Associate Professor

Basic Information

Personal Website:
Life Sciences, Rm B408
Lab office:
Life Sciences, Rm B410
Lab phone:
Research Interests:

The current research in my lab is directed to understand the establishment and maintenance of histone modifications in plants, their roles in regulating gene expression and development, and how they have contributed to the evolution of gene and genome functions. We use Arabidopsis and rice as model systems and employ a wide range of approaches, including genetic, molecular biology, biochemistry and genomic tools such as high-throughput sequencing and high-density tiling microarrays.

  • Schmitz RJ, Zhang X, Jackson D, Jackson S, Megraw M, Somatic Genetic and Epigenetic Variations in Long-lived Perennial Trees and their Interactions with the Environment, , NSF PGRP, 3/2018-2/2022.
  • Scanlon M, Zhang X, Muehlbauer, Yu, Schnable, Timmermans, Genetic networks regulating structure and function of the maize shoot apical meristem, NSF PGRP, 2/1/13-1/31/18


Selected Publications:
  • Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS, Bonasio R, Wagner D (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genetics 49(10):1546-1552
  • Chen LQ, Luo JH, Cui ZH, Xue M, Wang L, Zhang X, Pawlowski WP, He Y (2017) ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development. Plant Physiol. 174(3):1795-1806.
  • Ricci WA and Zhang X (2016) Public Service by a Selfish Gene: A Domesticated Transposase Antagonizes Polycomb Function. PLoS Genetics. 12(6):e1006014
  • Cui X, Lu F, Qiu Q, Zhou B, Gu L, Zhang S, Kang Y, Cui X, Ma X, Yao Q, Ma J, Zhang X, Cao X (2016) REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nature Genetics 48(6):694-9
  • Bewick AJ, Ji L, Niederhuth CE, Willing EM, Hofmeister BT, Shi X, Wang L, Lu Z, Rohr NA, Hartwig B, Kiefer C, Deal RB, Schmutz J, Grimwood J, Stroud H, Jacobsen SE, Schneeberger K, Zhang X, Schmitz RJ. (2016) On the Origin and Evolutionary Consequences of Gene Body DNA Methylation. Proc Natl Acad Sci 113(32):9111-6
  • Seymour M, Ji L, Santos AM, Kamei M, Sasaki T, Basenko EY, Schmitz RJ, Zhang X and Lewis ZA (2016) Histone H1 Limits DNA Methylation in Neurospora crassa. G3: GENES, GENOMES, GENETICS 6(7): 1879–1889
  • Bewick AJ, Hofmeister BT, Lee K, Zhang X, Hall SW, Schmitz RJ (2016) FASTmC: A Suite of Predictive Models for Nonreference-Based Estimations of DNA Methylation. G3: GENES, GENOMES, GENETICS 6(2): 447–452
  • Gent, J., Madzima, T., Bader, R., Kent, M., Zhang, X., Stam, M., McGinnis, K., Dawe, K. (2014). Accessible DNA and relative depletion of H3K9me2 at maize RdDM loci. The Plant Cell, 26(12), 4903-17.
  • Xu, Y., Gan, E., Zhou, E., Wee, W., Zhang, X., Ito, T. (2014). Arabidopsis MRG domain proteins bridge two histone modifications to elevate expression of flowering genes. Nucleic Acids Research, 42(17), 42(17):10960-74.
  • Joana Sequeira-Mendes, Irene Aragüez, Ramón Peiró, Raul Mendez-Giraldez, Xiaoyu Zhang, Steven E Jacobsen, Ugo Bastolla, Crisanto Gutierrez. (2014). The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs. The Plant Cell, 26(6), 2351-2366.
  • Zhang, X. (2014). Delayed gratification - waiting to terminate stem cell identity.. Science (New York, N.Y.), 343(6170), 498-9.
  • Consortium, A. G. S., Zhang, X. (2013). The Amborella Genome and the Evolution of Flowering Plants. Science (New York, N.Y.), 342(6165), 1241089.
  • Gent, J., Ellis, N., Guo, L., Harkess, A., Yao, Y., Zhang, X., Dawe, R. K. (2013). CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Research, 23, 628-637.
  • Zhang, X. (2012). Dynamic differential methylation facilitates pathogen stress response in Arabidopsis. Proc. Nat. Acad. Sci., USA, 109(32), 12842.
  • Eichten, S., Ellis, N., Makarevitch, I., Yeh, C., Gent, J., Guo, L., McGinnis, K., Zhang, X., Schnable, P., Vaughn, M., Dawe, R. K., Springer, N. (2012). Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genetics, 8(12), e1003127.

Ph.D Plant Molecular Biology, Epigenetics and Genomics, University of Georgia 2003