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, & Molecular Geneticist

Director of Genetics, Genomics and Bioinformatics Graduate Program

Gene regulation and signal transduction in plant immunity

Professor (2013-Present), UC Riverside
Associate Professor (2009-2013), UC Riverside
Assistant Professor (2004-2009), UC Riverside
Research Specialist (2000-2004), Plant Gene Expression Center, UC Berkeley. Postdoctoral Fellow (1996-1999), John Innes Center, UK. 

Ph.D. Plant Molecular Genetics (1996), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences.
B. Sc. Genetics (1991), Wuhan University, China

Biography & Research Interests

My laboratory studies the molecular mechanisms of small RNA-mediated gene regulation in plant disease resistance and defense responses. Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), have emerged as important regulators of eukaryotic gene expression by guiding mRNA cleavage, translational inhibition or chromatin modification. siRNA-induced gene silencing is a conserved regulatory process that has evolved as an antiviral defense mechanism in plants and animals. However, it is not known whether host cells also use siRNAs as an antibacterial or antifungal defense mechanism in eukaryotes.

The discovery of a bacteria-induced Arabidopsis siRNA in my lab provided the first example of the regulatory role of siRNAs in bacterial resistance and plant immunity. Functional analysis of the siRNA target identified a putative negative regulator of the resistance gene RPS2 signaling pathway. This study suggests a broader role forsiRNAs in host-defense mechanisms.The goal of my research is to identify and characterize pathogen-inducible endogenous small RNAs and understand their regulatory mechanisms in gene expression reprogramming during the host defense responses. We aim to identify novel signaling components within disease resistance network and to elucidate the crosstalk between multiple signal transduction pathways. A combination of functional genomics, molecular genetics and biochemical approaches are applied.


  • NSF IOS Award, 2013-2016
  • NIH R01 Award, 2010-2015
  • CDFA Specialty Crop Award, 2012-2015
  • NSF Career Award, 2007-2013
  • Awards from California Citrus Research Board, 2006-2013
  • University of California Riverside and Los Alamos National Lab Collaborative Award, 2008-2009
  • University of California Discovery Award, 2006-2009
  • Interdisciplinary Research Award, Institute for Integrative Genome Biology, UCR, 2007-2008
  • Hatch/AES-USDA Award, 2006-2015
  • Academic Senate Omnibus Research Award, 2005, 2007, 2009
  • Regents’ Faculty Fellowship/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
  • 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. 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, In press. 

  2. 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. [Highlighted in “This week in Science”, selected by Faculty of 1000. Also see Perspective by Baulcombe, 342 (6154) 45-46].
  3. Arne Weiberg, Ming Wang, Marschal Bellinger, and Hailing Jin: Small RNAs: A New Paradigm in Plant-Microbe Interactions. Annual Review of Phytopathology, 52:495-516. http://arjournals.annualreviews.org/eprint/rWwGmxW7EnRp7azMAWiw/full/10.1146/annurev-phyto-102313-045933

  4. Hailing Jin: From genomics and epigenomics to finding hidden regulators. Genome Biology, 2014, 15:302.

  5. Jang-Kyun Seo, Jianguo Wu, Yi Li*, Hailing Jin*: Contribution of small RNA pathway components in plant immunity. Mol Plant Microbe Interact. 2013, Mar 14. [Epub ahead of print].

  6. 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 Mar 1;123 (3):1057-67. doi: 10.1172/JCI65344.

  7. 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 Plant. 2013, Mar 15. [Epub ahead of print].

  8. 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, Jan 22. [Epub ahead of print].

  9. 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 (3): R20. 

  10. 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 (3):1279-92.

  11. 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(1):132.

  12. 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.

  13. 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. 2011, DOI: 10.1094/MPMI-01-11-0010.

  14. 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. 

  15. 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.

  16. 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. 

  17. 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. 

  18. Hailing Jin & Jian-Kang Zhu: A viral suppressor protein inhibits host RNA silencing by hooking up with Argonautes. Genes & Development, 2010, 24, 853-856.

  19. Hailing Jin* & Jian-Kang Zhu*: How many ways are there to generate small RNAs? Molecular Cell, 2010, 38, 775-777.

  20. Surekha Katiyar-Agarwal and Hailing Jin*: Role of Small RNAs in host-microbe interactions. Annu. Rev. Phytopathol. 2010, 48, 225-246.

  21. 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.

  22. 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.

  23. 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. 

  24. 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. 

  25. Iida K, Jin H, Zhu, JK. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana. BMC Genomics 2009, 10:155. 

  26. 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.

  27. 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. 

  28. 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 sativa. Genome Research, 2009, 19, 70-78

  29. 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.

  30. Hailing Jin*: Endogenous Small RNAs And Antibacterial Immunity in Plants. FEBS Letters, 2008, 582, 2679-84.

  31. 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.

  32. 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.

  33. 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.

  34. Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A Jr, Zhu JK, Staskawicz B*, Jin H.* 2006. A pathogen-inducible endogenous siRNA in plant immunity. Proc. Natl. Acad. Sci. USA 103: 1802-18007.

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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.

  40. 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.

  41. 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.

  42. 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.

  43. 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 Journal 2003, 34, 149-160.

  44. 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.

  45. 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.

  46. 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.

  47. Jin, H. and C. Martin. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol Biol. 1999, 41, 577-585.

  48. 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.

  49. 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.

  50. 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 RNA. Chinese Journal of Biotechnology 1995, 11, 20-26.  

  51. 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. RNA Abundance Analysis, a new volume for the "Methods in Molecular Biology"    book series, published by Humana Press, USA. 2012. Co-editors, Hailing Jin & Walter Gassmann.

Book Chapters:

  1. Yifan Lii and Hailing Jin*: Forward Chemical Screening of Small RNA Pathways. Plant Chemical Biology, Methods in Molecular Biology. Accepted.

  2. Hongwei Zhao, Yifan Lii, Pei Zhu, and Hailing Jin*:Isolation and Profiling of Protein-Associated Small RNAs. RNA Abundance Analysis, a new volume for the "Methods in Molecular Biology", 2012.

  3. Shang Gao and Hailing Jin*: Host small RNAs and plant innate immunity. Non Coding RNAs in Plants, RNA Technologies, 2011, DOI 10.1007/978-3-642-19454-2_2.

  4. Chellappan Padmanabhan and Hailing Jin*: Host endogenous small RNAs regulate plant innate immunity. Biology of Molecular Plant-Microbe Interactions, Volume 7. 2010.

  5. Padmanabhan Chellappan and Hailing Jin*: Discovery of plant microRNAs and short-interfering RNAs by deep parallel sequencing. Methods in Molecular Biology, 2009, 495, 121-132.

  6. Surekha Katiyar-Agarwal and Hailing Jin*: Discovery of Pathogen-Regulated Small RNAs in Plants. Methods in Enzymology, 2007, 427, 215-227.

  7. Hailing Jin*: Viral systemic movement and plant vascular development. Biology of Plant-Microbe Interactions, Volume 5. Published by International Society for Molecular-Microbe Interactions. St. Paul, Minnesota, USA. 2006, p423-426.

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