Project Summary
Chromosome breakage can generate extraordinary genetic novelty that is selected upon during
tumor progression. One commonly observed feature of cancer is the breakage-fusion-bridge
(BFB) cycle, where double-strand breaks set off a chain reaction that leads to copy number
variations and complex chromosome shattering events. The BFB cycle was first described in
maize by Barbara McClintock in the 1940s, and led to the discovery of transposable elements
(TEs). Two types of TEs, Activator/Dissociation (Ac/Ds) and Suppressor-mutator (En/Spm),
burst from her BFB samples, leading her to hypothesize that chromosome breakage can lead to
a genome-wide response she called “genome shock”. Her observation that BFB activates
previously dormant transposable elements suggests that major epigenetic changes accompany
BFB, likely compromising DNA methylation and heterochromatin. DNA demethylation and TE
activation are also observed in many cancers, but causal relationships between BFB and
demethylation have not been clearly established. Unlike in animals, maize tolerates the
transmission of major chromosomal abnormalities through gametogenesis, greatly facilitating
downstream studies. We have developed a system for inducing the BFB cycle in maize and
demonstrated its ability to induce genetic instability and large chromosomal abnormalities. In our
approach, an array of LexO repeats inserted on a chromosome arm is combined with a LexA-
CENH3 transgene and initiates a second centromere. With long read sequencing and ChIP-seq
assays, we will analyze the genomic and epigenomic changes that follow BFB over multiple
generations. We will also deploy high-sensitivity screens for TE activation. These approaches
will allow us to test at the molecular level the extent to which genome reordering by BFB leads
to genetic and epigenetic changes in otherwise wild type genetic backgrounds. The proposed
research will establish a new model for investigating BFB in complex eukaryotes and provide
greater insight into how the BFB cycle impacts epigenetic processes that have the potential to
further destabilize the genome. In addition, the work will provide a direct test of the genome
shock hypothesis, which has provided an important guidepost for interpreting the chromosome
rearrangements in cancer as well as hundreds of other genome restructuring events in animals,
plants, and fungi.