Research

High-throughput light-sheet microscopy and subcellular protein atlas

For our ultimate goal of painting a proteome-wide map of endogenous proteins inside human cells, we are developing three techniques:

1. new split-protein-based fluorescent probes that enable large-scale labeling of endogenous proteins in human cell lines via gene editing
2. new light-sheet microscopes for high-resolution 3D live cell imaging
3. deep-learning methods for efficient processing and quantitative interpretation of imaging data.

Combing these three technical advances, we are systematically analyzing the dynamic re-organization of various nuclear and cytoplasmic structures throughout the cell cycle.

• Yang et al., Nat. Methods (2019)
• Feng et al., Nat. Commun. (2017)
• Kamiyama & Sekine et al., Nat Commun. (2016)
• Leonetti & Sekine et al., PNAS (2016)

Protein phase-separation and the com­part­men­ta­tion of cell signaling

Cell signaling networks are the basis of cellular activities and, ultimately, the everyday life of an organism. As the activities in a signaling network are often highly dynamic in time and heterogeneous in space, with the same signaling molecule functioning differently among cellular compartments, we take a microscopy-based approach to map the localization and activities of endogenous signaling components. We are particularly interested in understanding how cytoplasmic protein granules organize cancer cell signaling in the RTK-RAS-MAPK signaling pathway.

• Tulpule et al., Cell (2021)
• Kamiyama et al., Dev. Cell (2015)
• Irannejad et al., Nature (2013)

Genome engineering and the spatial or­gan­i­za­tion of the genome

With our ever expanding knowledge on the genome from DNA sequencing, it is now clear that mechanisms regulating the functional output of the genome go far beyond its linear sequence. The packaging of the chromatin, its dynamic interactions with proteins and RNAs, and modifications to histones all play important roles during organism development, environment adaptation and cancer formation. For this purpose, we take the “imagenomics” approach, developing new tools to visualize the dynamics of specific genomic elements and their epigenetic status in living cells. These techniques will perfectly complement sequencing-based approaches and fundamentally advance our ability to understand the regulation of genome function. Highlights of our recent work include the development of the CRISPR imaging technology for endogenous gene loci.

• Chen et al., Cell (2013)
• Chen et al., Nucleic Acid Res. (2016)
• Guan et al., Biophys J. (2017)
• Chen et al., Nat. Commun (2019)

With support by