The major feature that stands out in the nucleus of all metazoan genomes are the chromosome territories (CTs), which have nonrandom radial positions that are conserved through evolution. We are using our custom Oligopaint FISH probes to identify signatures of chromosome arrangement across different cell cycle stages, tissues, and developmental time points in both Drosophila and mammalian cells.

Our approach leverages the flexibility and scalability of Oligopaints to generate low-cost chromosome paints for systematic analyses of chromatin folding and positioning. Typically, studies of chromosome positioning have been stymied by the lack of affordable, high-resolution FISH probes, which are usually targeted to only a few loci at a time. Moreover, not only are conventional technologies not a practical source of probe for use in high-throughput methodologies, they fall short of revealing the location of whole chromosomes or specific sub-chromosomal regions in interphase nuclei. In contrast to conventional approaches, Oligopaints are computationally designed, synthesized on microarrays, and generated via PCR amplification. This strategy provides precise control over the sequences they target and allows for multicolor imaging of regions ranging from a few Kb to whole chromosomes with the same basic protocol. Our previous work generated Oligopaints to the entire unique portion of the Drosophila genome in a chromosome arm-specific manner. Our experiments allow us to integrate levels of chromatin compaction, chromosome intermingling, and the epigenetic state of large domains in a single-cell and genome-wide manner. Using this approach, we are dissecting the contributions of putative architectural proteins to the radial positioning and folding of chromosomes as well as their function in genome integrity.

Oligopainting the Human Genome

More recently, we have also synthesized Oligopaints to three entire human chromosomes – chr18, 19, and 22 – in an effort to paint the entire the human genome. These paints are renewable, cost-effective, and versatile as they can be amplified to specifically label different 3D chromatin features (TADs, compartments, chromatin states etc.). Proper targeting of sequences to their respective chromatin environment is necessary for genome stability and gene regulation. These expanded high-resolution chromosome paints allow us to better visualize epigenome organization across individual chromosomes and study the regulation of architectural proteins and their effects on nuclear, cellular, and physiological phenotypes.

human paintsHumanCTs.

Please contact us if you would like to contribute to this effort by nominating and contributing to the synthesis of additional chromosomes.