Imaging gene regulation in live cells
We developed a method capable of discriminating specific DNA binding events at endogenous diploid allele sites from non-specific macro-molecular interactions in single-living embryonic stem cells (Chen, 2014); Following this direction, my lab further devised live-cell super-resolution assays to characterize the process by which transcription factor forms aggregates and hops between clustered binding sites in living cells (Li, 2016; Liu, 2018). These imaging strategies were widely used in the scientific community to probe biological processes in live cells. Through collaborations, we analyzed live-cell dynamics of CRSPR/Cas9, B-cell activation, MeCP2 and its Rett syndrome mutations, TF phase condensates, 'chemigenetic' sensors and ecDNAs.
3D genome organization
Another area that we focus on is to develop tools to study 3D genome architecture in the nucleus. To date, genome organization mechanisms have been largely investigated by genomic methods (e.g. Hi-C, 4C, 5C) derived from chromosome conformation capture (3C) assays. Due to population averaging, these methods are obscured from true 3D physical structures in the nucleus. We developed two super-resolution imaging methods to address this limitation. The first method utilizes live-cell 3D single-molecule localization by lattice light-sheet microscopy and residence-time thresholding to systematically map stable TF binding sites in single live cells (Liu, 2014). The second method – 3D ATAC-PALM combined ATAC (Assay for Transposase-Accessible Chromatin) with lattice light-sheet PALM microscopy to selectively image 3D nanometer-scale structure of the accessible genome in single cells (Xie & Peng, 2020). Coupled with chemical and genetic perturbations, these methods enabled investigation of molecular identities and interactions contributing to the formation and maintenance of 3D genome organization. For example, we found that Yap protein condensates induced by hyperosmotic stress promote de novo formation of accessible chromatin clusters in the nucleus (Cai, 2019). By analyzing auxin induced degron cell lines, we found that genome architectural protein CTCF decompacts accessible chromatin (Xie & Peng, 2020). On the contrary, Cohesin prevents spatial mixing of the accessible genome by counterbalancing chromatin-state specific affinity interactions mediated by Brd2 (Xie & Peng, 2022).
3D Sox2 Enhancer Clusters
Animal development and disease model
Our lab has a long standing interest as well as extensive experience in probing gene regulation during cell differentiation and animal development using both genomics and imaging approaches (Liu et al, 2012, Lolas et al, 2014). Currently, we are developing spatial multi-omics imaging techniques to further scale up and extend our research in vivo and into relevant disease models.
Risk-taking: We encourage lab members to explore their own ideas and turn their side projects into vertical breakthroughs in science (e.g. Ioannou, 2019).