PT  - JOURNAL ARTICLE
AU  - Brandon Fields
AU  - Son C. Nguyen
AU  - Guy Nir
AU  - Scott Kennedy
TI  - A Multiplexed DNA FISH strategy for Assessing Genome Architecture in <em>C. elegans</em>
AID  - 10.1101/397471
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 397471
4099  - http://biorxiv.org/content/early/2018/08/22/397471.short
4100  - http://biorxiv.org/content/early/2018/08/22/397471.full
AB  - Eukaryotic DNA is highly organized within nuclei and this genomic organization is important for genome function. Fluorescent in situ hybridization (FISH) approaches allow the 3D architecture of genomes to be visualized. Scalable FISH technologies, which can be applied to whole animals, are needed to help unravel how genomic architecture regulates, or is regulated by, development, growth, reproduction, and aging. Here, we describe a multiplexed DNA FISH Oligopaint library that targets the entire C. elegans genome at chromosome, three megabase, and 500 kb scales. We describe a hybridization strategy that provides flexibility to DNA FISH experiments by coupling a single primary probe synthesis reaction to dye conjugated detection oligos via bridge oligos, eliminating the time and cost typically associated with labeling probe sets for individual DNA FISH experiments. The approach allows visualization of genome organization at varying scales in all/most cells across all stages of development in an intact animal model system.