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Zhai Jixian

Associate Professor

Department of Biology

I received my graduate and postdoctoral training during an era in which the applications of “Next-Generation Sequencing” (NGS) have grown tremendously. I have applied these techniques to diverse biological questions, driving discovery across the field of plant epigenetics and genomics. My Ph.D. degree in Plant Biology and Master’s degree in Genetics have required extensive training in experimental or “wet lab” approaches; in addition, I earned two other Master’s degrees, one in Statistics and one in Bioinformatics, which greatly facilitated the development of my own “data-driven, hypothesis-generating” style of research.


Research Interests:
The application of high-throughput techniques to the study of plant epigenetics has been the primary focus of my research for the past ten years, a field that is the nexus of non-coding RNA, DNA methylation and chromatin modifications. Equipped with a interdisciplinary background that integrates both “wet lab” and “dry lab” techniques, and having worked in three leading academic laboratories, I am able to collaborate effectively and communicate smoothly with experts from different areas, and to incorporate into my work insights from multiple fields. Together with our group members, we are poised to offer our own unique perspective in addressing important biological questions in the big-data era.


Professional Experience:
2016 ~                Tenure-track Associate Professor, SUSTech
2013 ~ 2016        Postdoctoral Researcher         University of California, Los Angeles, USA                                                  
                          Advisor: Dr. Steven E. Jacobsen

Educational Background:
2008 ~ 2013        Ph.D. in Plant Biology and Genomics       University of Delaware, USA
                          Advisor: Dr. Blake C. Meyers
2011 ~ 2013        M.S. in Bioinformatics & Computational Biology       University of Delaware, USA
2009 ~ 2011        M.S. in Statistics       University of Delaware, USA
2005 ~ 2008        M.S. in Genetics       Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, China
                          Advisor: Dr. Xiaofeng Cao
2001 ~ 2005        B.S. in Biology       University of Science and Technology of China (USTC), China

Honors & Awards:
2014    Life Science Research Foundation Postdoctoral Fellowship
2012    W. J. Benton Graduate Student Award, University of Delaware
2007    Academy Scholarship for Outstanding Master Student, Chinese Academy of Sciences
2004    Outstanding Student Scholarship, USTC

Selected Publication:
First author research papers:
1.    Zhai J*, Bischof S*, Wang H, Feng S, Lee T, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson I, Meyers BC, Ausin I, Jacobsen SE (2015) A ‘One precursor, One siRNA’ model for Pol IV-dependent siRNA Biogenesis. Cell 163, 445–455 (*co-first author)
2.    Zhai J*, Zhang H*, Arikit S, Huang K, Nan G, Walbot V, Meyers BC (2015) Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction. PNAS 112(10): 3146-51 (*co-first author)
3.    Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay L, Ji L, et al. (2013) Plant microRNAs display differential 3’-truncation and tailing, modifications which are ARGONAUTE1-dependent and conserved across species. The Plant Cell 25(7):2417-28
4.    Zhai J, Jeong D-H, Paoli ED, Park S, Rosen BD, Li Y, González AJ, Yan Z, et al. (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes & Development 25(23):2540-53. 
5.    Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X, Cao X. (2008) Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genetics 4, e1000056.
6.    Song X*, Li P*, Zhai J*, Zhou M, Ma L, Liu B, Jeong DH, Cao S, Cui X et al. (2011) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. The Plant Journal 69, 462-474. (*co-first author)
7.    Zhai J, Arikit S, Simon SA, Kingham B, Meyers BC (2013) Construction of Parallel Analysis of RNA End (PARE) Library for Illumina Hi-Seq sequencing. Methods S1046-2023(13)00237-5
8.    Zhai J and Meyers BC (2013). Deep Sequencing from hen1 Mutants to Identify Small RNA 3' Modifications. Cold Spring Harb Symp Quant Biol 1943-4456


Co-authored papers (in reverse-chronological order):
9.    Groth M, Moissiard G, Wirtz M, Wang H, GarciaSalinas G, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Garza RID, Jacobsen SE (2016) MTHFD1 controls DNA methylation in Arabidopsis. Nature Communication (in press)
10.    Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor N, Bart R, Carrington JC, Jacobsen SE, Ausin I (2015) CG gene body DNA methylation changes and evolution of duplicated genes in cassava. PNAS 112(44):13729-34
11.    Yan Z, Hossain MS, Valdés-López O, Hoang NT, Zhai J, Wang J, Libault M, Joshi T, Brechenmacher L, Findley S, Qiu L, Sherrier DJ, Meyers BC, Xu D, Stacey G (2015) Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Plant Biotechnology Journal 10.1111/pbi.12387
12.    Tu B, Xu C, Liu L, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ren G, Yu B, Li S, Meyers BC, Mo B, Chen X (2015) Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genetics 11(4): e1005119
13.    Yan Z, Hossain MS, Arikit S, Valdé O, Zhai J, Wang J, Libault M, Ji T, Qiu L, Meyers BC, Stacey G (2015) Identification of MicroRNAs and their mRNA targets during soybean nodule development: Functional analysis of the role of miR393* in soybean nodulation. New Phytologist 10.1111/nph.13365
14.    Zhao M, Cai C, Zhai J, Lin F, Li L, Shreve J, Thimmapuram J, Hughes TJ, Meyers BC, Ma J (2015) Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Immune Responses: Insights from Analyses of Soybean Rps Gene Near-Isogenic Lines. The Plant Genome 10.3835
15.    Cantó-Pastor A, Mollá-Morales A, Ernst E, Dahl W, Zhai J, Yan Y, Meyers BC, Shanklin J, Martienssen RA (2015) Efficient transformation and artificial miRNA gene silencing in Lemna minor. Plant Biology 10.1111/plb.12215
16.    Arikit S, Xia R, Kakrana A, Huang K, Zhai J, Yan Z, Valdés-López O, Prince S, Musket TA, Nguyen HT, Stacey G, Meyers BC (2014) An atlas of soybean small RNAs demonstrates regulation by phased siRNAs of hundreds of coding genes. The Plant Cell 26: 4584-4601
17.    Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE (2014) Genome-wide Hi-C analyses in wild type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Molecular Cell 55(5):694-707
18.    Wong J, Gao L, Yang Y, Zhai J, Arikit S, Yu Y, Duan S, Xiong Q, Yan J, Li S, Liu R, Wang Y, Tang G, Meyers BC, Chen X, Ma W (2014) Roles of Small RNAs in Soybean Defense against Phytophthora sojae Infection. The Plant Journal 10.1111/tpj.12590
19.    Creasey KM, Zhai J, Borges F, Van EF, Meyers BC, Martienssen RA (2014) miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis. Nature 508 (7496):411-5
20.    Wei L, Gu L, Song X, Cui X, Lua Z, Zhou M, Wang L, Hu F, Zhai J, Meyers BC, Cao X (2014) Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. PNAS 111(10):3877-82
21.    Schapire A, Bologna NG, Moro B, Zhai J, Meyers BC, Palatnik JF (2013) Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. Methods doi:10.1016/j.ymeth.2013.08.032
22.    Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Paoli ED, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, and Green PJ (2013) Parallel Analysis of RNA Ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biology 14(12):R145
23.    Amborella Genome Project. (2013) The Amborella Genome and the Evolution of Flowering Plants. Science 342(6165):1241089
24.    Jeong DH, Thatcher SR, Brown RS, Zhai J, Park S, Meyers BC, Green PJ (2013) Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage. Plant Physiology 162(3):1225
25.    Raman V, Simon SA, Romag A, Demirci F, Mathioni SM, Zhai J, Meyers BC, Donofrio NM (2013) Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus Magnaporthe oryzae. BMC Genomics 14:326
26.    Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik J (2013) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Research (10):1675-89
27.    Arikit S, Zhai J, Meyers BC (2013) Biogenesis and function of rice small RNAs from non-coding RNA precursors. Current Opinion in Plant Biology 16(2):170-9. 
28.    Lee TF, Gurazada SG, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC (2012) RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 7(7):781-95
29.    Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh T, Meyers BC, Mo B, Chen X (2012) HESO1, a nucleotidyl transferase in Arabidopsis, uridylates unmethylated miRNAs and siRNAs to trigger their degradation. Current Biology 22(8):689-94
30.    The_International_Medicago_Initiative (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520-524 
31.    Jeong D-H, Park S, Zhai J, Gurazada SGR, Paoli ED, Meyers BC, Green PJ. (2011) Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage. The Plant Cell 23(12):4185-207.
32.    Yu B, Bi L, Zhai J, Agarwal M, Li S, Wu Q, Ding SW, Meyers BC, Vaucheret H, Chen X. (2010) siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Research 38(17):5844-5850.
33.    The International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763-768.
34.    Meyers BC, Simon SA, Zhai J. (2010) MicroRNA processing: battle of the bulge. Current Biology 20(2):R68-70. (review)
35.    Lee TF, Zhai J, Meyers BC. (2010) Conservation and divergence in eukaryotic DNA methylation. PNAS 107(20):9027-9028. (review)
36.    Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC. (2009) Short-read sequencing technologies for transcriptional analyses. Annual Review Plant Biology 60:305-333. (review)
37.    Park W, Zhai J, Lee JY. (2009) Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CAL genes. Plant Cell Rep 28(3):469-480. 
38.    De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, Meyers BC, Jorgensen RA, Green PJ. (2009) Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA 15(11):1965-1970.
39.    Simon SA, Zhai J, Zeng J, Meyers BC. (2008) The cornucopia of small RNAs in plant genomes. Rice 1(1):52-62. (review)
40.    Pei Y, Niu L, Lu F, Liu C, Zhai J, Kong X, Cao X. (2007) Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis. Plant Physiology 144, 1913-1923.
41.    Ding Y, Wang X, Su L, Zhai J, Cao S, Zhang D, Liu C, Bi Y, Qian Q, Cheng Z, et al. (2007) SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. The Plant Cell 19, 9-22.
42.    Xia R, Wang J, Liu C, Wang Y, Zhai J, Liu J, Hong X, Cao X, Zhu JK, Gong Z. (2006) ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. The Plant Cell 18, 85-103. 1(1):52-62.


1.    Meyers BC, Zhai J, Sherrier J. Use of phased small RNAs for suppression of plant defense and other plant genes. US Patent 20140356961
2.    Meyers BC, Zhai J, Walbot V. Regulatory non-coding RNAs as determinants of male sterility in grasses and other monocotyledonous plants. PCT/US2014/060081


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