Yijun QI, Ph.D.

Professor, Changjiang Scholar Recipient of The National Science Fund for Distinguished Young Scholars



Ph.D, Molecular Biology, Zhejiang University, China

M.Sc, Plant Virology, Zhejiang Agricultural University, China


B.Sc, Plant Pathology, Nanjing Argriculatural University, Nanjing, China


Professor, School of Life Sciences, Tsinghua University, China


Associate Investigator, National Institute of Biological Sciences, Beijing, China


Assistant Investigator, National Institute of Biological Sciences, Beijing, China


Postdoctoral fellow, Cold Spring Harbor Laboratory, USA


Postdoctoral researcher, The Ohio State University, USA



Research interest

Functions and mechanisms of small RNAs and long non-coding RNAs in plants, Mechanisms of epigenetics in plants



Selected publications

Fang, X.#, Zhao, G.#, Zhang S., Li, Y., Gu, H., Li, Y., Zhao, Q. and  Qi, Y.* (2018) Chloroplast-to-nucleus signaling regulates microRNA  biogenesis in Arabidopsis. Developmental Cell, DOI:  10.1016/j.devcel.2018.11.046

Zhao, X.#, Li, J.#, Lian, B.#, Gu, H., Li, Y.*and Qi, Y.*(2018) Global  identification of ArabidopsislncRNAs reveals the regulation of  MAF4by a natural antisense RNA. Nature Communications, DOI:  10.1038/s41467-018-07500-7

Li, Y.#, Yuan, Y.#, Fang, X.#, Lu, X., Lian, B., Zhao, G. and Qi, Y.* (2018) A role for MINIYO and QUATRE-QUART 2 in the assembly of RNA polymerases II, IV and V in Arabidopsis. The Plant Cell, 30: 466-480.

Liu, C.#, Xin, Y.#, Xu, L.#, Cai, Z., Xue, Y., Liu, Liu, C., Xin, Y., Xu, L., Cai, Z., Xue, Y., Liu, Y., Xie, D., Liu, Y. and Qi, Y.* (2018) Arabidopsis ARGONAUTE1 binds chromatin to promote gene transcription in response to hormone and stress stimuli. Developmental Cell, 44: 348-361.

Yuan, J. #, Li, J. #, Yang, Y., Tan, C., Zhu, Y., Hu, L., Qi, Y. * and Lu, Z.* (2018) Stress-responsive regulation of long noncoding RNA polyadenylation in Oryza sativa. The Plant Journal, 93: 814-827.

Xu, L.#, Hu, Y.#, Cao, Y., Li, J., Ma, L., Li, Y.* and Qi Y. * (2018) An expression atlas of miRNAs in Arabidopsis thaliana. Science China Life Sciences, 61: 178-189.

Liu, M., Ba, Z., Costa-Nunes, P., Wei, W., Li, L., Kong, F., Li, Y., Chai, J., Pontes, O. and Qi, Y. * (2017) IDN2 interacts with RPA and facilitates DNA double-strand break repair by homologous recombination in Arabidopsis. The Plant Cell, 29: 589-599.

Cui, Y.#, Fang, X.# and Qi, Y.* (2016) TRANSPORTIN1 Promotes the Association of MicroRNA with ARGONAUTE1 in Arabidopsis. The Plant Cell, 28: 2576-2585.

Fang, X. and Qi, Y.* (2016) RNAi in plants: An Argonaute-centered view. The Plant Cell, 28: 272-285. (invited review)

Ye, R.#, Chen, Z.#, Lian, B., Rowley, M., Xia, N., Chai, J., Li, Y., Wierzbicki A., and Qi, Y. * (2016) A Dicer-independent route for biogenesis of siRNAs that direct DNA methylation in Arabidopsis. Molecular Cell, 61: 222-235.

Fang, X., Cui, Y., Li, Y., and Qi, Y.* (2015) Transcription and processing of primary miRNAs are coupled by Elongator complex in Arabidopsis. Nature Plants, doi:10.1038/nplants.2015.75.

Fang, X., Lu, X., Chen, Z., and Qi, Y.* (2015) CMA33/XCT regulates small RNA production through modulating the transcription of Dicer-Like genes in Arabidopsis. Molecular Plant, 8: 1227-1236.

Yang, Y.* and Qi, Y.* (2015) RNA-directed repair of DNA double-strand breaks. DNA Repair, 32: 82-85.

Wu, J., Yang, Z., Wang, Y., Zheng, L., Ye, R., Ji, Y., Zhao, S., Ji, S., Liu, R., Xu, L., Zheng, H., Zhou, Y., Zhang, X., Cao, X., Xie, L., Wu, Z. *, Qi, Y.*, and Li, Y.* (2015) Viral-Inducible Argonaute18 confers broad-spectrum virus resistance in rice by sequestering a host microRNA. eLife, 10.7554/eLife.05733.

Gao, M. #, Wei, W. #, Li, M. #, Wu, Y., Ba, Z., Jin K.-X., Li, M.-M., Liao, Y.-Q., Adhikari S., Chong, Z., Zhang, T., Guo, C.-X., Tang, T.-S., Zhu, B.-T., Xu, X.-Z., Mailand, N., Yang, Y.*, Qi, Y.*, and Rendtlew Danielsen, J. (2014) Ago2 Facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination. Cell Research,24: 532-541.

Li, J., Wu, Y., and Qi, Y.* (2014) MicroRNAs in a multicellular green alga Volvox carteri. Science China Life Sciences, 57: 36-45.

Ba, Z., and Qi, Y.* (2013) Small RNAs: Emerging key players in DNA double-strand break repair. Science China Life Sciences, 56: 933-936.

Zhong, S., Liu, J., Jin, H., Lin, L., Li, Q., Chen, Y., Yuan, Y., Wang, Z., Huang, H., Qi, Y., Chen. X., Vaucheret H., Chory J., Li, J., and He. Z.* (2013). Warm temperatures induce transgenerational epigenetic release of RNA silencing by inhibiting siRNA biogenesis in Arabidopsis. PNAS, 110(22): 9171-9176.

Wu, X., Shi, Y., Li, J., Xu, L., Fang, Y., Li, X., and Qi, Y.* (2013). A role for the RNA-binding protein MOS2 in microRNA maturation in Arabidopsis. Cell Research,23: 645-657.

Ye, R. #, Wang, W. #, Iki, T., Liu, C., Wu, Y., Ishikawa M., Zhou, X., and Qi, Y.* (2012). Cytoplasmic assembly and selective nuclear import of Arabidopsis ARGONAUTE4/siRNA complexes. Molecular Cell, 46: 859-870.

     Highlighted in Molecular Cell 46: 719-721, 2012   

Wei, W. #, Ba, Z. #, Gao, M., Wu, Y., Ma, Y., Amiard, S., White, C., Danielsen, J., Yang, Y., and Qi, Y.* (2012). A role for small RNAs in DNA double-strand break repair. Cell, 149: 101-112.

     Highlighted in Nature Review Genetics 13:299, 2012; Nature Reviews Molecular Cell Biology 13: 282, 2012; and Nature Structural & Molecular Biology 19: 470, 2012

     Recommended on Faculty of 1000 ( http://f1000.com/prime/14263986)

Wu, L.*, Mao, L., and Qi, Y. (2012) Roles of DICER-LIKE and ARGONAUTE proteins in TAS-derived small interfering RNA-triggered DNA methylation. Plant Physiology, 160: 990-999.

Shen, H., He, H., Li, J., Chen, W., Wang, X., Guo, L., Peng, Z., He, G., Zhong, S., Qi, Y., Terzaghi, and W., Deng, X.* (2012) Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 24: 875-892.

Wang, W. #, Ye, R. #, Xin, Y., Feng, X., Li, C., Zhou, X., and Qi, Y.* (2011). An Importin β protein negatively regulates microRNA activity in Arabidopsis. The Plant Cell, 23: 3565-3576. (Cover story)

Wang, Y., Itaya, A., Zhong, X., Wu, Y., Zhang, J., van der Knaap, E., Olmstead, R., Qi, Y., and Ding, B.* (2011). Function and evolution of a microRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. The Plant Cell, 23: 3185-3203.

Wu, L. #, Zhou, H. #, Zhang, Q., Ni, F., Liu, C., and Qi, Y.* (2010). DNA methylation mediated by a microRNA pathway. Molecular Cell, 38: 465-475. (Cover story)

     Highlighted in Cell, 141: 556, 2010.

Li, Y., Zhang, Q., Zhang, J., Wu, L., Qi, Y., and Zhou, J.* (2010). Identification of miRNAs involved in Pathogen-Associated Molecular Pattern-triggered plant innate immunity. Plant Physiology, 152: 2222-2231.

He, G., Zhu, X., Elling, A.A., Chen, L., Wang, X., Guo, L., Liang, M., He, H., Zhang, H., Chen, F., Qi, Y., Chen R., Deng, X.W.* (2010). Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. The Plant Cell, 22: 17-33.

Qi, Y.* and Mi, S. (2010). Purification of Arabidopsis Argonaute complexes and associated small RNAs. Methods in Molecular Biology, 592:243-254.

Wu, L., Zhang, Q., Zhou, H., Ni, F., Wu, X., and Qi, Y.* (2009). Rice microRNA effector complexes and targets. The Plant Cell, 21: 3421-3435.

Wei, B., Cai, T., Zhang, R., Li, A., Huo, N., Li, S., Gu, Y. Q., Vogel, J, Jia J., Qi, Y.*, Mao, L.* (2009). Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional and Integrative Genomics, 9: 499-511. (*co-corresponding authors)

Wang, X., Elling, A. A., Li, X., Li, N., Peng, Z., He, G., Sun, H., Qi, Y., Liu, S., Deng, X.W.* (2009). Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. The Plant Cell, 21: 1053-1069.

Zhao, T., Wang, W., Bai, X., and Qi, Y.* (2009). Gene silencing by artificial microRNAs in Chlamydomonas. The Plant Journal, 58: 157-164.

Gruntman, E. #, Qi, Y. #, Slotkin, R., Roeder, T., Martienssen, R., and Sachidanandam, R.* (2008) Kismeth: Analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics, 9:371. (*co-first authors)

Meyers, B.C.*, Axtell, M.J.*, Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., and Zhu, J.K. (2008). Criteria for annotation of plant microRNAs. The Plant Cell, 20: 3186-3190.

Mi, S. #, Cai, T. #, Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G., and Qi, Y.* (2008) Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5’ terminal nucleotide. Cell, 133: 116-127. 

     This work was featured in Cell 133:25-26, 2008.

Zhao, T. #, Li, G. #, Mi, S., Li, S., Hannon, G., Wang, X.-J.*, and Qi, Y*. (2007). A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes and Development, 29: 1190-1203. (*co-corresponding authors)  

     Highlighted in: Cell 129:1029, 2007; Genes and Development 21: 1153-1156, 2007; Nature 447: 5, 2007; Nature 447: 518, 2007; Nature Review Genetics 8: 406, 2007; ACS Chemical Biology 2: 436-437, 2007


Contact information

Email: qiyijunATtsinghua.edu.cn