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Plant RNA Biology

Beyond the Central Dogma of Molecular Biology

Publications

Recent Publications:
  1. Li X*, Zhong S*, Li C, Yan X, Zhu J, Li Y, Wang Z, Peng X, Zhang X. 2024. RNA helicase Brr2a promotes miRNA biogenesis by properly remodelling secondary structure of pri-miRNAs. Nature Plants. doi: 10.1038/s41477-024-01788-8. Online ahead of print. PMID: 39271943.
  2. Li, X. and Zhang, X. The spliceosome factor and RNA helicase Brr2a moonlights in miRNA production. Nature Research Briefing. Oct. 8. 2024.7. Volume 10, Pages:1444–1445. 
  3. Yan X*, Li C*, Liu K, Zhang T, Xu Q, Li X, Zhu J, Wang Z, Yusuf A, Cao S, Peng X, Cai JJ, Zhang X.
    2024. Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis. Nature Plants. doi: 10.1038/s41477-024-01725-9. Online ahead of print. PMID: 38918606.
  4. Yan, X. and Zhang, X., 2024. Exploring the landscape of miRNA production and the structural rules that shape it. Nature Research Briefing. Volume 10, pages 1060-1061.
  5. Zhang T*, Li C*, Zhu J* **, Li Y, Wang Z, Tong CY, Xi Y, Han Y, Koiwa H, Peng X, Zhang X**. 2024. Structured 3′ UTRs destabilize mRNAs in plants. Genome Biol. 2024 Feb 22;25(1):54. doi: 10.1186/s13059-024-03186-x.PMID: 38388963
  6. Shang B, Li C, Zhang X. 2024. How intrinsically disordered proteins order plant gene silencing.  Trends Genet. Jan 30:S0168-9525(23)00284-6. doi: 10.1016/j.tig.2023.12.009. PMID: 38296708
  7. Wang Z, Castillo-González CM, Zhao C, Tong CY, Li C, Zhong S, Liu Z, Xie K, Zhu J, Wu Z, Peng X, Jacob Y, Michaels SD, Jacobsen SE, Zhang X. 2023. H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome. Nature Commun.14(1):7484. doi: 10.1038/s41467-023-43311-1. PMID: 37980416
  8. Meehan J, McDermott SM, Ivens A, Goodall Z, Chen Z, Yu Z, Woo J, Rodshagen T, McCleskey L, Sechrist R, Stuart K, Zeng L, Rouskin S, Savill NJ, Schnaufer A, Zhang X, Cruz-Reyes J. Trypanosome RNA helicase KREH2 differentially controls non-canonical editing and putative repressive structure via a novel proposed ‘bifunctional’ gRNA in mRNA A6. Nucleic Acids Res. 2023 May 29:gkad453. doi: 10.1093/nar/gkad453. PMID: 37246647.

  9. Shang B*, Wang L*, Yan X*, Li Y, Li C, Wu C, Wang T, Guo X, Choi SW, Zhang T, Wang Z, Tong CY, Oh T, Zhang X, Wang Z, Peng X, Zhang X. Intrinsically disordered proteins SAID1/2 condensate on SERRATE for dual inhibition of miRNA biogenesis in Arabidopsis. Proc Natl Acad Sci U S A. 2023 Apr 4;120(14):e2216006120. doi: 10.1073/pnas.2216006120. PMID: 36972460

  10. Li X, Li C, Zhu J, Zhong S, Zhu H, Zhang X. Functions and mechanisms of RNA helicases in plants. J Exp Bot. 2022 Nov 23:erac462. doi: 10.1093/jxb/erac462. PMID: 36416783
  11. Yang X, Unver T, Zhang X, Li L. 2022. Editorial: Roles and regulatory mechanisms of microRNA in plant development, evolution, and adaptation. Front Plant Sci. 2022 Aug 15;13:995517. doi: 10.3389/fpls.2022.995517. PMID: 36046595.

  12. Zhu J, Yan X, Zhang X. The R-loop influences miRNA birth place. Nature Plants. 2022 Apr;8(4):320-321. doi: 10.1038/s41477-022-01124-y. PMID: 35449403

  13. Xu Q, Yang Y, Zhang X, Cai JJ. Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis. Immunoinformatics (Amst). 2022 Apr 10:100013. doi: 10.1016/j.immuno.2022.100013. PMID: 3543469.
  14. Wang L*, Yan X*, Li Y, Wang Z, Chhajed S, Shang B, Wang Z, Choi SW, Zhao H, Chen S, Zhang X. PRP4KA phosphorylates SERRATE for degradation via 20S proteasome to fine-tune miRNA production in Arabidopsis. Sci Adv. 2022 Mar 25;8(12):eabm8435. doi: 10.1126/sciadv.abm8435. Epub 2022 Mar 25. PMID: 35333566
  15. Xu Q, Li G, Osorio D, Zhong Y, Yang Y, Lin YT, Zhang X, Cai JJ. scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation. Genes. 2022 Feb 18;13(2):371. doi: 10.3390/genes13020371. PMID: 35205415 Free PMC article.
  16. Sun D, Li Y, Ma Z, Yan X, Li N, Shang B, Hu X, Cui K, Koiwa H, Zhang X. The epigenetic factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene silencing in Arabidopsis. Science Adv. 2021 Aug 4;7(32):eabf3898. doi: 10.1126/sciadv.abf3898. Print 2021 Aug. PMID: 3434889
  17. Sun, D., and Zhang, X. HASTY moves to chromatin for miRNA production. Mol Plant. 2021 Jan 22:S1674-2052(21)00012-5. doi: 10.1016/j.molp.2021.01.012. PMID: 33493678
  18. Zhu, J., Li, C., Peng, X., and Zhang, X. Architecture of RNA influences plant biology. J Exp Bot. 2021 Jan 23:erab030. doi: 10.1093/jxb/erab030. PMID: 33484251
  19. Li Y, Sun D, Yan X, Wang Z, and Zhang X. In vitro Reconstitution Assays of Arabidopsis 20S Proteasome. Bio Protoc. 2021 Apr 5;11(7):e3967. doi: 10.21769/BioProtoc.3967. eCollection 2021 Apr 5. PMID: 33889661.
  20. Sun, D., Ma, Z., Zhu, J., and Zhang, X. Identification and Quantification of Small RNAs. Methods Mol Biol. 2021;2200:225-254. doi: 10.1007/978-1-0716-0880-7_11. PMID: 33175381
  21. Kumar, V., Ivens, A., Goodall, Z., Meehan, J., Doharey, P.K., Hillhouse, A., Hurtado, DO., Cai, J.J., Zhang, X., Schnaufer. A., and Cruz-Reyes, J. Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes. RNA. 2020 Dec;26(12):1862-1881. doi: 10.1261/rna.076513.120.
  22. Li. Y.*, Sun, D.*, Ma, Z., Yamaguchi, K., Wang, L, Zhong, S. Yan, X., Shang, B., Nagashima, Y., Koiwa, H., Han, J., Xie, Qi., Zhou, M., Wang, Z.**, and Zhang, X.** Degradation of Serrate via ubiquitin-independent 20S proteasome to survey RNA metabolism. Nature Plants.
    2020 Aug;6(8):970-982. doi: 10.1038/s41477-020-0721-4.
  23. Nagashima, Y., Ma, Z., Zhang, X., von Schaewen, A., Koiwa, H. Lack of endoplasmic reticulum quality control (ERQC) promotes tonoplast (TP) targeting of KORRIGAN 1 (KOR1). Plant Signal Behav. 2020 Apr 2;15(4):1744348. doi: 10.1080/15592324.2020.1744348. Epub 2020 Mar 20. PMID: 32195619
  24. Nagashima, Y., Ma, Z., Liu, X., Qian, X., Zhang, X., von Schaewen, A., Koiwa, H. Multiple Quality Control Mechanisms in the ER and TGN Determine Subcellular Dynamics and Salt-Stress Tolerance Function of KORRIGAN1. Plant Cell. 2020 Feb;32(2):470-485. doi: 10.1105/tpc.19.00714. Epub 2019 Dec 18. PMID: 31852774
  25. Hu, T., Huang, C., He, Y., Castillo-González, C., Gui, X., Wang, Y.**, Zhang X.**, and Zhou X**. βC1 protein encoded in geminivirus satellite concertedly targets MKK2 and MPK4 to counter host defense. PLoS Pathog. 2019 Apr 18;15(4):e1007728. doi: 10.1371/journal.ppat.1007728.
  26. Wang, Z., Wang, M., Wang. T., Zhang, Y., Zhang, X. Genome-wide probing RNA structure with the modified DMS-MaPseq in Arabidopsis. Methods. 2019. Feb 15;155:30-40. doi: 10.1016/j.ymeth.2018.11.018.
  27. Njaci, I., Williams, B., Castillo-González, C., Dickman, M., Zhang, X., and Mundree, S. Genome-wide investigation of the role of microRNAs in desiccation tolerance in the resurrection grass Tripogon loliiformis. Plants. 2018. 7(3), 68. doi: 10.3390/plants7030068
  28. Castillo-González, C., and Zhang, X. The Trojan horse of the plant kingdom. Cell Host & Microbe. 2018. Jul 11; 24(1): 1-3. doi: 10.1016/j.chom.2018.06.015.
  29. Ma Z., Castillo-González, C., Wang, Z., Sun, D., Hu, X., Shen, X., Potok, M.E., and Zhang, X. Arabidopsis SERRATE coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression. Dev Cell. 2018. Jun 18; 45(6): 769-784.e6. doi: 10.1016/j.devcel.2018.05.023.
  30. Ma, Z., and Zhang, X. Actions of plant Argonautes: predictable or unpredictable? Curr Opin Plant Biol. 2018 May 29;45(Pt A):59-67. doi: 10.1016/j.pbi.2018.05.007
  31. Wang, Z., Ma, Z., Castillo-González, C., Sun, D., Li, Y., Yu, B., Li, P., and Zhang,X., SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via SE to impede miRNA production.Nature, 2018. 10.1038/s41586-018-0135-x
  32. Castillo-González C, Zhang X. Transactivator: A New Face of Arabidopsis AGO1.Dev Cell. 2018 Feb 5;44(3):277-279. doi: 10.1016/j.devcel.2018.01.014.
  33. Mei Y, Yang X, Huang C, Zhang X, Zhou X. Tomato leaf curl Yunnan virus-encoded C4 induces cell division through enhancing stability of Cyclin D 1.1 via impairing NbSKη -mediated phosphorylation in Nicotiana benthamiana.PLoS Pathog. 2018 Jan 2;14(1):e1006789. doi: 10.1371/journal.ppat.1006789
  34. Fukudome A, Sun D, Zhang X, Koiwa H. Salt Stress and CTD PHOSPHATASE-LIKE4 Mediate the Switch between Production of Small Nuclear RNAs and mRNAs.Plant Cell. 2017 Dec;29(12):3214-3233. doi: 10.1105/tpc.17.00331.
  35. Zhang X. Tough GC beats transgene silencing. Nature Plants. 2017 Nov;3(11):850-851. doi: 10.1038/s41477-017-0048-y.
  36. Guo X, Ma Z, Zhang Z, Cheng L, Zhang X*, Li T*. Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple.Front Plant Sci. 2017 May 29;8:873. doi: 10.3389/fpls.2017.00873.
  37. Zhang Z**, Hu F**, Sung MW, Shu C, Castillo-González C, Koiwa H, Tang G, Dickman M, Li P*, Zhang X*.RISC-interacting clearing 3′- 5′ exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana.eLife. 2017 May 2;6. pii: e24466. doi: 10.7554/eLife.24466.
  38. Zhang Z**, Guo X**, Ge C**, Ma Z, Jiang M, Li T, Koiwa H, Yang SW, Zhang X. KETCH1 imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis.Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):4011-4016. doi: 10.1073/pnas.1619755114
  39. Li S**, Castillo-González C**, Yu B*, Zhang X*.The functions of plant small RNAs in development and in stress responses.Plant J. 2017 May;90(4):654-670. doi: 10.1111/tpj.13444.
  40. Zhang Z**, Liu X**, Guo X, Wang XJ*, Zhang X*.  Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nature Plants 2016 Apr. doi:10.1038/nplants.2016.49.
  41. Williams B, Njaci I, Moghaddam L, Long H, Dickman MB, Zhang X, Mundree S.  Trehalose Accumulation Triggers Autophagy during Plant Desiccation. PLOS Genetics 2015 Oct. doi: http://dx.doi.org/10.1371/journal.pgen.1005705.
  42. Castillo-González C, Liu X, Huang CJ, Zhao CJ, Ma Z, Hu T, Sun F, Zhou J, Wang XJ, Zhou X, Zhang X.  Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense. eLife 2015 Oct. doi: http://dx.doi.org/10.7554/eLife.06671.
  43. Wang T, Castillo-González C, You L, Li R, Wen L, Zhu HL*, Zhang X*.In vitro Reconstitution Assay of miRNA Biogenesis by Arabidopsis DCL1. Bio-protocol 2015 Apr. Vol. 5 Iss. 8.
  44. Zhou Y, Honda M, Zhu H, Zhang Z, Guo X, Li T, Li Z, Peng X, Nakajima K, Duan L, Zhang X. Spatiotemporal Sequestration of miR165/166 by Arabidopsis Argonaute10 Promotes Shoot Apical Meristem Maintenance. Cell Reports 2015 Mar 17. pii: S2211-1247(15)00205-3. doi: 10.1016/j.celrep.2015.02.047. PMID: 25801022.
  45. Zhu H, Zhou Y, Castillo-González C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJ, Wang XJ, Zhang X.Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nature Structure & Molecular Biology 2013 Sep 20(9):1106-15. doi: 10.1038/nsmb.2646. Epub 2013 Aug 11. PMID: 23934148.
  46. Zhang Z, Zhang X.Argonautes compete for miR165/166 to regulate shoot apical meristem development. Current Opinion in Plant Biology 2012 Dec;15(6):652-8. doi: 10.1016/j.pbi.2012.05.007. Epub 2012 Jun 21. Review. PMID: 22727764.
  47. Zhu H**, Hu F**, Wang R**, Zhou X, Sze SH, Liou LW, Barefoot A, Dickman M, Zhang X.Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell. 2011 Apr 15;145(2):242-56. doi: 10.1016/j.cell.2011.03.024. PMID: 21496644.  Paper Flick!  http://www.youtube.com/watch?v=VuQvQCxHo-c
  48. Wang H**, Zhang X**, Liu J, Kiba T, Woo J, Ojo T, Hafner M, Tuschl T, Chua NH, Wang XJ.  Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions.  Plant Journal 2011 Jul;67(2):292-304. doi: 10.1111/j.1365-313X.2011.04594.x. Epub 2011 May 10. PMID: 21457371.
  49. Catala R, Ouyang J, Abreu IA, Hu Y, Seo H, Zhang X, Chua NH. The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell. 2007 Sep;19(9):2952-66. Epub 2007 Sep 28. PubMed PMID: 17905899; PubMed Central. PMCID: PMC2048692.
  50. Zhang X, Henriques R, Lin SS, Niu QW, Chua NH. Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nat Protoc. 2006;1(2):641-6. Epub 2006 Jun 29. PubMed PMID: 17406292.
  51. Zhang X, Buehner NA, Hutson AM, Estes MK, Mason HS. Tomato is a highly effective vehicle for expression and oral immunization with Norwalk virus capsid protein. Plant Biotechnol J. 2006 Jul;4(4):419-32. PubMed PMID: 17177807.
  52. Zhang X, Yuan YR, Pei Y, Lin SS, Tuschl T, Patel DJ, Chua NH. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 2006 Dec 1;20(23):3255-68. PubMed PMID:17158744; PubMed Central PMCID: PMC1686603.
  53. Zhang X, Mason H. Bean Yellow Dwarf Virus replicons for high-level transgene expression in transgenic plants and cell cultures. Biotechnol Bioeng. 2006 Feb 5;93(2):271-9. PubMed PMID: 16187337.
  54. Zhang X, Garreton V, Chua NH. The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation. Genes Dev. 2005 Jul 1;19(13):1532-43. PubMed PMID: 15998807; PubMed Central PMCID: PMC1172060.
 
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