Yanhai Yin, GDCB chair

Yanhai Yin

Position
  • Professor and Chair

Contact Info

1035D Roy J Carver Co-Lab
Ames
,
IA
50011-1085
Email
yin@iastate.edu
Phone
515-294-4971

Education

  • B.S., Biology, Sichuan University, Chendu, China, 1985
  • M.S., Cell Biology and Genetics, Institute of Botany, Chinese Academy of Sciences, Beijing, China, 1988
  • Ph.D., Macromolecular and Cellular Structure and Chemistry, The Scripps Research Institute, La Jolla, 1997

More Information

Research Description

My laboratory is interested in understanding the molecular mechanisms and gene regulatory networks through which plant steroid hormone, Brassinosteroid (BRs), regulate plant growth and stress responses. We use a combination of genetics, genomics, computational modeling and predicative phenomics approaches and model plant Arabidopsis thaliana in our research. Our long-term goal is to apply the knowledge generated from model systems to improve crop production under adverse climate conditions. There are several lines of research supported by grants from NIH, NSF and Plant Sciences Institute (PSI) at Iowa State University:

1. Investigate the mechanisms and networks for BR regulated plant growth and stress responses using genomics, computational modeling and phenomics: We have previously established that BRs function through BES1/BZR1 family transcriptional factors to mediate BR responses (Yin et al., 2002, 2005). We have identified many BES1 interacting proteins and target genes, based on which we have established BR Gene Regulatory Networks (GRNs, Yu et al., 2011, Guo et al, 2013, Nolan et al., 2017, Ye et al., 2017, Chen, et al., 2017, Chockalingam et al., 2017, Xie et al., 2018, Jiang et al., 2019, Nolan et al., 2020, Clark et al., 2021). We are currently investigating the functions of genes in the BR GRNs and the mechanisms of actions in plant growth and stress responses. We are also developing new phenotyping tools that can be used to study the functions of a large number of genes in GRNs (Bao et al., 2019, Xiang et al., 2021). Our collaborators include J. Walley, L. Tang, P. Schnable, S. Sarkar, B. Ganapathysubramanian, D. Nettleton, S. Howell, M. Aluru, and S. Aluru. Supported by NSF and PSI.

2. Explore the crosstalk between brassinosteroid and autophagy signaling pathways: We have recently found that BR signaling component BES1 is targeted to autophagy pathway for degradation under drought and carbon starvation conditions through E3 ubiquitin ligases SINAT2 and BAF1 and ubiquitin receptor DSK2 (Nolan et al., 2017, Yang et a., 2017, Wang et al., 2021).  In collaboration with D. Bassham and J. Walley labs, we are investigating the detailed molecular mechanisms and regulatory networks underlying autophagy and BR crosstalk. Supported by NIH and PSI.

3. Define the functions and signaling pathways for FERONIA (FER) and HERCULES Receptor-Like Kinases (HERKs): Leading by Hongqing (Michelle) Guo (https://www.gdcb.iastate.edu/people/hongqing-michelle-guo), we have previously discovered that several CrRLK1L family receptor kinase genes, including HERK1, THE1 (THESEUS 1) and FER, are regulated by BRs and involved in plant growth and immunity (Guo et al., 2009; Guo et al., 2018).  We are using multidisciplinary approaches to study signaling transduction pathways for these receptor kinases. Our current collaborators on this project include J. Walley and Y. Lee. Supported by LAS Signature Research Initiative (SRI) and PSI.

4. Determine the functions of brassinosteroid in crops: In collaborating with E. Vollbrecht, P. Becraft, C. Chu, and T. Lubberstedt, we are investigating the BR functions in maize and rice using CRISPR-cas9, Genome-Wide Association Studies (GWAS) and functional genomics approaches (Kir et al., 2015, Tong et al, 2014, Hu et al, 2017). Supported by PSI.

Publications

Complete list: https://scholar.google.com/citations?user=l8d1bLcAAAAJ&hl=en&oi=ao

  • Nolan, TM, N Vukašinović, C-W Hsu, J Zhang, I Vanhoutte, R Shahan, IW Taylor, L Greenstreet, M Heitz, A Afanassiev, P Wang, P Szekely, A Brosnan, Y Yin, G Schiebinger, U Ohler, E Russinova, PN Benfey. 2023. Brassinosteroid gene regulatory networks at cellular resolution. Science. DOI: 10.1126/science.adf4721
  • Guo H , Y Yin*  (2023) Redesigning green revolution trait with increased grain yield and nitrogen utilization efficiency by reducing brassinosteroid signaling in semidwarf wheat. Sci China Life Sci. https://doi.org/10.1007/s11427-023-2401-3.
  • Liao CY, Y Pu, TM Nolan, C Montes, H Guo, JW Walley, Y Yin, and DC Bassham. 2023. Brassinosteroids modulate autophagy through phosphorylation of RAPTOR1B by the GSK3-like kinase BIN2 in Arabidopsis. Autophagy. 19:1293-1310. https://doi.org/10.1080/15548627.2022.2124501.
  • Wang P, Clark MC, Nolan TM, Song G, Bartz PM, Liao CY, Montes C, Katz E, Polko JK, Kieber JJ, Kliebenstein DJ, Bassham DC, Walley JW, Yin Y*, Guo H*. 2022. Integrated  omics reveal novel functions of FERONIA receptor kinase in Arabidopsis thaliana.  Plant Cell. 34: 2594–2614. https://doi.org/10.1093/plcell/koac111
  • Montes C, P Wang, CY Liao, TM Nolan, G Song, NM Clark, JM Elmore, H Guo, DC Bassham, Y Yin, JW Walley. 2022. Integration of multi-omics data reveals interplay between brassinosteroid and TORC signaling in Arabidopsis. New Phytol, 236: 893–910. https://doi.org/10.1111/nph.18404.
  • Wang P, NM Clark, TM Nolan, G Song, OG Whitham, CY Liao, C Montes-Serey, DC Bassham, JW Walley, Y Yin, H Guo* (2022) Feronia functions through Target of Rapamycin (TOR) to negatively regulate autophagy. Front Plant Sci, 13:961096. https://doi.org/10.3389/fpls.2022.961096. 
  • Wang P, TM Nolan, NM Clark, H Jiang, C Montes, H Guo, DC Bassham, JW Walley, Y Yin*. 2021. The F-box E3 ubiquitin ligase BAF1 mediates the degradation of the brassinosteroid-activated transcription factor BES1 through selective autophagy in Arabidopsis. Plant Cell. 33:3532-3554.doi: 10.1093/plcell/koab210
  • Clark NM, TM Nolan, P Wang, G Song, C Montes, H Guo, R Sozzani, Y Yin, JW Walley. 2021. Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. Nature Communications 12, 5858. https://doi.org/10.1038/s41467-021-26165-3.
  • Liu D, Zhao H, Xiao Y, Zhang G, Cao S, Yin W, Qian Y, Yin Y, Zhang J, Chen S, Chu C, Tong H. 2021 A Cryptic Inhibitor of Cytokinin Phosphorelay Controls Rice Grain Size. Mol Plant. S1674-2052(21) 00370-1. doi: 10.1016/j.molp.2021.09.010.
  • Liu H, Liu L, Liang D, Zhang M, Jia C, Qi M, Liu Y, Shao Z, Meng F, Hu S, Yin Y, Li C, Wang Q. 2021 SlBES1 promotes tomato fruit softening through transcriptional inhibition of PMEU1. iScience. 24(8):102926. doi: 10.1016/j.isci.2021.102926.
  • Xiang L, TM Nolan, Y Bao, M Elmore, T Tuel, J Gai, D Shah, NM Huser, AM Hurd, SA McLaughlin, SH Howell, JW Walley, Y Yin*, L Tang* 2021. Robotic Assay for Drought (ROAD): an automated phenotyping system for brassinosteroid and drought response. Plant Journal. 107:1837-1853. doi:10.1111/tpj.15401.
  • Jiang H. and Yin Y*. Brassinosteroids. 2021. In “Encyclopedia of Biochemistry 3rd Edition” Joseph Jez ed. Elsevier Inc. eBook ISBN: 9780128220405.
  • Klionsky, D. J. et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 17, 1-382.
  • D Zhang, W Tan, F Yang, Q Han, X Deng, H Guo, B Liu, Y Yin, H Lin. 2021. A BIN2-GLK1 Signaling Module Integrates Brassinosteroid and Light Signaling to Repress Chloroplast Development in the Dark. Developmental Cell. 56: 310-324. doi: 10.1016/j.devcel.2020.12.001 
  • Nolan TM, Vukašinović N, Liu D, Russinova E, Yin Y*. 2020. Brassinosteroids: Multidimensional Regulators of Plant Growth, Development, and Stress Responses. Plant Cell. 32:295-318. doi: 10.1105/tpc.19.00335.
  • A Kono, Y Yin*. 2020. Updates on BES1/BZR1 Regulatory Networks Coordinating Plant Growth and Stress Responses. Frontiers in Plant Science 11, 1948. doi: 10.3389/fpls.2020.617162
  • Liang T, Shi C., Peng Y, Tan H, Xin P, Yang Y, Wang F, Li X, Chu J, Huang J, Yin Y, Liu H. 2020 BES1 coordinates growth and UV-B stress responses. Plant Cell. tpc.00048.2020; DOI: 10.1105/tpc.20.00048
  • Li T, Lei W, He R, Tang X, Han J, Zou L, Yin Y, Lin H, Zhang D. (2020) Brassinosteroids regulate root meristem development by mediating BIN2-UPB1 module in Arabidopsis. PLoS Genet 16(7): e1008883. https://doi.org/10.1371/journal.pgen.1008883
  • Xie Z., Nolan TM, Jiang H, Tang B, Zhang M, Li Z and Yin Y*. 2019. The AP2/ERF Transcription Factor TINY Modulates Brassinosteroid-Regulated Plant Growth and Drought Response in Arabidopsis. Plant Cell. 31: 1788-1806. doi:10.1105/tpc.18.00918.
  • Guo H, Yin Y (2019) Measuring protein half-life in Arabidopsis thaliana. Bio-protocol, 9(15): e3318. doi:10.21769/BioProtoc.3318.
  • Bao Y, Zarecor S, Shah D, Tuel T, Campbell DA, Chapman AVE, Imberti D, Kiekhaefer D, Imberti H, Lübberstedt T, Yin Y, Nettleton DS, Lawrence-Dill CJ, Whitham SA, Tang L, Howell SH (2019) Assessing plant performance in the Enviratron. Plant Methods, 15: 117. doi:10.1186/s13007-019-0504-y.
  • Jiang H, Tang B, Xie Z, Nolan TM, Ye H, Song G, Walley JW, Yin Y* (2019) GSK3-like kinase BIN2 phosphorylates RD26 to potentiate drought signaling in Arabidopsis. Plant J. doi:10.1111/tpj.14484.
  • Zhang L, Han Q, Xiong J, Zheng T, Han V, Zhou H, Lin H, Yin Y, Zhang D (2019) Sumoylation of BRI1-EMS-SUPPRESSOR 1 (BES1) by the SUMO E3 ligase SIZ1 negatively regulates brassinosteroids signaling in Arabidopsis thaliana. Plant Cell Physiol, 60(10): 2282-2292. doi:10.1093/pcp/pcz125.
  • Xie Z., Nolan TM, Jiang H, Yin Y*. 2019.  AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Frontiers in Plant Science. 10: 228. doi:10.3389/fpls.2019.00228.
  • Wang P, Nolan TM, Yin Y, Bassham DC. 2019. Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis. Autophagy. doi:10.1080/15548627.2019.1598753.
  • Hansen RL, Guo H, Yin Y, Lee YJ. 2018. FERONIA mutation induces high levels of chloroplast‐localized Arabidopsides which are involved in root growth. The Plant Journal. 97(2): 341-351.
  • Guo H*, Nolan TM, Xie Z, Song G, Walley JW, Yin Y*. 2018. FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana. Current Biology. 28: 3316-3324.
  • Tan W, Zhang D, Zhou H, Zheng T, Yin Y, Lin H (2018) Transcription factor HAT1 is a substrate of SnRK2.3 kinase and negatively regulates ABA synthesis and signaling in Arabidopsis responding to drought. PLoS Genet, 14(4): e1007336.
  • Liang T, Mei S, Shi, Yang Y, Peng Y, Ma L, Wang F, Li X, Huang X, Yin Y, Liu H. 2018. UVR8 Interacts with BES1 and BIM1 to Regulate Transcription and Photomorphogenesis in Arabidopsis. Dev. Cell. 44: 512-523.
  • Nolan, T.M., Brennan, B., Yang, M., Chen, J., Zhang, M., Li, Z., Wang, X., Bassham, D., Walley, J. and Yin Y*. 2017. Selective Autophagy of BES1 Mediated by DSK2 Balances Plant Growth and Survival. Dev. Cell.  41: 33-46.
  • Ye, H., Liu, S., Tang, B., Chen, J., Xie, Z., Nolan. T.M., Jiang, H., Guo, H., Lin, H.-Y., Li, L., Wang, Y., Tong, H., Zhang, M., Li, Z., Chu, C., Aluru, M., Aluru, S., Schnable, P. S. S., Yin, Y*. 2017. RD26  mediates crosstalk between drought and brassinosteroid signaling pathway. Nature Communications. 8:14753.
  • Chen, J., Nolan. T.M., Ye, H., Zhang, M., Tong, H., Xin, P., Chu, J., Chu, C., Li, Z., Yin, Y*. 2017. Arabidopsis WRKY46, WRKY54 and WRKY70 Transcription Factors Are Involved in Brassinosteroid-Regulated Plant Growth and Drought Response. Plant Cell. 29: 1425-1439.
  • Chen J, Yin Y*. (2017) WRKY transcription factors are involved in brassinosteroid signaling and mediate the crosstalk between plant growth and drought tolerance. Plant Signal Behav. 2017 12: e1365212. doi: 10.1080/15592324.2017.1365212.
  • Yang, M., Li, C., Cai, Z., Hu, Y., Nolan, T., Yu, F., Yin, Y., Xie, Q., Tang, G., Wang, X. 2017. SINAT E3 ligases control the light-mediated stability of the brassinosteroid-activated transcription factor BES1 in Arabidopsis. Dev. Cell.  41: 47-58.
  • Nolan, T. M., Chen, J. and Yin, Y*. 2017. Cross-talk of Brassinosteroid Signaling in Controlling Growth and Stress Responses. Biochem. J. 474: 2641-2661.
  • Chockalingam, S. P., Aluru, M., Guo, H., Yin, Y., Aluru, S. 2017. Reverse Engineering Gene Networks: A Comparative Study at Genome-scale. The 8th ACM International Conference. DOI: 10.1145/3107411.3107428.
  • Jiang, H., Wang X., Nolan, T.M., Yin, Y.  Aluru M.R., L. Dong. (2017) Automated microfluidic plant chips-based plant phenotyping system. NEMS: 756-760.
  • Hu S, Sanchez DL, Wang C, Lipka AE, Yin Y, Gardner CAC, Lübberstedt T. Brassinosteroid and gibberellin control seedling traits in maize (Zea mays L.). Plant Sci. 263:132-141. doi: 10.1016/j.plantsci.2017.07.011.
  • Hu S, Wang C, Sanchez DL, Lipka AE, Liu P, Yin Y, Blanco M, Lübberstedt T. 2017. Gibberellin promote brassinosteroid action and both increase heterosis for plant height in maize (Zea mays L.). Front Plant Sci. 8:1039. doi: 10.3389/fpls.2017.01039. 
  • Nolan, T., Liu, S., Guo, H., Li, L., Schnable, S. & Yin, Y*. 2017. Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High­throughput Sequencing (ChIP­seq) and RNA­seq. Method in Molecular Biology. 1564: 63-79.
  • Deng, X.G., Zhu, T., Peng, X.J., Xi, D.H., Guo, H., Yin, Y., Zhang D.W., Lin, H.H. 2016. Role of brassinosteroid signaling in modulating Tobacco mosaic virus resistance in Nicotiana benthamiana. Sci Rep. 2016 Feb 3; 6: 20579.
  • Kir, G., Ye, H., Nelissen, H., Neelakandan, A.K., Kusnandar, A.S., Luo, A., Inze, D., Sylvester, A., Yin, Y., Becraft, P.W. (2015) RNAi knockdown of BRI1 in maize (Zea mays) reveals novel functions for brassinosteroid signaling in controlling plant architecture. Plant Physiol. 169: 826-839.
  • Wang, X., Chen J., Xie, Z., Liu, S., Nolan, T., Ye, H., Zhang, M., Guo, H., Schnable, P.S., Li, Z. and Yin, Y. 2014. Histone Lysine Methyltransferase SDG8 Is Involved in Brassinosteroid Regulated Gene Expression in Arabidopsis thaliana. Molecular Plant. 7: 1303-1315.
  • Tong, H., Xiao, Y., Liu, D., Gao, S., Liu, L., Yin, Y., Jin, Y. Qian, Q., and Chu, C. 2014. Brassinosteroid regulates cell elongation by modulating gibberellin metabolism in rice. Plant Cell, 26: 4376-93.
  • Mantilla Perez, M.B., Zhao, J., Yin, Y., Hu, J., Salas Fernandez, M.G. 2014. Association mapping of brassinosteroid candidate genes and plant architecture in a diverse panel of Sorghum bicolor. Theor Appl Genet. 127: 2645-62.
  • Zhang, D., Yuan, S., Xu, F., Zhu, F., Yuan, M., Ye, H., Guo, H., Lv, X., Yin, Y. and Lin, H. 2014. Light intensity affects chlorophyll synthesis during greening process by metabolite signal from mitochondrial alternative oxidase in Arabidopsis. Plant Cell & Environment. 39: 12-25.
  • Zhang, D., Ye, H., Guo, H., Johnson, A., Zhang, M., Lin, H., and Yin, Y. 2014. Transcription Factor HAT1 is Phosphorylated by BIN2 Kinase and Mediates Brassinsteroid Repressed Gene Expression in Arabidopsis. Plant J. 77: 59-70
  • Zhang, D., Ye, H., Guo, H., Johnson, A., Zhang, M., Lin, H., and Yin, Y. 2014. Transcription factors involved in brassinosteroid repressed gene expression and their regulation by BIN2 kinase. Plant Signal Behav. 9: e27849
  • Guo H, Li L, Aluru M, Aluru S, Yin Y. 2013. Mechanisms and networks for brassinosteroid regulated gene expression. Curr Opin Plant Biol. 16:545-53.
  • Hao J. Yin, Y., Fei, S. 2013. Brassinosteroid Signaling network: implications on yield and stress tolerance.  Plant Cell Report. 32: 1017-1030.
  • Ye, H., Li, L., Guo, H., Yin Y. (2012) MYBL2 is a substrate of GSK3-like kinase BIN2 and acts as a corepressor of BES1 in brassinosteroid signaling pathway in Arabidopsis. Proc Natl Acad Sci U S A. 109: 20142-20147.
  • Tong, H., Liu, L., Jin, Y., Du, L., Yin Y., Qian, Q., Zhu, L. and Chu, C. 2012. DWARF AND LOW-TILLERING Acts as a Direct Downstream Target of a GSK3/SHAGGY-Like Kinase to Mediate Brassinosteroid Responses in Rice. Plant Cell. 24: 2562-2577.
  • Ye H, Li L, Yin Y (2011) Recent advances in the regulation of brassinosteroid signaling and biosynthesis pathways. J. Integr. Plant Biol. 53, 455–468.
  • Yu, X*, Li, L*, Zola, J, Aluru, M, Ye, H, Foudree, A, Guo, H, Anderson, S, Aluru, S, Liu, P, Rodermel, S, and Yin, Y. (2011) A Brassinosteroid transcriptional network revealed by genome-wide identification of BES1 target genes in Arabidopsis thaliana. Plant J. 65: 634-646. (*co-first authors).
  • Li, L., Yu, X., Ye, H., Guo, H., Yin, Y. (2010). Arabidopsis IWS1 interacts with transcription factor BES1 and is involved in Brassinosteroid regulated gene expression. Proc Natl Acad Sci U S A. 107: 3918-3923.
  • Ye, Q., Zhu, W., Li, L.,Yin, Y., Ma, H., Wang, X. 2010. Brassinosteriods control male fertility by regulating the expression of key genes involved in Arabidopsis anther and pollen development. Proc Natl Acad Sci USA 107: 6100-6105.
  • Guo, H., Li, L., Ye, H., Yu, X., Algreen, A.,Yin, Y. 2009. Three related receptor-like kinases are required for optimal cell elongation in Arabidopsis thaliana. Proc Natl Acad Sci USA 106: 7648-7653.
  • Li, L., Yu, X., Thompson, A., Guo, M. Yoshida, S., Asami, T., Chory, J., Yin, Y. 2009. Arabidopsis MYB30 is a direct target of BES1 and cooperates with BES1 to regulate brassinosteroid target gene expression. Plant J. 58: 275-286.
  • Guo, H., Ye, H., Li, L.,Yin, Y. 2009. A Family of Receptor-Like Kinases Are Regulated by BES1 and Involved in Plant Growth in Arabidopsis thaliana. Plant Signaling & Behavior 4: 784-786.
  • Srivastava, R., Liu, J., Guo, H., Yin, Y., Howell, S. 2009. Regulation and processing of a plant peptide hormone, AtRALF23, in Arabidopsis. Plant J. 59: 930-939.
  • Tong, H., Jin, Y., Liu, W., Li, F., Yin Y., Qian, Q., Zhu, L. and Chu, C. 2009. Dwarf and low-tillering, a new member of the GRAS family, plays positive roles in brassinosteroid signaling in rice. Plant J. 58: 803-816.
  • Salas Fernandez, M.G., Becraft, P.W., Yin, Y., Lübberstedt, T. 2009. From dwarves to giants? Plant height manipulation for biomass yield.Trend Plant Sci 14: 454-461.
  • Yu, X., Li, L., Li, L., Guo, H., Chory, J., Yin, Y. 2008. Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc Natl Acad Sci USA 105: 7618-7623.
  • Yin, Y. Vafeados, D., Tao, Y., Yoshida, S., Asami, T., Chory, J. 2005. A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell 120: 249-259.
  • Mora-Garcia, S., Vert, G., Yin, Y., Cano-Delgado, A., Cheong, H., and Chory, J. 2004. Nuclear protein phosphotases with Kelch-repeat domains modulate the response to bassinosteroids in Arabidopsis. Genes & Development 18: 448-460.
  • Caño-Delgado, A.*, Yin, Y.*, Yu, C.*, Vafeados, D., Mora-García, S., Cheng, J-C., Nam, K.H.2, Li, J. and Chory, J. 2004. BRL1 and BRL3 are novel brassinosteroid receptors that function in vascular differentiation in Arabidopsis. Development 131: 5341-5351 (*cofirst authors).
  • Yin, Y., Cheong, H., Friedrichsen, D., Zhao, Y., Hu, J., Mora-Garcia, S., and Chory, J. 2002. A crucial role for putative Arabidopsis topoisomerase VI in plant growth and development. Proc Natl Acad Sci USA 99: 10191-10196.
  • Yin, Y., Wang , Z-Y., Mora-Garcia, S., Li, J., Yoshida, S., Asami, T., and Chory, J. 2002. BES1 acccumulates in the nucleus in response to brassinosteroid to regulate gene expression and promotes stem elongation. Cell 109: 181-191.
  • Yin, Y., Zhu, Q., Dai, S., Lamb, C. and Beachy, R.N. 1997. RF2a, a bZIP transcriptional activator of the phloem-specific rice tungro bacilliform virus promoter, functions in vascular development. EMBO J. 16: 5247-5259.