Education

Ph.D. candidate in Biostatistics, USC

B.S. in Biology, Nanjing University, 2012

 

Research Area

Stem cell genomics 

 

Research Summary

4C-seq

Circularized Chromosome Conformation Capture combined with high-throughput next generation sequencing (4C-seq) is a cost-effective and powerful technique to uncover chromatin folding and genome contact profile within the nucleus. Besides, we know that regulatory DNA elements (enhancers, promoters) can control the expression of distal genes through physical interaction, so 4C-seq is also applied to explore gene regulation in some cell types. Conventional 4C approaches used restriction enzyme digestion to fragment chromatin, while our lab applied a sonication approach which have some advantages over the enzymatic method. We developed a customized experimental and analytical pipeline for sonication based 4C-seq and performed a comprehensive comparison between two methods. 

In Collaboration with Dr. Wange Lu's lab, we focus on enhancers of some key pluripotent genes, like Oct4 (Pou5f1) and Sox2. With bioinformatic tool and statistical model, we study which genemic regions interact with the targeted "bait" region on a genome-wide scale. Furthermore, we characterize the interactome by examining the "4C sites" association with histone marks, transcription factor binding, DNA replication timing, gene structure, gene onthology, and so on. Associated genes are candidate for subsequent functional validation.  

 

Demo results
 
Circos plot showing inter-chromosomal (blue) and intra-chromosomal (red) interacting regions with bait region of Oct4 distal enhancer 

 

 

Heat map showing significant interacting regions across genome

 

RNA-seq

We explore the transcriptional landscape of different cell types. In collaboration with Dr. Wange Lu, we examine the difference of gene expression signatures bewteen cells with certain gene knock-out (KO) and cells of wild-type (WT).

 

Other

We also use other tools like ChIP-seq and ChIA-PET-seq to study genome-wide regulation of certain gene expression in pluripotent cells.