Yijun Qi, Ph.D.

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Scientists&Research

Associate Investigator, NIBS, Beijing, China

Research Description

RNA interference (RNAi) is a general phenomenon in eukaryotic organisms and plays important roles in diverse biological processes including developmental regulation, antiviral defense and chromatin remodeling. The key features of RNAi include the production of ~21-25 nt small RNAs by Dicer and the formation of Argonaute (AGO)-containing RNA-induced silencing complexes (RISCs) that carry out gene silencing at the transcriptional or post-transcriptional level.

In plants, there are several RNAi pathways. These include post-transcriptional gene silencing (PTGS) directed by small interfering RNAs and microRNA through mRNA cleavage or translational repression, and transcriptional gene silencing (TGS) that is associated with siRNA-directed chromatin remodeling including DNA and histone methylation.

We study the mechanisms of RNAi in plants using integrated genetic, molecular and biochemical approaches. Of particular interest are how RISC complexes are formed, how small RNAs guide and reinforce the chromatin remodeling at the homologous loci, and how RNAi components are specialized for distinct pathways.

The discovery of RNAi has not only expanded our understanding of the regulatory roles of RNA in gene expression, but also offered us a powerful genetic tool to study gene functions. We are interested in the application of RNAi in plant functional genomics.

Publications:

1.

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. This work was selected as the cover story and featured in Cell, 141: 556, 2010.

2.

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.

3.

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.

4.

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

5.

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.

6.

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)

7.

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.

8.

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

9.

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

10.

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.

11.

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.

12.

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 algaChlamydomonas reinhardtii. Genes and Development, 29: 1190-1203.(*co-corresponding authors) This work was featured in: Cell129:1029, 2007; Genes and Development 21: 1153-1156, 2007; Nature447: 5, 2007; Nature 447: 518, 2007; Nature Review Genetics 8: 406, 2007; ACS Chemical Biology 2: 436-437, 2007

13.

Itaya, A., Zhong, X., Bundschuh, R., Qi, Y., Wang, Y., Takeda, R., Harris, A., Molina, C., Nelson, R. and Ding, B. (2007) A structured viroid RNA serves as a substrate for Dicer-Like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. Journal of Virology 81(6):2980-2994.

14.

Qi, Y., He, X., Wang X-J., Kohany, O., Jurka, J. and Hannon, G. (2006)Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature, 443: 1008-1012.

15.

Zhong, X., Leontis, N., Qian, S., Itaya, A., Qi, Y., Boris-Lawrie, K. and Ding, B. (2006) Tertiary structural and functional analyses of a viroid RNA motif by Isostericity Matrix and mutagenesis reveal its essential role in replication. Journal of Virology 80(17):8566-8581.

16.

Qi, Y.*and Hannon, G*. (2005) Uncovering RNAi mechanisms in plants: Biochemistry enters the foray. FEBS Letters, 579: 5899-5903.(*co-corresponding author)

17.

Qi, Y., Denli, A. and Hannon, G.(2005). Biochemical specialization within Arabidopsis RNA silencing pathways. Molecular Cell , 19: 421-428.

18.

Qi, Y., Pélissier, T., Itaya, A., Hunt, E., Wassenegger, M. and Ding, B. (2004). Direct role of a viroid RNA motif in mediating directional RNA trafficking across a specific cellular boundary. The Plant Cell, 16(6): 1741-1752.

19.

Qi, Y.* Zhong, X., Itaya, A. and Ding, B.*(2004). Dissecting RNA silencing in protoplasts uncovers novel effects of viral suppressors on the silencing pathway at the cellular level. Nucleic Acids Research32(22):e179. (*co-corresponding authors)

20.

Qi, Y. and Ding, B. (2003). Differential subnuclear localization of RNA strands of opposite polarity derived from an autonomously-replicating viroid. The Plant Cell, 15(11): 2566-2577.

21.

Qi, Y. and Ding, B. (2003). Inhibition of cell growth and shoot development by a specific nucleotide sequence in a noncoding viroid RNA. The Plant Cell,15(6): 1360-1374.

22.

Ding, B., Itaya, A., and Qi, Y. (2003). Symplasmic protein and RNA traffic: regulatory points and regulatory factors. Current Opinion in Plant Biology, 6(6): 596-602.

23.

Qi, Y. and Ding, B. (2002). Replication of Potato spindle tuber viroid in cultured cells of tobacco and Nicotiana benthamiana: the role of specific nucleotides in determining replication levels for host adaptation.Virology, 302: 445-456.

24.

Qi, Y., Zhou, X., Huang, X., and Li, G. (2002). In vivo accumulation ofBroad bean wilt virus 2 VP37 protein and its ability to bind single-stranded nucleic acids. Archives of Virology, 147(5): 917-928.

25.

Zhu, Y., Qi, Y., Xun, Y., Owens, R., and Ding, B. (2002). Movement ofPotato spindle tuber viroid reveals regulatory points of phloem-mediated RNA traffic. Plant Physiology, 130(1): 138-146.

26.

Itaya, A., Ma, F., Qi, Y., Matsuda, Y., Zhu, Y., Liang, G. and Ding, B.(2002). Plasmodesma-mediated selective protein traffic between “symplasmically isolated” cells probed by a viral movement protein.The Plant Cell, 14(9): 2071-2083.

27.

Xie, Y., Zhou, X., Zhang, Z., and Qi, Y. (2002). Tobacco curly shoot virusisolated in Yunnan is a distinct species of Begomovirus. Chinese Science Bulletin, 47(3): 197-200.

28.

Zhou, X., Xie, Y., Zhang, Z., Qi, Y. and Wu, J. (2001). Molecular characterization of a novel defective DNA isolated from tobacco tissues infected with Tobacco leaf curl virus. Acta Virologica, 45(1): 45-50.

29.

Qi, Y., Zhou, X., and Li, D. (2000). Complete nucleotide sequence and infectious cDNA clone of the RNA1 of a Chinese isolate of Broad bean wilt virus 2. Virus Genes, 20(3): 201-207.

30.

Qi, Y., Zhou, X., Xue, C., and Li, D. (2000). Nucleotide sequence and polyprotein processing sites of the RNA2 of a Chinese isolate of Broad bean wilt virus 2. Progress in Natural Science, 10(7): 680-686.

31.

Qi, Y., Zhou, X., and Li, D. (2000). Characterization and RNA2 nucleotide sequence of Broad bean wilt virus isolate P158. Journal ofZhejiang University (Science), 1(4): 437-441.

32.

Xue, C., Zhou, X., Chen, Q., Qi, Y., and Li, D. (2000). Rapid construction of full-length cDNA clones of Tobacco mosaic virus and the infectivity assays of their in vitro transcripts. Acta Biochimica et Biophysica Sinica, 32(3): 270-274.

33.

Qing, L., Wu, J., Qi, Y., Zhou, X., and Li, D. (2000). Production of monocolonal antibodies against Broad bean wilt virus and their application in virus detection. Acta Microbiologica Sinica, 40(2): 166-173.

34.

Li, F., Zhou, X., Qi, Y., and Li, D. (2000). Characterization of an isolate of Cucumber mosaic virus subgroup III collected from tobacco inYunnan, China. Acta Microbiologica Sinica, 40(4): 346-351.

35.

Xue, C., Zhou, X., Chen, Q., Qi, Y., and Li, D. (2000). Complete nucleotide sequence and genomic organization of a Chinese isolate ofTomato mosaic virus. Science in China, 43(2): 200-208.

36.

Qi, Y., Zhou, X., and Li, D. (1999). Characterization of Broad bean wilt virus isolated from Glycine max. Chinese Journal of Applied and Environmental Biologym, 5(1): 69-72.

37.

Qi, Y., Zhou, X., Tao, X. and Li, D. (1999). Comparison of biological and serological characteristics of two isolates of Broad bean wilt virus.Journal of Zhejiang Agliculatural University, 25(3): 236-238.

38.

Zhou, X. and Qi, Y. (1999). Extraction methods of genomic DNA ofCotton leaf curl virus from infected cotton leaves. Chinese Journal of Agricultural Biotechnology, 7(2): 169-172.

39.

Zhou, X., Yu, Y., Qi, Y., and Li, D. (1997). Detection of Broad bean wilt virus in fields by double-antibody-sandwich ELISA. Acta Phytopathologica Sinica, 26(4): 247-352.

2001	Ph.D, Molecular Biology, Zhejiang University, Hangzhou,China
1995	B.Sc, Plant Pathology, Nanjing Argriculatural University,Nanjing, China

2010-2012	Associate Investigator, National Institute of Biological Sciences, Beijing, China
2006-2010	Assistant Investigator, National Institute of Biological Sciences, Beijing, China
2004-2006	Postdoctoral fellow, Cold Spring Harbor Laboratory, USA
2001-2004	Postdoctoral researcher, The Ohio State University, USA

1.	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. This work was selected as the cover story and featured in Cell, 141: 556, 2010.
2.	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.
3.	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.
4.	Qi, Y. and Mi, S. (2010). Purification of Arabidopsis Argonaute complexes and associated small RNAs. Methods in Molecular Biology,592:243-254.
5.	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.
6.	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)
7.	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.
8.	Zhao, T., Wang, W., Bai, X., and Qi, Y. (2009). Gene silencing by artificial microRNAs in Chlamydomonas. The Plant Journal, 58: 157-164.
9.	Gruntman, E., Qi, Y., Slotkin, R., Roeder, T., Martienssen, R., and Sachidanandam, R. (2008) Kismeth: Analyzer of plant methylation status through bisulfite sequencing. BMC Bioinformatics, 9:371. (*co-first authors)
10.	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.
11.	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.
12.	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 algaChlamydomonas reinhardtii. Genes and Development, 29: 1190-1203.(co-corresponding authors) This work was featured in: Cell129:1029, 2007; Genes and Development 21: 1153-1156, 2007; Nature447: 5, 2007; Nature 447: 518, 2007; Nature Review Genetics 8: 406, 2007; ACS Chemical Biology 2: 436-437, 2007
13.	Itaya, A., Zhong, X., Bundschuh, R., Qi, Y., Wang, Y., Takeda, R., Harris, A., Molina, C., Nelson, R. and Ding, B. (2007) A structured viroid RNA serves as a substrate for Dicer-Like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. Journal of Virology 81(6):2980-2994.
14.	Qi, Y., He, X., Wang X-J., Kohany, O., Jurka, J. and Hannon, G. (2006)Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature, 443: 1008-1012.
15.	Zhong, X., Leontis, N., Qian, S., Itaya, A., Qi, Y., Boris-Lawrie, K. and Ding, B. (2006) Tertiary structural and functional analyses of a viroid RNA motif by Isostericity Matrix and mutagenesis reveal its essential role in replication. Journal of Virology 80(17):8566-8581.
16.	Qi, Y.and Hannon, G. (2005) Uncovering RNAi mechanisms in plants: Biochemistry enters the foray. FEBS Letters, 579: 5899-5903.(*co-corresponding author)
17.	Qi, Y., Denli, A. and Hannon, G.(2005). Biochemical specialization within Arabidopsis RNA silencing pathways. Molecular Cell , 19: 421-428.
18.	Qi, Y., Pélissier, T., Itaya, A., Hunt, E., Wassenegger, M. and Ding, B. (2004). Direct role of a viroid RNA motif in mediating directional RNA trafficking across a specific cellular boundary. The Plant Cell, 16(6): 1741-1752.
19.	Qi, Y.* Zhong, X., Itaya, A. and Ding, B.(2004). Dissecting RNA silencing in protoplasts uncovers novel effects of viral suppressors on the silencing pathway at the cellular level. Nucleic Acids Research32(22):e179. (co-corresponding authors)
20.	Qi, Y. and Ding, B. (2003). Differential subnuclear localization of RNA strands of opposite polarity derived from an autonomously-replicating viroid. The Plant Cell, 15(11): 2566-2577.
21.	Qi, Y. and Ding, B. (2003). Inhibition of cell growth and shoot development by a specific nucleotide sequence in a noncoding viroid RNA. The Plant Cell,15(6): 1360-1374.
22.	Ding, B., Itaya, A., and Qi, Y. (2003). Symplasmic protein and RNA traffic: regulatory points and regulatory factors. Current Opinion in Plant Biology, `6(6): 596-602.`
23.	Qi, Y. and Ding, B. (2002). Replication of Potato spindle tuber viroid in cultured cells of tobacco and Nicotiana benthamiana: the role of specific nucleotides in determining replication levels for host adaptation.Virology, 302: 445-456.
24.	Qi, Y., Zhou, X., Huang, X., and Li, G. (2002). In vivo accumulation ofBroad bean wilt virus 2 VP37 protein and its ability to bind single-stranded nucleic acids. Archives of Virology, 147(5): 917-928.
25.	Zhu, Y., Qi, Y., Xun, Y., Owens, R., and Ding, B. (2002). Movement ofPotato spindle tuber viroid reveals regulatory points of phloem-mediated RNA traffic. Plant Physiology, 130(1): 138-146.
26.	Itaya, A., Ma, F., Qi, Y., Matsuda, Y., Zhu, Y., Liang, G. and Ding, B.(2002). Plasmodesma-mediated selective protein traffic between “symplasmically isolated” cells probed by a viral movement protein.The Plant Cell, 14(9): 2071-2083.
27.	Xie, Y., Zhou, X., Zhang, Z., and Qi, Y. (2002). Tobacco curly shoot virusisolated in Yunnan is a distinct species of Begomovirus. Chinese Science Bulletin, 47(3): 197-200.
28.	Zhou, X., Xie, Y., Zhang, Z., Qi, Y. and Wu, J. (2001). Molecular characterization of a novel defective DNA isolated from tobacco tissues infected with Tobacco leaf curl virus. Acta Virologica, 45(1): 45-50.
29.	Qi, Y., Zhou, X., and Li, D. (2000). Complete nucleotide sequence and infectious cDNA clone of the RNA1 of a Chinese isolate of Broad bean wilt virus 2. Virus Genes, 20(3): 201-207.
30.	Qi, Y., Zhou, X., Xue, C., and Li, D. (2000). Nucleotide sequence and polyprotein processing sites of the RNA2 of a Chinese isolate of Broad bean wilt virus 2. Progress in Natural Science, 10(7): 680-686.
31.	Qi, Y., Zhou, X., and Li, D. (2000). Characterization and RNA2 nucleotide sequence of Broad bean wilt virus isolate P158. Journal ofZhejiang University (Science), 1(4): 437-441.
32.	Xue, C., Zhou, X., Chen, Q., Qi, Y., and Li, D. (2000). Rapid construction of full-length cDNA clones of Tobacco mosaic virus and the infectivity assays of their in vitro transcripts. Acta Biochimica et Biophysica Sinica, 32(3): 270-274.
33.	Qing, L., Wu, J., Qi, Y., Zhou, X., and Li, D. (2000). Production of monocolonal antibodies against Broad bean wilt virus and their application in virus detection. Acta Microbiologica Sinica, 40(2): 166-173.
34.	Li, F., Zhou, X., Qi, Y., and Li, D. (2000). Characterization of an isolate of Cucumber mosaic virus subgroup III collected from tobacco inYunnan, China. Acta Microbiologica Sinica, 40(4): 346-351.
35.	Xue, C., Zhou, X., Chen, Q., Qi, Y., and Li, D. (2000). Complete nucleotide sequence and genomic organization of a Chinese isolate ofTomato mosaic virus. Science in China, 43(2): 200-208.
36.	Qi, Y., Zhou, X., and Li, D. (1999). Characterization of Broad bean wilt virus isolated from Glycine max. Chinese Journal of Applied and Environmental Biologym, 5(1): 69-72.
37.	Qi, Y., Zhou, X., Tao, X. and Li, D. (1999). Comparison of biological and serological characteristics of two isolates of Broad bean wilt virus.Journal of Zhejiang Agliculatural University, 25(3): 236-238.
38.	Zhou, X. and Qi, Y. (1999). Extraction methods of genomic DNA ofCotton leaf curl virus from infected cotton leaves. Chinese Journal of Agricultural Biotechnology, 7(2): 169-172.
39.	Zhou, X., Yu, Y., Qi, Y., and Li, D. (1997). Detection of Broad bean wilt virus in fields by double-antibody-sandwich ELISA. Acta Phytopathologica Sinica, 26(4): 247-352.