Looking at Chromosomes

Our studies of genome organization have led us in a number of directions, including super-resolution imaging of the genome, Hi-C analysis of homolog pairing, and computational analysis of sequence ultraconservation. Regarding imaging, we have developed an approach that enables the tracing of megabases of the human genome at super-resolution using sequence-specific fluorescent in situ hybridization Oligopaint probes and single-molecule localization microscopy (OligoSTORM and OligoDNA-PAINT). Here, we have observed the 3D organization of chromosomal regions contributing to loops, contact domains, and compartments and, using homolog-specific Oligopaint (HOP) probes, have further observed differential packaging of maternal and paternal chromosomal regions. Then, through integrative modeling of genomic regions (IMGR), we have combined our images with Hi-C contact data to generate 3D models of homologous chromosomal regions. Regarding Hi-C analysis of homolog pairing, we have examined both hybrid Drosophila embryos and a newly established hybrid Drosophila cell line to elucidate the structure of homolog pairing and how that pairing accommodates cis interactions in a manner that is correlated with gene expression. Time-permitting, this presentation will also touch on sequence ultraconservation and how its potential underlying mechanism may contribute to the maintenance of genome integrity. This work has benefitted from several collaborations and funding (for the Wu laboratory) from the William Randolph Hearst Foundation to RBM, EMBO (ALTF 186-2014) to JE, and NIH (DP1GM106412, R01HD091797-03, R01GM123289-02) to C-tW.