43a, and the Ecol\lacZ allele symbol is of the format Ecol\lacZ^h-L43a.
• The reporter gene reflects the expression of a gene without causing a mutant allele of that gene. The resulting insertion will be described with the format P{PZ}P2023-44, where P2023-44 reflects the insertion identifier, and the Ecol\lacZ allele symbol is of the format Ecol\lacZ^hh-P2023-44.
• The reporter gene reflects the expression of an undescribed gene/enhancer. The resulting insertion will be described with the format P{lacW}1.28, and the Ecol\lacZ allele symbol is of the format Ecol\lacZ^1.28.

Promoter analysis results:

• Generally some fragment of a gene promoter/intron/3'-region is fused to the reporter gene. In this case the allele symbol is of the form 'gene symbol.fragment descriptor' e.g., Ecol\lacZ^eve.prox54. The fragment descriptor reflects that used in the publication, even though this may be long and cumbersome (this may not be strictly true for such alleles curated early in the FlyBase project).
• Where a reporter gene is simply described in a publication as being driven by, e.g., an arm promoter, the symbol of the Ecol\lacZ allele is 'arm.PI', where I is the first letter of the surname of the first author of the paper, e.g., Ecol\lacZ^arm.PV for 'Ecol\lacZ arm promoter construct of Vincent'.
• For logistical reasons some promoter fusions involving reporter genes such as Ecol\lacZ, though technically protein fusions, are simply treated as alleles of the reporter gene. The symbol for the additional gene(s) contributing to the fusion is indicated as part of a superscript, e.g., Ecol\lacZ^P\T.A92. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name.

G.1.2. Alleles of ectopically expressed Drosophila gene products

Products of genes may be ectopically expressed due either to juxtaposition with different regulatory sequences in the genome (as a result of being inserted into different-than-wild-type locations by chromosome rearrangement or P element transposition) or due to in vitro construction creating a different constellation of regulatory sequences than in wild type.

By analogy with alleles of Ecol\lacZ for enhancer traps, P-element-borne insertions of genes e.g., w or ve that have a qualitatively distinct _position-dependent_ mutant phenotype will be curated as new alleles of e.g., w or ve, e.g., veStg caused by a particular insertion of P{HS-rho}, P{HS-rho}Stg.

The 'in vitro construct' ectopic expression alleles currently fall into two main classes, one component or two component systems:

One component systems:

• Gene A is expressed from a promoter of gene B. The allele is typically generated by in vitro construction. In such cases the allele symbol is of the format 'gene-A^gene-B.PI', e.g., phyl^sev.PC or 'gene-A^{gene-B.fragment descriptor}' where the author includes a promoter fragment descriptor, e.g., phyl^ninaE.GMR.
• An occasional exception is made for promoter fusions that are widely used to provide essentially wild-type gene function; these alleles have the mini-gene '+m construct' designation (see below) prepended to an, e.g., heat shock designation, e.g., w^+mW.hs.
• It is common that authors report a construct where e.g., ftz is expressed under a 'heat shock' or Hsp70 promoter, while providing no further details about the nature of the promoter. For these cases the allele symbol hs.PI is employed, e.g., Ant^phs.PZ for 'Antp heat shock construct of Zeng'. An 'hs' designation should be reserved for when the heat inducible, not just the minimal, promoter fragment is used.
• Where the allele is both altered in its coding region and being expressed from an ectopic promoter the sequence 'alteration.promoter' is used in the allele designation, e.g., tor^13D.hs.sev to denote the coding sequence of tor13D expressed from a heat shock (undefined) promoter with a sev enhancer. An exception to this rule is made for Tags, which appear as the last component of the allele symbol (see below).

Two component systems:

• GAL4-UAS The allele symbol for the gene whose expression is dependent upon Scer\GAL4 shall include 'Scer\UAS' and an identifier. The identifier should reflect the construct as named by author e.g., l(1)sc^{DeltaB.Scer\UAS}. In the absence of any other identifier '.cIa' is used, where 'c' stands for construct, I for the first author's last name initial and 'a' for the first in the series (subsequent ones will be b, c, etc). e.g., ase^Scer\UAS.cBa for 'Scer\UAS construct a of Brand'.
• FLP-FRT Alleles of Scer\FLP are named as outlined above for reporter genes, and allele symbols of genes whose expression is dependent upon that of Scer\FLP include 'Scer\FRT'.

G.1.3. Alleles of ectopically expressed non-Drosophila effector products

A note on ribozymes: FlyBase has a foreign ribozyme gene, symbol LTSV\RBZ. Alleles of LTSV\RBZ capture the different variants, e.g., for a heat inducible ftz-targeted ribozyme: LTSV\RBZ^hs.ftz (syntax 'promoter.target gene') will be named.

'+m' minigenes

The minigene allele designation is used in its narrow sense, i.e., where the only difference between the allele and the wild type is the removal of more or less non-essential sequences. Thus the minigene allele symbol designation reserved for those cases where the gene's own promoter is driving its expression.

The minigene allele symbols begin with 'm', for minigene, and are followed by the construct symbol used in the publication. If no construct symbol has been used, the string 'mIa' where 'm' stands for minigene, 'I' for the first author's last name initial and 'a' for the first in the series is used. If the function of the minigene is stated to be indistinguishable from that of the wild type allele, the 'm' is preceded by a '+'.

Tags

Genes can be modified by the addition of a tag allowing the product to be identified, purified, or targeted to a particular subcellular distribution. Tagged alleles have the syntax 'gene-symbol x.T:y' , where x is an identifier and y is the name of the tag, e.g., Hsap\MYC, T:Ivir\HA1, SV40\nls2, e.g., dap1gm.T:Hsap\Myc. Where a tag is artificial, the species prefix Zzzz is used, e.g. T:Zzzz\His6.

G.1.4. Classical alleles engineered into transgene constructs, including rescue constructs

A class of alleles are named to capture fragments of genomic DNA used in rescue constructs. The symbol for the rescuing allele symbol begins with '+t'. This is followed by length as stated by authors, construct symbol if length is not given or '+tIa', where 't' stands for transgene, 'I' for the first author's last name initial and 'a' for the first in the series (if neither length nor construct symbol is stated). When rescue is incomplete, the construct is considered as carrying a mutant allele. Allele designator is construct symbol, 'length of genomic insert.tIa' if no symbol is given or 'tIa' where neither length nor construct symbol is stated.

When a classical allele, e.g., w^a, is put into a transgene construct it will get a new designation, e.g., w^a.tIa, to reflect its transgenic environment, where 't' stands for transgene, 'I' for the first author's last name initial and 'a' for the first in the series

FlyBase is, of course, happy to discuss and advise on use of nomenclature of these non-traditional alleles.