After some discussion with various people working on cloned Mu elements, I suggest the following system of nomenclature for discussion. This nomenclature is directed at giving specific names to individual cloned Mu elements cloned from various sites in the genome. Assigning each new Mu clone a specific name should increase the accessibility of the Mu literature to non-experts, in contrast to the "Tower of Babel" when each lab assigns its own names.
The Mu family of transposable elements is to include all DNA sequences with homology to a terminal inverted repeat of the cloned and sequenced Mu1 element from the Adh1-S3034 allele (Bennetzen et al., 1984, PNAS 81:4125; Barker et al., 1984, Nucl. Acids Res. 12:5955). This particular Mu element would retain the colloquial name Mu1, but all other elements would have descriptors added to indicate the length of the Mu element in kb, the laboratory of origin, and either the allele from which it was isolated or a numerical designation (order of recovery) in a particular lab. For example, Mu1 would have the specific name Mu1.4MF-Adh1-S3034. Individual derivative alleles of S3034 which retained the 1.4kb Mu element would be named as they are now by appending a letter designation: Mu1.4MF-Adh1-S3034a. Revertants in which the Mu element is now gone would be designated by an R placed at the end of the name.
If an element is cloned from a region of DNA that does not contain a known gene, the cloned element would be named for its size, the laboratory of origin, and a number, beginning with one, reflecting the order in which individual Mu elements at unknown locations were cloned by that laboratory. For example, Mu1.7VW-1 is the name of the first 1.7 kb Mu element cloned in our lab; it is from an unknown location.
If DNA hybridization studies indicate that a particular mutable allele contains a particular type of Mu element, but the Mu element has not yet been cloned, the mutable allele should be assigned a name based on current conventions, but the Mu element should be referred to simply as an element resident in the allele, for example, the 1.4kb element in bz1-mu1.
Based on what is currently known about the Mu family of transposable elements, size class designations of Mu1.4, Mu1.7, and Mu1.0 would be required. More classes could be conveniently added to take into account additional isolates that differ in their length. A special designation for the presence of just one Mu terminal inverted repeat end (with essentially no middle sequence) would be MuE-. Mu-homologous sequences cloned from non-Mutator standard lines of maize (lines lacking a high mutation rate and a high copy number of Mu elements) would be named for the line from which they were isolated, i.e. Mu1.4VW-B37.
This nomenclature does not imply that all elements of 1.4kb in length are identical. It requires that an element be cloned before it is named; this is done to avoid ambiguities that might result from examination of the restriction profiles of modified elements resulting in an erroneous assignment of size (see Chandler and Walbot, 1986, PNAS, in press). One potential difficulty is that two labs could independently isolate precisely the same Mu insert from related biological material. To aid in detecting such duplications, descriptions of the initial isolation of individual Mu elements should include a pedigree of the stock and a restriction map of the element and some flanking sequences.
This nomenclature does not indicate which elements are autonomous and which are defective, because the nature of the presumed autonomous element regulating Mu element activity is as yet unknown. Upon discovery the nomenclature might be revised to indicate autonomous and non-autonomous elements.
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