Specialized Chromosomes and Their Uses in Caenorhabditis elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 48

wormbase.org ) . Genome sequencing can identify CNV as well as base pair differ-
ences and can therefore potentially identify all genomic alterations in a rearranged
chromosome regardless of type or complexity.

1. Advantages and Disadvantages
The major advantage of genome sequencing is the ability to rapidly and accurately
accumulate a complete sequence analysis of the entire spectrum of alterations in the
genome, something that has not previously been possible. The technology is evolv-
ing rapidly making this approach much more accessible to individual researchers.
However, one still needs to have access to high-level bioinformatic analysis in order
to interpret the data. This is though a very powerful approach, providing a compre-
hensive view of the genome and may become increasingly accessible for analysis of
SCs in the near future.

IV. Engineered Constructs: Transgenic Arrays

A. Experimental Applications of Transgenic Arrays
Transgenic arrays have been used for a range of research purposes including, but
not limited to, discovery of the molecular identity of a mutated gene and cloning it by
rescue of the mutant phenotype, study of overexpression or ectopic expression of
genes, manipulation and investigation of gene structure and function, discovery and
analysis of cis-acting regulatory motifs and their trans-acting control factors, and
creation of tagged proteins for specific manipulation or study. In addition, they can
be used in genetic screens and for mosaic analysis. In this section, we will highlight
how transgenic arrays have been used for C. elegans research as well as the various
techniques and approaches available for the generation and manipulation of these
arrays.

1. Mutant Rescue

Rescuing a mutant phenotype is one of the most common uses of transgenic arrays
in C. elegans research. Rescuing arrays contain a wild-type copy of the gene of interest.
Libraries of both cosmid ( http://www.sanger.ac.uk/technology/clonerequests/ ) and
fosmid ( http://elegans.bcgsc.bc.ca/ ) clones exist and these resources can be mined
for a suitable clone containing the genomic fragment of the gene of interest including
its surrounding promoter elements. Cosmids and Fosmids generally work well for
mutant rescue because they contain a relatively large amount of DNA (35 kb) and are
therefore likely to contain all the enhancer elements required for faithful expression of
the gene ( Tur sun et al., 2009 ). Full-length cDNAs can also be used for rescue exper-
iment, though the cDNA will need to be cloned into a vector containing a suitable
promoter. This type of construct is useful when the gene spans a large genomic region
or for genes for which no other genomic clone is available. Alternatively, a