The genome stores, propagates and expresses genetic information. One big challenge in modern biology is to understand the genome spatial organization and temporal dynamics that instruct fundamental DNA-templated processes including the precise transcriptional regulation in development. As a postdoc in the Tjian lab and a visiting scholar at the Janelia research campus (hosted by James Liu’s group), I develop new molecular imaging tools and integrate multidisciplinary approaches (imaging, genomics, biochemistry and computation et al.) to address these challenges.

To globally visualize the 3D organization of cis-regulatory DNA elements at nanometer scale, I developed a super-resolution imaging method–3D ATAC-PALM in collaboration with James Liu’s group at Janelia Research Campus and Howard Chang’s group at Stanford (Xie et al. Nature Method, 2020, https://www.nature.com/articles/s41592-020-0775-2). This technology employs the hyperactive Tn5 transposase to insert photo-activatible Janelia Fluor 549 (PA-JF₅₄₉) labeled oligo probes into the accessible chromatin genome-wide and achieves precise 3D localization under the maximal photon budget by the Lattice light sheet microscopy. This method provides a new revenue to study the architecture, mechanism and function of the cis-regulatory genome in single cells (manuscript under preparation, also see Xie et al. biorxiv, https://www.biorxiv.org/content/10.1101/678649v1).

To ‘zoom in’ the spatiotemporal regulation of transcription by cis-DNA elements, I characterized a long-range enhancer cluster (~50-70kb) regulating the naïve pluripotency gene Klf4  in mouse embryonic stem cells and identified the highly dynamic yet intrinsically ordered nature of key pluripotency transcription factors (ESRRB, STAT3, SOX2, OCT4) engaging pluripotency enhancers by  live-cell single-molecule imaging, genomics and in vitro biochemistry (Xie et al. Genes and Development, 2017, http://genesdev.cshlp.org/content/31/17/1795). To dissect the spatiotemporal dynamics of cis-regulatory chromatin at single cell single allele resolution, I am combining MS2-based RNA labeling, TetO array based DNA labeling, and HaloTag based protein labeling to understand gene activation dynamics in single live cells, with surprising observations and novel mechanistic insights continuing to unfold.