Oligopaints
One of the main approaches I use in my research is Oligopaint DNA FISH (originally developed in Ting Wu’s lab at Harvard). Unlike BAC-based FISH probes, Oligopaints are computationally designed probes based on genomic sequence. This allows for only unique, single copy sequences to be labeled, significantly increasing the specificity and resolution of FISH. The flexibility and scalability of the Oligopaint design pipeline can be leveraged to generate chromosome paints for any species with a sequenced genome. These paints can then be used to image chromosomes or sub-chromosomal regions in any tissue type, cell cycle stage, or developmental stage of interest to address fundamental questions of chromosome organization and cell biology.
More information about Oligopaints can be found at the following sites:
Genomics
In addition to imaging-based approaches, my research takes advantage of genomics technologies such as Chromatin immunoprecipition (ChIP)-seq, RNA-seq, and Assay for Transposase-Accessible Chromatin (ATAC)-seq. Moving forward, I will also incorporate genomics approaches that use proximity-ligation to measure 3D genome interactions in cell populations, like High-throughput Chromosome Conformation Capture (Hi-C). Together, these approaches allow me to map architectural protein binding sites throughout the genome and directly correlate this with 3D chromatin organization and gene expression. By combining these tools with the single-cell nature of microscopy, I am able to gather a more complete picture of chromatin organization and function.
Hi-C image above published in Rosin et al., 2019, eLife
Live Imaging
In addition to fixed imaging techniques, my future work will employ live imaging approaches. While the snapshots obtained by imaging fixed cells can provide a lot of information, live imaging allows cell dynamics to be captured in four dimensions.