1Present and 2Past WormBase Gene Name Curators.
New methods for genome engineering (TALENs, CRISPR-Cas9, etc.) are increasingly being applied to C. elegans. These entail some additional recommendations to the standard Genetic Nomenclature Guidelines (http://www.wormbase.org/about/userguide/nomenclature), as described below. The aim is to provide compact and unambiguous ways of describing and referring to engineered changes to endogenous loci, as distinct from transgenic constructs that are inserted elsewhere in the genome.
Each engineered modification to an endogenous locus (point mutations, deletions, insertions or combinations thereof) should receive a unique allele designation, using the standard allele designation of the originating laboratory. For example: bus-50(e5000).
Optional brackets can be employed to provide additional information.
Example: bus-50(e5000[T110E]) (an engineered missense mutation).
An engineered fusion of GFP to the C-terminus of BUS-50 would be:
As a shorter and more convenient form, and where unambiguous, this could be referred to as:
bus-50::gfp. Such abbreviations should be clearly defined where first used in a paper.
An engineered insertion of GFP plus the unc-119(+) selectable marker, flanked by loxP sites, would be:
bus-50(e5002[bus-50::gfp + loxP unc-119(+) loxP]).
Each additional engineering of the endogenous locus requires a new allele number. In the example of bus-50(e5002), following Cre-mediated recombinase removal of unc-119(+) so that a single loxP site remains, the new genotype would be bus-50(e5003[bus-50::gfp +loxP]) or bus-50(e5003) for short.
Engineered insertions in apparent intergenic regions are given standard Is insertion names, for example eIs2002. Optional descriptors can include the nature of the insertion, e.g., [unc-119::gfp] and the position in the genome, e.g., [III:2992500], to give eIs2002[unc-119::gfp] or eIs2002[unc-119::gfp, III:2992500].
Engineered changes to existing Is (or Si) insertions should receive new Is numbers using originating lab’s prefix. The original Is insertion can be indicated in brackets with a preceding asterisk (*), in order to allow searches for all derivatives from a given insertion.
For example, an engineered change from GFP to mCherry in eIs2002 might be named as ozIs909, or ozIs909[unc-119::mCherry *eIs2002].
Articles submitted to the Worm Breeder's Gazette should not be cited in bibliographies. Material contained here should be treated as personal communication and cited as such only with the consent of the author.
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