Xuehua Zhong

Associate Professor



Mechanisms and roles of epigenetic modifications underpinning various biological processes

Wisconsin Institutes for Discovery, room 2114
Ph.D., The Ohio State University (2007), Postdoctoral Research, University of California, Los Angeles (2008-2013)
Lab Website
Research Interests
Our research focuses on epigenetic regulation of plant traits and environmental adaptation. By understanding how plants reprogram epigenetic landscapes to meet growth and survival needs, we aim to develop innovative tools to edit and engineer epigenomes for biomass production and agricultural improvement.
Research Fields
Epigenetics, Gene Expression, Genome editing and engineering, Genomics & Proteomics, Environmental Stress, Plants

Research Description:
Epigenetic Regulation in Plant Growth and Development

A functional plant or human body develops from a single cell. This cell divides and produces millions of cells that make up a body. If all cells that come from this very first cell were identical, there would be just a mass of cells and no body parts or organs. So subsequent to cell division, cells gradually become different from each other, a process called differentiation. These different cells build different organs that perform different functions. The burning question is: how do cells that ultimately come from a single cell become so different? A simple answer is that during specific stages of development the cells express different genes. This leads to the formation of distinct types of cells. Then, how do cells know what genes to express to make them distinct? One of the answers is epigenetic regulation, the chemical modification on chromatin, that switch gene ‘on’ or ‘off’ without changing the underlying DNA sequences. Epigenetic regulation is not only critical for the proper development of an organism, but also plays important roles in cross talk to the environment. The overall goal of our research is to uncover how versatile developmental and environmental signals trigger epigenetic modifications, how environmental conditions feed back to the epigenetic landscape, and how cells are instructed to deposit the modification correctly in the genome. By understanding how plants reprogram epigenetic landscapes to meet growth and survival needs, we are developing innovative tools to edit and engineer epigenomes for biomass production and agricultural improvement.

Representative Publications:
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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