The research in our group is mainly focusing on the epigenetic regulation of chromatin higher-order structures on transcription, and their biological functions in cell fate determination during programming and reprogramming of embryonic stem (ES) cells. Our research mainly includes three directions as follows:

1. Structure of 30-nm Chromatin Fibers and their epigenetic regulations

        During programming and reprogramming of stem cells, the transcriptional signatures are regulated by epigenetic mechanisms, including DNA methylation, histone variants and histone modifications. In the meanwhile, the dynamics of chromatin structures, which correlate with the transcriptional activity of genes, can be regulated by many epigenetic factors. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, which comprises 146 base pairs of DNA wrapped in 1.7 superhelical turns around an octamer of histones, there is still much discussion on the higher-order levels of chromatin structure, including 30-nm chromatin fiber, the second structural level of DNA organization. It has been clear that the plasticity of and the dynamics of higher-order chromatin fiber are key regulators of transcription and other biological processes inherent to DNA. Elucidating just how a nucleosomal array can be compacted into higher-order chromatin structures is central to understanding the dynamics of chromatin structure. In our group, we have developed the chromatin in-vitro reconstitution and structural analysis system with techniques including EM/Cryo-EM, AUC, single-molecule(sm)-magnetic tweezers, FRET/sm-FRET. We focus on the investigation on the 3D structure of 30-nm chromatin fibers, their structural plasticity/dynamics and epigenetic regulations.

2. The structure and function of chromatin in centromere

        Centromeres are the specialized chromosomal loci that drive the assembly of the kinetochores and allow the accurate chromosome segregation during mitosis and meiosis. A unique histone H3 variant known as CENP-A, which is therefore proposed as the epigenetic mark of the centromere, is responsible for centromere identity. However, up to date, the composition and the structure of centromeric chromatin are still unclear. The studies on nucleosome composition, dynamic assembly, higher order chromatin organization, epigenetic regulation of CENP-A containing chromatin at centromeres during cell cycles remain rather limited. In our group, by using our established an in vitro chromatin reconstitution system together with the in vivo cell assay and the biophysical, biochemical, molecular biology techniques, we will extensively investigated the structure of centromeric nucleosome, the recognition and dynamic assembly of CENP-A on centromeres, the cooperatively regulation of CENP-A and other histone variants in nucleosome dynamics and higher-order chromatin structure of centromere, the dynamic deposition and maintenance of CENP-A throughout the cell cycle, the biological functions of centromere in stem cell biology and diseases such as cancer and ageing.

3. The Dynamic Interactions between Chromatin and Nuclear Envelope during Stem Cell Differentiation

        In eukaryotic cell, other than the 30-nm fibers, chromatin can be hierarchically compacted into further complicated folding levels and organized in three dimensions via interacting with other nuclear structures within the nucleus. The nuclear lamina, a filamentous protein network that provides a structural scaffold for the inner nuclear membrane, has been shown to dynamically interact with specific chromatin domains and regulate gene expression and stem cell differentiation. Molecular mapping indicated that lamina-genome interactions are dynamic and play essential roles in the regulation of gene expression programs during lineage commitment and terminal differentiation. However, it remains unclear by which mechanisms the chromatin organization and nuclear architecture might regulate the gene expression. Our group is investigating the establishment and maintenance of chromatin underlining the nuclear envelope/nuclear lamina and their dynamic changes during cell lineage commitment, terminal differentiation and diseases such as progeria.