Xuehua Zhong

Epigenetic regulation of plant genome integrity, developmental and environmental interaction

Years at WID

2013 - present


  • B.S., Wuhan University, China M.S., Wuhan University, China
  • Ph.D., The Ohio State University
  • Postdoctoral Research, University of California, Los Angeles

Research Description

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.


  • NIH Ruth L. Kirschstein National Research Service Award (2011)
  • NSF Faculty Early Career Development (CAREER) Award (2015)
  • Alfred Toepfer Faculty Fellow Award (2016)
  • NIH Maximizing Investigators’ Research Award (2017)

Selected Publications

  • Yang Z*, Qian S*, Scheid RN, Lu L, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J#, Zhong X# (2018) EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nature Genetics, doi: 10.1038/s41588-018-0187-8. *Equal contribution; #Corresponding author
  • Qian S*, Lv X*, Scheid RN*, Lu L, Yang Z, Chen W, Liu R, Boersma MD, Denu JM, Zhong X#, Du J# (2018) Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nature Communications, doi: 10.1038/s41467-018-04836-y. *Equal contribution; #Corresponding author
  • Lu L*, Chen X*, Qian S, Zhong X (2018) Plant-specific histone residue Phe41 is important for genome-wide H3.1 distribution. Nature Communications, doi: 10.1038/s41467-018-02976-9.
  • Chen X, Lu L, Qian S, Scalf M, Smith LM, Zhong X (2018) Canonical and non-canonical actions of Arabidopsis histone deacetylases in ribosomal RNA processing. The Plant Cell, 30: 1-19.
  • Sanders D, Qian S, Fieweger R, Lu L, Dowell JA, Denu JM, Zhong X (2017) Histone lysine-to-methionine mutations reduce histone methylation and cause developmental pleiotropy. Plant Physiology, 173 (4): 2243-52.
  • Kim Y, Wang R, Gao L, Li D, Xu C, Mang H, Jeon J, Chen X, Zhong X, Kwak J, Mo B, Xiao L, Chen X (2016) POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. PNAS, 113 (51): 14858-63.
  • Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X (2016) POWERDRESS interacts with histone deacetylase 9 to promote aging in Arabidopsis. eLife, doi: 10.7554/eLife.17214.
  • Zhong X (2016) Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation. New Phytologist, 21: 76-80.
  • Lu L, Chen X, Sanders D, Qian S, Zhong X (2015) High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns in Arabidopsis and rice. Epigenetics, 10: 1044-53.
  • Zhong X* #, Hale CJ*, Nguyen M, Ausin I, Groth M, Hetzel J, Vashisht AA, Henderson IR, Wohlschlegel JA, Jacobsen SE#. (2015) DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis. PNAS, 112: 911-6. #Corresponding author
  • Zhong X*, Du J*, Hale CJ, Gallego-Bartolome J, Feng S, Vashisht AA, Chory J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell, 157: 1050-60.
  • 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. *Equal contribution
  • 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 Struct & Mol Biol, 19: 870-75. *Equal contribution

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