Deciphering nanoscale 3D genome-organization in single cells using super-resolution imaging

Faculty : Mohit Kumar Jolly (BSSE) and Mahipal Ganji (BC)

In this project, we will investigate the interrelation between the 3D position of genes relative to the nuclear bodies and epigenetic marks and their transcriptional activity is lacking. The project will utilize the DNA-PAINT super-resolution approach – a microscopy technique that uses barcoded DNA sequences for imaging many targets – to obtain the nanoscale distribution of many genes and their transcriptional levels, nuclear bodies, and epigenetic marks in single-cells. Each gene body and its mRNA species will be in-situ hybridized with oligonucleotides containing a unique sequence-signature. Furthermore, nuclear bodies and epigenetic marks will be immunolabeled with DNA-barcoded antibodies. As each component’s identity is encoded into the unique DNA sequence-signature, individual components’ positions in the nucleus can be determined with an ultra-high-resolution (~10 nm) using Exchange-PAINT. We propose to adopt a multiplexed encoding scheme to image hundreds of nuclear components within only a few rounds of imaging. Analysis of such systems-level data will enable us to dissect the underlying principles of functional genome-organization in its native-state.