Research

Although genome is a blueprint for making an organism, epigenome governs the functional expression of genes and ultimately shapes the organism. Our overall research goal is to understand the fundamental mechanisms and biological roles of epigenetic modifications underpinning various biological processes.

Epigenetic regulation is a process whereby genes can inherit different states of activity in the absence of any changes in the DNA sequences. One such epigenetic system involves the addition of a chemical mark on DNA, so-called DNA methylation, which causes silencing of underlying genes. DNA methylation has evolved to play significant roles in gene regulation that control many biological processes including genome integrity, imprinting, cellular differentiation, development, and X chromosome inactivation. Global alterations of DNA methylation are now widely recognized as a contributing factor in many types of cancers and cardiovascular.

Epigenetic modifications of histones (proteins that package and organize DNA), such as methylation and acetylation, play crucial roles in regulating all DNA-dependent processes including transcription, replication, DNA repair and recombination in diverse organisms. Mis-regulation and abnormalities of histone modifications are often observed in plant and animal diseases.

Given the great importance of epigenetic regulation of gene expression in many aspects of biology, ranging from genome integrity, imprinting, cellular differentiation, normal growth and development, disease formation, to potential biotechnological applications, our research goal is to understand the fundamental mechanisms of chromatin-based gene regulation. We study how various chromatin factors are recruited to chromatin to “read” and ‘translate” epigenetic information into differential gene expression patterns under normal growth and development as well as stress conditions. Knowledge gained from such studies should have high and broad impacts on our understanding of how distinct chromatin modifications coordinate with each other to regulate gene expression critical for diverse biological processes. They may also contribute to the development of new tools for applied research.

Some outstanding questions we are interested in answering are:

  • How does dynamic epigenetic modification regulate gene expression for proper growth and development?
  • How do chromatin alternations lead to changes in stable gene expressions?
  • How do different developmental and environmental stimuli influence the chromatin dynamics?
  • How are chromatin modifications established and maintained under stress conditions?
  • Are altered chromatin structures stable and inheritable?

To address these questions, we use Arabidopsis thaliana as our main experimental model system because of its amenability to genetic manipulations, small genome, availability and viability of most epigenetic mutants. Experimentally, we will use a combination of molecular, genetic, genomic, proteomic, biochemical and structural approaches.