Specialized Chromosomes and Their Uses in Caenorhabditis elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 30

Specialized chromosomes also have an accepted nomenclature. Df for deficiencies
or deletions that are known to affect multiple genes, Dp for duplications, T for
translocations, In for inversions, and C for crossover suppressors (of unknown struc-
ture). Extrachromosomal transgenic arrays are designated Ex, while transgenic con-
structs that are inserted into a chromosome are designated Is. Transgenes integrated
by a recently developed transposon-based method, MosSCI ( Frokjaer-Jensen et al.,
2008 ), are designated by the two letters Si. Full names include the laboratory allele
prefix, the two letters, and a number. For example, a MosSCI insert from the
Jorgensen lab(ox) will be named oxSi31. As for alleles, the name is preceded by
the small letter italic designation of the originating laboratory. If the SC carries a
mutation in a known gene, the gene is described using square brackets following the
SC name, for example, the reciprocal translocation eT1, which has a breakpoint in
unc-36 (III), is eT1[unc-36] (III;V). The components of a reciprocal translocation can
be identified by their pairing properties. Chromosome identity in C. elegans is
defined by the end of the autosome that pairs with its homolog and that contains a
pairing center, also known as the homolog recognition region (HRR) ( McKim et al.,
1988b ). Thus, eT1 (III) pairs with the normal chromosome III, and eT1 (V) with the
normal chromosome V. In some cases, half-translocations can be maintained as
extrachromosomal duplications and may in these cases be given a Dp designation.
For example, a half-translocation from the reciprocal translocation hT1(I;V) that was
isolated in the Rose laboratory at the University of British Columbia (h), recombines
and segregates from chromosome I. It can be maintained as a duplication of regions of
chromosomes I and V in addition to the normal diploid complement and has been
designated hDp133, rather than the precise but more cumbersome hT1(I R V L ).
These standardized nomenclature guidelines have been modified and adopted to
describe genetic constructs marked with a reporter gene; the most commonly used is
the green fluorescent protein (GFP) ( Chalfie et al., 1994 ). In these cases, double
colons are used to indicate the covalent linkage to the reporter, for example, a
promoter engineered to connect 5 0 to a GFP is written promoter::GFP.
II. Chromosomal Rearrangements
Gross rearrangements refer to chromosomes that involve an extensive alteration
to the content or structure of the genome. Such rearrangements can arise naturally,
although many have been engineered purposefully by the use of mutagenesis.
Translocations, inversions, duplications, and deletions all fall into this category
and each have specific properties that make them useful for a variety of housekeep-
ing tasks and experimental approaches in C. elegans research.
A. Translocations
Translocations involve the displacement of a segment of DNA from one region of
the genome to another. Consequently, nonhomologous DNA aligns during meiotic