Rapid progress in technology advancement has greatly increased our capacity in addressing important biological questions previously considered impossible. Our lab strives to develop and adapt novel technologies to address important questions relevant to epigenetics, reprogramming, development and neurobiology.
To understand the mechanism and function of active DNA demethylation, we utilized DIP-seq to analyze the genomic distribution of 5hmC, 5fC and 5caC (1,2). For 5fC and 5caC profiling at single-base resolution, we developed MAB-seq (3) and extended the method to low-input and single-cell level (4).
To understand the chromatin dynamics in biological contexts with limited cell numbers, we developed a liDNase-seq method and applied it to understand the chromatin regulatory landscape during mouse preimplantation development (5). In addition, we have also adopted other methods such as low-input RNA-seq, ChIP-seq, BS-seq and HiC and used them to discover a new imprinting mechanism (6). Other state-of-art techniques used in our study include live cell imaging, SCNT, and IVG (in vitro oocyte growth).
We have also set up different single-cell RNA-seq platforms to dissect biological systems with cellular heterogeneity. Using Drop-seq, we have comprehensively profiled mouse hypothalamus under normal and food deprivation conditions (7). In addition, we used the 10x genomics platform to classify the cell types of the brain reward system and examined the response of various cell types to drug self-administration.
1. Shen, L. et al. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153, 692-706 (2013).
2. Wu, H. et al. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev 25, 679-84 (2011).
3. Wu, H., et al. Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing. Nat Biotechnol 32, 1231-40 (2014).
4. Wu, X., et al. Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells. Genes Dev 31, 511-523 (2017).
5. Lu, F. et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell 165, 1375-88 (2016).
6. Inoue, A., et al. Maternal H3K27me3 controls DNA methylation-independent genomic imprinting. Nature (2017)
7. Chen, R., et al. Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity. Cell Rep 18, 3227-3241 (2017).