Plant Pathology Graduate Program

Hailing Jin

Hailing Jin
Office: 951-827-7995
3234B Genomics Bldg.
Office Hours: M,W, not specified - not specified
Email: hailingj@ucr.edu

Hailing Jin

Professor, & Cy Mouradick Endowed Chair
Director of Genetics,Genomics and Bioinformatics Graduate Program
Department of Plant Pathology and Microbiology
Center for Plant Cell Biology
Institute for Integrative Genome Biology

Biography & Research Interests

My lab studies the molecular mechanisms of plant immunity and pathogen virulence, 
 with an overall goal to develop effective and environmentally friendly strategies to control plant diseases and to ensure sufficient food production.  

Our research projects include:

  • Small RNAs and Cross-Kingdom RNAi in Plant - Pathogen Interactionsfigure 1

Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are important regulators of eukaryotic gene expression by guiding mRNA cleavage, translational inhibition or chromatin modification. We utilize genomics, genetics, molecular and biochemical approaches to identify and functionally characterize infection-regulated small RNAs, including those from plant hosts and from eukaryotic pathogens. My lab provided the first example of a plant endogenous siRNA that regulates plant immune responses. We further discovered that some small RNAs from aggressive fungal pathogens are delivered into host cells to hijack host RNAi machinery to suppress host immunity genes. These studies have added small RNAs to the list of pathogen effectors, which unveiled a novel virulence mechanism in aggressive eukaryotic pathogens. The transport of small RNAs from fungal pathogens to plant hosts also represents a naturally occurring cross-kingdom RNAi event. We recently show that such cross-kingdom RNAi is bi-directional, plants are also capable of delivery small RNAs into fungal pathogens to attenuate their virulence. 

  • Regulatory mechanisms of RNAi machinery in plant - pathogen interactions

My lab also studies the function and regulation of RNAi pathway components, mostly Argonaute (AGO) proteins in plant immunity. AGO proteins are the core components of RNAi complexes, which selectively bind with small RNAs and silence target genes with complementary sequences. We discovered that Arabidopsis AGO2 positively regulates antibacterial immunity by associating with miR393*, which targets a Golgi-localized SNARE gene MEMB12 and leads to increased secretion of antimicrobial peptide and confers resistance. Since miR393 also contributes to antibacterial immunity by suppressing auxin receptors, miR393*/miR393 represent a novel example of a miRNA*/miRNA pair that functions in the same cellular pathway (host immunity) through two distinct AGOs. We further demonstrated that small RNA duplex structures and AGO PIWI domain contribute to the selective loading of small RNAs in different AGO proteins, AGO1 and AGO2. We currently focus on the regulation and modification of AGO proteins in responses to pathogen attacks.

  • Epigenetic regulation of plant immune responses 

Surveillance of pathogen infection is mediated by intracellular NOD-like nucleotide-binding/leucine-rich-repeat receptors (NLRs) in both plants and animals. We recently discovered that some NBS-LRR genes, are under the control of specific plant chromatin remodeling proteins, as well as RNA-directed DNA methylation (RdDM) pathway. Such epigenetic regulation ensures precise expression of these resistance genes to avoid autoimmune responses or disease. 


  • Cy Mouradick  Endowed Chair , 2016

  • Elected Fellow of American Association for the Advancement of Science (AAAS), 2015

    UC President's Endowed Chair, 2015

    NSF Career Award, 2007-2013

    Academic Senate Omnibus Research Award, 2005, 2007, 2009

    Regents’ Faculty Development Award, 2004, 2006

    NSF Travel Award, Keystone Symposia, 2002

    EMBO Fellowship, European Molecular Biology Organization, 1999

    Excellent Performance Award, John Innes Center, Biotechnology and Biological Sciences Research Council, UK, 1997

    Beckman Excellent Ph.D. Dissertation Award, Beckman Instruments, Inc., China Office, 1995

    Outstanding Graduate Student Award, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 1992 and 1995



  1. Ming Wang and Hailing Jin*. "Spray-Induced Gene Silencing: a Powerful Innovative Strategy for Crop Protection". Trends in Microbiology (2016).
  2. Wang, M., A. Weiberg, F. M. Lin, B. P. Thomma, H. D. Huang and H. Jin*. "Bidirectional Cross-Kingdom Rnai and Fungal Uptake of External Rnas Confer Plant Protection." Nature Plants 2,  (2016): 16151.
  3. Dongdong Niu, Yifan E. Lii, Padmanabhan Chellappan, Lei Lei, Karl Peralta, Chunhao Jiang, Jianhua Guo, Gitta Coaker and Hailing Jin*: miRNA863-3p sequentially targets negative immune regulator pseudokinases ARLPKs and positive regulator SERRATE upon bacterial infection. Nature Communications, 2016, 7: 11324.
  4. Dong OX, Meteignier LV, Plourde MB, Ahmed B, Wang M, Jensen C, Jin H*, Moffett P, Li X, Germain H.: Arabidopsis TAF15b Localizes to RNA Processing Bodies and Contributes to snc1-Mediated Autoimmunity. Mol Plant Microbe Interact, 2016, 29: 247-257.
  5. Niu D, Xia J, Jiang C, Qi B, Ling X, Lin S, Zhang W, Guo J*, Jin H*, Zhao H.*: Bacillus cereus AR156 primes induced systemic resistance by suppressing miR825/825* and activating defense related genes in Arabidopsis. J Integr Plant Biol, 2015, 58: 426-439.
  6. Arne Weiberg, Hailing Jin*. Small RNAs — the secret agents in the plant–pathogen interactions. Current Opinion in Plant Biology, 2015, 26: 87-94.
  7. Arne Weiberg, Marshall Bellinger, Hailing Jin*: Conversations between kingdoms: small RNAs. Current Opinion Biotechnology, 2015, 32: 207-215.
  8. Ming Wang, Arne Weiberg, Hailing Jin*. Pathogen small RNAs: a new class of effectors for pathogen attacks. Mol Plant Pathol, 2015, 16: 219-223.
  9. Xiaoming Zhang, DongDong Niu, Alberto Carbonell, Airong Wang, Angel Lee, Vinnary Tun, Zonghua Wang, James C. Carrington, Chia-en A. Chang, Hailing Jin*: ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis. Nature Communications, 2014, 5: 5468.
  10. Arne Weiberg, Ming Wang, Marschal Bellinger, and Hailing Jin*Small RNAs: A New Paradigm in Plant-Microbe Interactions. Annual Review of Phytopathology, 2014, 52:495-516.
  11. Hailing Jin*: From genomics and epigenetics to finding hidden regulators. Genome Biology, 2014, 15:302.
  12. Yifan Lii and Hailing Jin*: Forward Chemical Screening of Small RNA Pathways. Plant Chemical Biology, Methods in Molecular Biology, 2014, 1056:95-101.
  13. Arne Weiberg, Ming Wang, Feng-Mao Lin, Hongwei Zhao, Zhihong Zhang, Isgouhi Kaloshian, Hsien-Da Huang, Hailing Jin*: Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science, 2013, 342 (6154) 118-123. 
    [Hightlighted in "This week in Science", selected by Faculty of 1000. Also see Perspective by Baulcombe, 342 (6154) 45-46.]
  14. Jang-Kyun Seo, Jianguo Wu, Yi Li*, Hailing Jin*: Contribution of small RNA pathway components in plant immunity. Mol Plant Microbe Interact. 2013,  26: 617-625.
  15. Chen Z, Lai TC, Jan YH, Lin FM, Wang WC, Xiao H, Wang YT, Sun W, Cui X, Li YS, Fang T, Zhao H, Padmanabhan C, Sun R, Wang DL, Jin H, Chau GY, Huang HD, Hsiao M, Shyy JY: Hypoxia-responsive miRNAs target argonaute 1 to promote angiogenesis. J Clin Invest. 2013, 123:1057-67.
  16. Xiaoming Zhang, Yifan Lii, Zhigang Wu, Stefano Lonardi, Jian-kang Zhu, Renyi Liu* and Hailing Jin*: Mechanisms of siRNA generation from cis-NATs in response to stresses. Molecular Plant2013,  6: 704-715.
  17. Zhao H., Sun R, Albrecht U, Padmanabhan C, Wang A, Coffey MD, Girke T, Wang Z, Close TJ, Roose M, Yokomi RK, Folimonova S, Vidalakis G, Rouse R, Bowman KD, Jin H*: Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus Huanglongbing disease. Molecular Plant. 2013, 6: 301-310. 
  18. Zhang X, Xia J, Lii Y, Barrera-Figueroa B, Zhou X, Gao S, Lu L, Niu D, Liang W, Chen Z, Leung C, Wong T, H. Zhang, Guo J, Li Y, Liu R, Zhu JK, Zhang W*, Jin H*: Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol. 2012, 13: R20. 
  19. Li W, Cui X, Meng Z, Huang X, Xie Q, Wu H, Jin H, Zhang D, Liang W: Transcriptional regulation of Arabidopsis MIR168a and ARGONAUTE1 homeostasis in ABA and abiotic stress responses. Plant Physiol. 2012, 158:1279-92.
  20. Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R, Zhu JK: High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. BMC Plant Biol. 2012, 12:132.
  21. Xiaoming Zhang, Hongwei Zhao, Shang Gao, Wei-Chi Wang, Surekha Katiyar-Agarwal, Hsien-Da Huang, Natasha Raikhel and Hailing Jin*: Arabidopsis Argonaute 2 regulates innate immunity via miRNA393*-mediated silencing of a Golgi-localized SNARE gene MEMB12. Molecular Cell, 2011, 42: 356-366.
  22. Panagiotis F. Sarris, Shang Gao, Konstantinos Karademiris, Hailing Jin, Kriton Kalantidis and Nickolas J. Panopoulos: Phytobacterial Type III Effectors HopX1, HopAB1 and HopF2 Enhance Sense-Post Transcriptional Gene Silencing Independently of Plant R Gene-Effector Recognition. Mol Plant Microbe Interact. 2012, 24: 907-917.
  23. Hongwei Zhao, Yifan Lii, Pei Zhu, and Hailing Jin*: Isolation and Profiling of Protein-Associated Small RNAs. RNA Abundance Analysis, Methods in Molecular Biology, 2012, 883:165-176
  24. Weixiong Zhang*, Shang Gao, Xiang Zhou, Padmanabhan Chellappan, Zheng Chen, Xuefeng, Zhou, Xiaoming Zhang, Nyssa Fromuth, Gabriela Coutino, Michael Coffey, and Hailing Jin*: Bacterial-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Molecular Biology, 2011, 75: 93-105.
  25. Niu DD, Liu HX, Jiang CH, Wang YP, Wang QY, Jin H, Guo J.: The Plant Growth-Promoting Rhizobacterium Bacillus cereus AR156 Induces Systemic Resistance in Arabidopsis thaliana by Simultaneously Activating Salicylate- and Jasmonate/Ethylene-dependent Signaling Pathways. Mol Plant Microbe Interact. 2011, 24: 533-42.
  26. Zhang W*, Gao S, Zhou X, Xia J, Chellappan P, Zhou X, Zhang X, Jin H.*: Multiple distinct small RNAs originated from the same microRNA precursors. Genome Biol. 2010, 11: R81.
  27. Padmanabhan Chellappan, Jing Xia, Xuefeng Zhou, Shang Gao, Xiaoming Zhang, Gabriela Coutino, Franck Vazquez, Weixiong Zhang and Hailing Jin*: siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acid Research, 2010, 38: 6883-94.
  28. Hailing Jin & Jian-Kang Zhu: A viral suppressor protein inhibits host RNA silencing by hooking up with Argonautes. Genes & Development, 2010, 24: 853-856.
  29. Hailing Jin* & Jian-Kang Zhu*: How many ways are there to generate small RNAs? Molecular Cell, 2010, 38: 775-777.
  30. Surekha Katiyar-Agarwal and Hailing Jin*: Role of Small RNAs in host-microbe interactions. Annu. Rev. Phytopathol. 2010, 48: 225-246.
  31. Zhihuan Gao, Hai-Liang Liu, Lucia Daxinger, Olga Pontes, Xinjian He, Weiqiang Qian, Mingtang Xie, Zdravko J. Lorkovic, Shoudong Zhang, Dominique Pontier, Thierry Lagrange, Steven E. Jacobsen, Hailing Jin, Antonius J.M. Matzke, Marjori Matzke, Craig S. Pikaard, and Jian-Kang Zhu: An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature, 2010, 465: 106-110. 
  32. Agee AE, Surpin M, Sohn EJ, Girke T, Rosado A, Kram BW, Carter C, Wentzell AM, Kliebenstein DJ, Jin HC, Park OK, Jin H, Hicks GR, Raikhel NV: MODIFIED VACUOLE PHENOTYPE1 is an Arabidopsis myrosinase-associated protein involved in endomembrane protein trafficking. Plant Physiol., 2010, 152: 120-32.
  33. Atsunari Tsuchisaka, Guixia Yu, Hailing Jin, Jose M. Alonso, Joseph R. Ecker, Xiaoming Zhang, Shang Gao and Athanasios Theologis: A Combinatorial Interplay Among the 1-Aminocyclopropane-1-carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana. Genetics, 2009, 183: 979-1003. 
  34. He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK: An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell, 2009,137: 498-508. 
  35. Iida K, Jin H, Zhu, JK: Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana. BMC Genomics, 2009, 10:155.
  36. Ni Li, Carolyn Jablonowski, Hailing Jin and Wenwan Zhong: Stand-Alone Rolling Circle Amplification Combined with Capillary Electrophoresis for Specific Detection of Small RNA. Analytical Chemistry 2009. 81: 4906-13.
  37. Padmanabhan Chellappan, Xiaoming Zhang and Hailing Jin*: Host small RNAs are big contributors in plant innate immunity. Current Opinion in Plant Biology, 2009, 12: 465-72. 
  38. Xuefeng Zhou, Ramanjulu Sunkar, Hailing Jin, Jian-Kang Zhu and Weixiong Zhang: Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativaGenome Research, 2009, 19, 70-78.
  39. Hailing Jin* (co-corresponding author), Vladimir Vacic, Thomas Girke, Stefano Lonardi and Jian-Kang Zhu*: Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Molecular Biology, 2008, 9:6. 
  40. Hailing Jin*: Endogenous Small RNAs And Antibacterial Immunity in Plants. FEBS Letters, 2008, 582, 2679-84. 
  41. Wen-Xue Li, Youko Oono, Jianhua Zhu, Xin-Jian He, Jian-Min Wu, Iida Kei, Xiao-Yan Lu, Xinping Cui, Hailing Jin and Jian-Kang Zhu: Transcriptional and posttranscriptional regulation of a transcription factor important for drought resistance in Arabidopsis. Plant Cell, 2008, 20, 2238-51. 
  42. Surekha Katiyar-Agarwal, Shang Gao, Adam Vivian-Smith and Hailing Jin*: A novel class of bacteria-induced small RNAs in Arabidopsis. Genes & Development 2007, 21, 3123-3134.
  43. Vladimir Vacic, Hailing Jin, Jian-Kang Zhu and Stefano Lonard: A probabilistic method for small RNA flowgram matching. Pacific Symposium on Biocomputing, 2008, 13, 75-86.
  44. Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A Jr, Zhu JK, Staskawicz B*, Jin H.*: A pathogen-inducible endogenous siRNA in plant immunity. Proc. Natl. Acad. Sci. USA. 2006,103, 1802-18007.
  45. Kim Baumann, Maria Perez-Rodriguez, Desmond Bradley, Julien Venail, Paul Bailey, Hailing Jin, Ronald Koes, Keith Roberts and Cathie Martin: Control of cell and petal morphogenesis by R2R3 MYB transcription factors. Development 2007, 134, 1691-1701.
  46. Surekha Katiyar-Agarwal and Hailing Jin*: Discovery of Pathogen-Regulated Small RNAs in Plants. Methods in Enzymology, 2007, 427, 215-227.
  47. Hailing Jin*, Songtao Li and Andy Villegas Jr.: Down Regulation of 26S Proteasome Subunit RPN9 Inhibits Viral Systemic Transport and Alters Plant Vascular Development. Plant Physiology, 2006, 142, 651-661. 
  48. Rojo E, M.R., Carter C, Zouhar J, Pan S, Plotnikova J, Jin H, Paneque M, Sanchez-Serrano JJ, Baker B, Ausubel FM, Raikhel NV: VPEgamma Exhibits a Caspase-like Activity that Contributes to Defense against Pathogens. Current Biology, 2004, 14, 1897-906. 
  49. Gianinna Brigneti, Ana M. Martín-Hernández, Hailing Jin, Judy Chen, David C. Baulcombe, Barbara Baker and Jonathan D.G. Jones: Virus-Induced Gene Silencing in Solanum Species.The Plant Journal. 2004, 39, 264-272.
  50. Ronning, C.M., S. Stegalkina, R. Ascenzi, O. Bougri, A. Hart, T. Utterbach, S. Vanaken, S.,  Riedmuller, J. White, J. Cho, G. Pertea, Y. Lee, S. Karamycheva, R. Sultana, J. Tsai, J. Quackenbush, K. Myers, S. Restrepo, C. Smart, W. Fry, R. van der Hoeven, S. Tanksley, P. Zhang, H. Jin, M. Yamamoto, B. Baker, and C.R. Buell: Comparative Analyses of Potato Expressed Sequence Tag Libraries. Plant Physiology 2003, 131, 419-429.
  51. Jin, H., M.J. Axtell, D. Dahlbeck, O. Ekwenna, S. Zhang, B. Staskawicz, and B. Baker: NPK1, an MEKK1-like mitogen-activated protein kinase kinase kinase, regulates innate immunity and development in plants. Developmental Cell 2002, 3, 291-297. 
  52. Cathie Martin, Kiran Bhatt, Kim Baumann, Hailing Jin, Sabine Zachgo, Keith Roberts, Zsuzsanna Schwarz-Sommer, Beverley Glover and Maria Perez-Rodrigues: The mechanics of cell fate determination in petals. Philos Trans R Soc Lond B Biol Sci. 2002, 357, 809-813.
  53. Jin, H., Y. Liu, K.-Y. Yang, C.-Y. Kim, B..Baker, and S. Zhang: Function of a mitogen-activated protein kinase pathway in N gene-mediated resistance in tobacco. The Plant Journal 2003, 33, 719-731. 
  54. Liu, Y., H. Jin, K.-Y. Yang , C.-Y. Kim, B. Baker, and S. Zhang: Interaction between two mitogen-activated protein kinases during tobacco defense signaling. The Plant Journal2003, 34, 149-160.
  55. Cathie Martin, Hailing Jin, Kathy Schwinn: Chapter Eight Mechanisms and applications of transcriptional control of phenylpropanoid metabolism. Recent Advances in Phytochemistry, 2001, 35:155-169.
  56. Jin, H., E. Cominelli, P. Bailey, A. Parr, F. Mehrtens, C. Tonelli, B. Weisshaar, and C. Martin: Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis.  EMBO Journal 2000, 19, 6150-6161.
  57. Meissner, R., H. Jin (co-first author), E. Cominelli, M. Denekamp, et.al.: Function search in a large transcription factor gene family in Arabidopsis: Assessing the potential of reverse genetics to identify insertional mutants in R2R3 MYB genes. Plant Cell 1999, 11, 1827-1840.
  58. Kranzl, H.D., M. Denekamp, R. G., H. Jin, A. Leyva, R. Meissner, K. Petroni, A. Urzainqui,  M.Bevan, C. Martin, S. Smeekens, C. Tonelli, J. Paz-Ares, B. Weisshaar.  Towards functional characterisation of the members of the R2R3- MYB gene family from Arabidopsis thaliana. The Plant Journal 1998, 16, 263-276.
  59. Jin, H. and C. Martin. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol. 1999, 41, 577-585.
  60. Song, R.-T., J. Li, H. Jin, Q.-Q. Zhang, and Z.-K. Xu. Influence of substrate and ribozyme sequences on the functions of ribozyme.  ACTA Biochimica et Biophysica Sinica 1997, 29, 61-67.
  61. Jin, H., Q.-Q. Zhang, R.-T. Shong, and Z.-K. Xu. Complementary expression of two defective TMV particles in tobacco.  Chinese Journal of Biochemistry and Biophysics 1996, 29(2): 131-139.
  62. Li, J., H. Jin, Q.-Q. Zhang, R.-T. Song, and Z.-K. Xu. Di-component ribozyme can function as two independent ribozymes on tobacco mosaic virus RNAChinese Journal of Biotechnology 1995, 11, 20-26.  
  63. Jin, H., H.-S. Shang, Q.-Q. Zhang, and Z.K. Xu. Cloning and expression of an antifreeze peptide gene of Winter Flounder in E.coli.  ACTA Biologiae Experimentalis Sinica 1995, 28, 77-83.

*: Corresponding author

Book Edited:

  1. Olga Pontes and Hailing Jin (Co-editors): Nuclear Functions in Plant Transcription and Signaling. Published by Springer, ISBN 978-1-4939-2385-4, 275 P., 18 Illus. in color., 2015.
  2. Hailing Jin & Walter Gassmann (Co-editors): RNA Abundance Analysis, a new volume for the "Methods in Molecular Biology" book series, published by Humana Press, USA. 2012. 

Book Chapters:

  1. Chellappan Padmanabhan and Hailing Jin: Host endogenous small RNAs regulate plant innate immunity. Biology of Molecular Plant-Microbe InteractionsVolume 7. 2010.
  2. Hailing Jin: Viral systemic movement and plant vascular development. Biology of Plant-Microbe InteractionsVolume 5. Published by International Society for Molecular-Microbe Interactions. St. Paul, Minnesota, USA. 2006, p423-426.Cathie Martin, Hailing Jin, Kathy Schwinn: Chapter Eight: Mechanisms and applications of transcriptional control of phenylpropanoid metabolism. Recent Advances in Phytochemistry, 2001, 35:155-169.
  3. Cathie Martin, Hailing Jin, Kathy Schwinn: Chapter Eight: Mechanisms and applications of transcriptional control of phenylpropanoid metabolism. Recent Advances in Phytochemistry, 2001, 35:155-169.

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