What We Do

Transcription factors and chromatin complexes play important roles in cell fate decisions. Recent technology development in genomics, especially in single-cell genomics, has allowed us to investigate different transcription factors and chromatin complexes at an unprecedented level. We are developing low-input and single cell epigenetic technologies to study chromatin accessibility and genome-wide binding events of key transcription factors and chromatin complexes. We apply these new techniques to investigate the transcriptional mechanisms of cell fate decision and memory during cellular differentiation.

We have two main areas in the lab:

1. Simple, robust and flexible single cell epigenetic and transcriptomic methods development

We are developing simple, robust and flexible methods that can be done in a plate-based small-scale format and in a high-throughput format. They have different pros and cons, but both are essential for the research. By combining upfront mini-bulk reaction with single cells or single nuclei isolation, we have developed a few methods that allow us profiling chromatin status and gene expression in a straightforward and economical way.

Relevant work

• ISSAAC-seq
• 3’ SMART-seq
• Plate-based scATAC-seq v2
• Plate-based scATAC-seq

2. Epigenetic changes during early embryogenesis and ESC differentiation

During early embryo development, the chromatin of gametes and zygotes undergoes rapid and dramatic changes. How embryonic cells acquire different cell fates and the spatial temporal changes of chromatin during this process is of great interest. We apply our single cell epigenetic techniques to zebrafish and mouse models as well as in vitro ESC differentiation to unravel the key events during early embryo development, including chromatin accessibility, transcription factor binding and histone modifications.

Relevant work

• Dpf2 in mESC differentiation
• Chromatin accessibility in zebrafish early embryogenesis