Assistant Professor, Genetics, Epigenetics
- 330 North Orchard Street
- Madison WI 53715
- Room 2114
- B.S., Wuhan University, China
- M.S., Wuhan University, China
- Ph.D., The Ohio State University
- Postdoctoral Research, University of California, Los Angeles
Epigenetic Regulation in Plant Growth and Development
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-based gene silencing can be very stable and in many cases mitotically heritable. 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.
- Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel DJ, Jacobsen SE (2014) The roles of non-CG methylation in Arabidopsis. Nat Struct & Mol Biol, 21: 64-72.
- Johnson LJ, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE (2014) SRA- and SET-domain-containing proteins link RNA Polymerase V occupancy to DNA methylation. Nature, Doi:10.1038/nature12931
- Du J*, Zhong X*, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell, 151: 167-80. *These authors contributed equally and are listed alphabetically.
- Zhong X*, Hale CJ*, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE (2012) DDR complex facilitates genome-wide association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struc Mol Biol., 19: 870-5. *These authors contributed equally.
- Henderson IR, Deleris A, Wong W, Zhong X, Chin HG, Horwitz G, Kelly KA, Pradhan S, Jacobsen SE (2010) The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet, 6(10): e1001182.
- Qian S, Zhong X, Yu L, Ding B, Haan PD, Boris-Lawrie K (2009) HIV-1 Tat RNA silencing suppressor activity is conserved across kingdoms and counteracts translational repression of HIV-1. Proc Natl Acad Sci USA, 106: 605-10.
- Zhong X, Archual A, Amin A, Tao X and Ding B (2008) A genomic map of viroid RNA motifs critical for replication and systemic trafficking. Plant Cell, 20: 35-47.
- Zhong X*, Tao X*, Stombaugh J, Leontis N, Ding B (2007) Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking. EMBO J, 26: 3836-46. * These authors contributed equally.
- Zhong X, Leontis N, Qian S, Itaya A, Qi Y, Boris-Lawrie K, Ding B (2006) Tertiary structural and functional analyses of a viroid RNA motif by isostericity matrix and mutagenesis reveal its essential role in replication. J Virol, 80: 8566-81.