Self-introduction
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
2024 ~ present Professor, Southern University of Science and Technology of China

2016 ~ 2024 Associate Professor, Southern University of Science and Technology of China
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

(#co-first authors, *corresponding author)

At SUSTech

1. Chen, X.#; Yuan, X.#; Liu, S.#; Cui, X.; Cao, N.; Chen, Y.; Chen, Y.; Yi, M.; Xu, H.; Yao, N.; Yu, U.; Chen, S.; Liu, C.; Zhang, M.; Song, J.; Jiang, X.; Wang, Y.; Xiao, L.; Zheng, B.; Zhang, H.; Huang, X.; Yang, M.; Zhai, J.*; Liu, Z.*; Wen, F.* (2026). Circulating Immune Cell Membrane–Cloaked Tumor Cells exhibit Metastasis–Initiation Capacity. Cell Research. Accepted.

2. Liu, Z.#; Li, Z.#; Wang, Y.#; Long, Y.#; Zhao, H.; Qin, Y.; Zhu, X.; Guo, H.*; Jiang, K.*; Zhai, J.* (2026b). Cell-type specific early perception of nine phytohormones revealed by single-nucleus transcriptomics in Arabidopsis. Nature Communications, 17, 9288. doi: 10.1038/s41467-026-76284-y.

3. Lei, H.#; Long, Y.#; Wu, S.#; Wang, X.#; Peng, Y.#; Liu, Z.; Lu, W.; Shu, Y.; Zhu, H.; Zou, M.; Gao, Y.; Xia, Y.; Li, S.; Ren, L.; Fu, Y.*; Zhang, Z.*; Li, Y.*; Zhai, J.* (2026a). Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance. Nature Communications, 17, 5323. doi: 10.1038/s41467-026-71703-6.

4. Chen, Y.#; Lu, W.#; He, H.#; Zheng, L.; Pan, X.; Sun, T.; Bu, F.; Fang, Y.; Sun, Y.; Long, Y.; Wang, M.; Wu, S.; Liu, L.; Jia, J.; Jiao, Y.; Hu, Z.; Zhang, Y.*; Zhai, J.* (2026b). A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails. Genome Biology, 27, 146. doi: 10.1186/s13059-026-04040-y.

5. Jin, X.#; Li, J.#; Lu, W.; Deng, X.; Wei, Y.; Shu, Y.; Liu, B.; Liu, Z.; Long, Y.; Zhu, X.; Fei, Q.; Xia, Y.; Li, Q. Q.; Michaels, S. D.; Cao, X.; Lenhard, M.; Zhai, J.* (2025b). Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination. Nature Communications, 16, 7086. doi: 10.1038/s41467-025-62555-7.

6. Qin, Y.#; Liu, Z.#; Gao, S.#; Martínez-Vasallo, C.#; Long, Y.#; Zhu, X.; Liu, B.; Gao, Y.; Xu, X.; Nohales, M. A.*; Xie, Q.*; Zhai, J.* (2025a). 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis. Nature Communications, 16, 4171. doi: 10.1038/s41467-025-59424-8.

7. Li, Z.; Zheng, L.; Zhai, J.*; Long, Y.* (2024). Analysis of DNA 5-methylcytosine Using Nanopore Sequencing. Bio-protocol, 14, e4943. doi: 10.21769/BioProtoc.4943.

8. Liu, Z.#; Yang, J.#; Long, Y.#; Zhang, C.#; Wang, D.; Zhang, X.; Dong, W.; Zhao, L.; Liu, C.; Zhai, J.*; Wang, E.* (2023c). Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago. Nature Plants, 9, 1734–1748. doi: 10.1038/s41477-023-01524-8.

9. Mo, W.#; Shu, Y.#; Liu, B.; Long, Y.; Li, T.; Cao, X.; Deng, X.*; Zhai, J.* (2023b). Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis. Nature Plants, 9, 1439–1450. doi: 10.1038/s41477-023-01498-7.

10. Liu, Z.#; Kong, X.#; Long, Y.#; Liu, S.; Zhang, H.; Jia, J.; Cui, W.; Zhang, Z.; Song, X.; Qiu, L.; Zhai, J.*; Yan, Z.* (2023a). Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. Nature Plants, 9, 515–524. doi: 10.1038/s41477-023-01387-z.

11. Zhang, H.; Jia, J.; Zhai, J.* (2023). Plant Intron-Splicing Efficiency Database (PISE): exploring splicing of ∼1,650,000 introns in Arabidopsis, maize, rice, and soybean from ∼57,000 public RNA-seq libraries. Science China Life Sciences, 66, 602–611. doi: 10.1007/s11427-022-2193-3.

12. Jia, J.#; Lu, W.#; Liu, B.; Fang, H.; Yu, Y.; Mo, W.; Zhang, H.; Jin, X.; Shu, Y.; Long, Y.; Pei, Y.; Zhai, J.* (2022). An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length. Nature Plants, 8, 1118–1126. doi: 10.1038/s41477-022-01224-9.

13. Li, Z.#; Long, Y.#; Yu, Y.; Zhang, F.; Zhang, H.; Liu, Z.; Jia, J.; Mo, W.; Tian, S. Z.; Zheng, M.; Zhai, J.* (2022b). Pore‐C simultaneously captures genome‐wide multi‐way chromatin interaction and associated DNA methylation status in Arabidopsis. Plant Biotechnology Journal, 20, 1009–1011. doi: 10.1111/pbi.13811.

14. Yu, Y.#; Zhang, H.#; Long, Y.; Shu, Y.; Zhai, J.* (2022a). Plant Public RNA‐seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA‐Seq libraries. Plant Biotechnology Journal, 20, 806–808. doi: 10.1111/pbi.13798.

15. Mo, W.#; Liu, B.#; Zhang, H.; Jin, X.; Lu, D.; Yu, Y.; Liu, Y.; Jia, J.; Long, Y.; Deng, X.; Cao, X.; Guo, H.; Zhai, J.* (2021b). Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing. Genome Biology, 22, 322. doi: 10.1186/s13059-021-02543-4.

16. Long, Y.#; Jia, J.#; Mo, W.; Jin, X.; Zhai, J.* (2021). FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing. Nature Protocols, 16, 4355–4381. doi: 10.1038/s41596-021-00581-7.

17. Hu, D.#; Yu, Y.#; Wang, C.#; Long, Y.; Liu, Y.; Feng, L.; Lu, D.; Liu, B.; Jia, J.; Xia, R.; Du, J.; Zhong, X.; Gong, L.; Wang, K.*; Zhai, J.* (2021). Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions. The Plant Cell, 33, 2950–2964. doi: 10.1093/plcell/koab162.

18. Long, Y.#; Liu, Z.#; Jia, J.#; Mo, W.; Fang, L.; Lu, D.; Liu, B.; Zhang, H.; Chen, W.; Zhai, J.* (2021a). FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants. Genome Biology, 22, 66. doi: 10.1186/s13059-021-02288-0.

19. Jia, J.#; Ji, R.#; Li, Z.; Yu, Y.; Nakano, M.; Long, Y.; Feng, L.; Qin, C.; Lu, D.; Zhan, J.; Xia, R.; Meyers, B. C.; Liu, B.*; Zhai, J.* (2020). Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats. The Plant Cell, 32, 3662–3673. doi: 10.1105/tpc.20.00562.

20. Zhang, H.#; Zhang, F.#; Yu, Y.#; Feng, L.; Jia, J.; Liu, B.; Li, B.; Guo, H.; Zhai, J.* (2020). A Comprehensive Online Database for Exploring ∼20,000 Public Arabidopsis RNA-Seq Libraries. Molecular Plant, 13, 1231–1233. doi: 10.1016/j.molp.2020.08.001.

21. Jia, J.#; Long, Y.#; Zhang, H.; Li, Z.; Liu, Z.; Zhao, Y.; Lu, D.; Jin, X.; Deng, X.; Xia, R.; Cao, X.; Zhai, J.* (2020a). Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. Nature Plants, 6, 780–788. doi: 10.1038/s41477-020-0688-1.

22. Feng, L.#; Zhang, F.#; Zhang, H.; Zhao, Y.; Meyers, B. C.; Zhai, J.* (2020). An Online Database for Exploring Over 2,000 Arabidopsis Small RNA Libraries. Plant Physiology, 182, 685–691. doi: 10.1104/pp.19.00959.

23. Zhang, Y.#; Harris, C. J.#; Liu, Q.#; Liu, W.; Ausin, I.; Long, Y.; Xiao, L.; Feng, L.; Chen, X.; Xie, Y.; Chen, X.; Zhan, L.; Feng, S.; Li, J. J.; Wang, H.*; Zhai, J.*; Jacobsen, S. E.* (2018). Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. Proceedings of the National Academy of Sciences, 115, E1069–E1074. doi: 10.1073/pnas.1716300115.

24. Fang, H.; Liu, Z.; Long, Y.; Liang, Y.; Jin, Z.; Zhang, L.; Liu, D.; Li, H.; Zhai, J.*; Pei, Y.* (2017). The Ca2+/calmodulin2‐binding transcription factor TGA3 elevates LCD expression and H2S production to bolster Cr6+ tolerance in Arabidopsis. The Plant Journal, 91, 1038–1050. doi: 10.1111/tpj.13627.

25. Qi, Y.*; Chen, Y.*; Guo, H.*; Guo, H.*; Hang, R.*; Jia, G.*; Li, Y.*; Mo, B.*; Wang, Z.*; Wu, L.*; Xia, Y.*; Yang, X.*; Zhai, J.*; Zheng, B.*; Zhu, D.*; Cao, X.* (2026). RNA regulation in plants. Science China Life Sciences. Advance online publication. doi: 10.1007/s11427-026-3331-5.

26. Shi, Y.#; Liu, H.#; Yang, W.*; Zhai, J.*; Wang, H.* (2026a). Advances in single-cell and spatial omics for studying symbiotic nitrogen fixation: comparative cellular and evolutionary perspectives. Genome Biology, 27, 134. doi: 10.1186/s13059-026-04024-y.

27. Xue, Y.*; Cao, X.*; Chen, X.*; Deng, X.*; Deng, X. W.*; Ding, Y.*; Dong, A.*; Duan, C.-G.*; Fang, X.*; Gong, L.*; Gong, Z.*; Gu, X.*; He, C.*; He, H.*; He, S.*; He, X.-J.*; He, Y.*; He, Y.*; Jia, G.*; Jiang, D.*; Jiang, J.*; Lai, J.*; Lang, Z.*; Li, C.*; Li, Q.*; Li, X.*; Liu, B.*; Liu, B.*; Luo, X.*; Qi, Y.*; Qian, W.*; Ren, G.*; Song, Q.*; Song, X.*; Tian, Z.*; Wang, J.-W.*; Wang, Y.*; Wu, L.*; Wu, Z.*; Xia, R.*; Xiao, J.*; Xu, L.*; Xu, Z.-Y.*; Yan, W.*; Yang, H.*; Zhai, J.*; Zhang, Y.*; Zhao, Y.*; Zhong, X.*; Zhou, D.-X.*; Zhou, M.*; Zhou, Y.*; Zhu, B.*; Zhu, J.-K.*; Liu, Q.* (2025). Epigenetics in the modern era of crop improvements. Science China Life Sciences, 68, 1570–1609.
doi: 10.1007/s11427-024-2784-3.

28. Jiang, K.*; Guo, H.; Zhai, J.* (2023). Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity. Journal of Integrative Plant Biology, 65, 381–398. doi: 10.1111/jipb.13384.

29. Qin, Y.; Long, Y.; Zhai, J.* (2022). Genome-wide characterization of nascent RNA processing in plants. Current Opinion in Plant Biology, 69, 102294. doi: 10.1016/j.pbi.2022.102294.

30. Lu, D.; Zhai, J.*; Xi, M.* (2022). Regulation of DNA Methylation During Plant Endosperm Development. Frontiers in Genetics, 13, 760690. doi: 10.3389/fgene.2022.760690.

31. Yu, Y.; Zhai, J.* (2020b). The chromatin will never forget. Nature Plants, 6, 1396–1397. doi: 10.1038/s41477-020-00803-y.

32. Kuo, H. Y.#; Jacobsen, E. L.#; Long, Y.; Chen, X.; Zhai, J.* (2017). Characteristics and processing of Pol IV-dependent transcripts in Arabidopsis. Journal of Genetics and Genomics, 44, 3–6. doi: 10.1016/j.jgg.2016.10.009.