Specialized Chromosomes and Their Uses in Caenorhabditis elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 47

C. Inverse PCR

In the case of a balancer in which the location of one breakpoint has been mapped
to a small region of the genome that information can be used to perform inverse PCR
of the rearranged chromosomes. This approach will identify the remaining break-
point position. In the case for eT1, which breaks in unc-36 (III), PCR across the 7 kb
long gene was used to locate the chromosome III breakpoint to a 450 bp interval.
Inverse PCR was subsequently used to identify the sequence of the fusion between
chromosome III and chromosome V ( Zhao et al., 2006 )( Fig. 9 ). This information
was useful for developing a PCR assay to rapidly identify the eT1 chromosomes in
genetic crosses ( Zhao et al., 2006 ).

D. Whole Genome Sequencing
Advances in sequencing technology have made whole genome sequencing experi-
ments feasible. There are a growing number of C. elegans whole genome sequences
available ( Hillier et al., 2007, 2008; Rose et al., 2010 ), in addition to the canonical
assembled and aligned sequence in WormBase ( Harris et al., 2010 )( www.

Fig. 9 iPCR scheme is used to isolate eT1 breakpoint. See text for details.