Publications

(# for equal contribution; * for corresponding authors)

    2022

  1. Zhu S#, Gu J#, Yao J, Li Y, Zhang Z, Xia W, Wang Z, Gui X, Li L, Li D, Zhang H*, Liu C* (2022) Liquid-liquid phase separation of RBGD2/4 is required for heat stress resistance in Arabidopsis. Developmental Cell, 57(5):583-597.e6. [PMID: 35231447][Citations]
  2. Kiani-Pouya A#, Li L#, Rasouli F, Zhang Z, Chen J, Yu M, Tahir A, Hedrich R, Shabala S*, Zhang H* (2022) Transcriptome analyses of quinoa leaves revealed critical function of epidermal bladder cells in salt stress acclimation. Plant Stress, 100061. [PMID: ][Citations]
  3. Guo J, Chai X, Mei Y, Du J, Du H, Shi H, Zhu JK, Zhang H* (2022) Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response. Stress Biology, 2:1. [PMID: ][Citations]
  4. Bazihizina N#, Böhm J#, Messerer M#, Stigloher C*, Müller HM, Cuin TA, Maierhofer T, Cabot J, Mayer KFX, Fella C, Huang S, Al-Rasheid KAS, Alquraishi S, Breadmore M, Mancuso S, Shabala S, Ache P, Zhang H, Zhu J-K, Hedrich R*, Scherzer S* (2022) Stalk cell polar ion transport provide for bladder-based salinity tolerance in Chenopodium quinoa. New Phytologist, 05 May 2022. [PMID: 35510810][Citations]
  5. Jiang W, Li C, Li L, Li Y, Wang Z, Yu F, Yi F, Zhang J, Zhu J-K, Zhang H, Li Y, Zhao C* (2022) Genome-wide analysis of CqCrRLK1L and CqRALF gene families in Chenopodium quinoa and their roles in salt stress response. Frontiers in Plant Science, 21 June 2022. [PMID: ][Citations]
  6. 2021

  7. Rasouli F, Kiani-Pouya A, Shabala L, Li L, Tahir A, Yu M, Hedrich R, Chen Z, Wilson R, Zhang H*, Shabala S* (2021) Salinity Effects on Guard Cell Proteome in Chenopodium quinoa. Int J Mol Sci, 22(1):428. [PMID: 33406687][Citations]
  8. Song C#, Lv W#, Li Y#, Nie P, Lu J, Geng Y*, Zhang H*, Song L* (2021) Alleviating the effect of quinoa and the underlying mechanism on hepatic steatosis in high-fat diet-fed rats. Nutrition & Metabolism, 18(1):106. [PMID: 34922572][Citations]
  9. Fan P#, Aguilar E#, Bradai M, Xue H, Wang H, Rosas-Diaz T, Tang W, Wmn,olf S, Zhang H, Xu L, Lozano-Durán R* (2021) The receptor-like kinases BAM1 and BAM2 are required for root xylem patterning. Proc Natl Acad Sci U S A, 118(12):e2022547118. [PMID: 33723062][Citations]
  10. Niu Q#, Song Z#, Tang K, Chen L, Wang L, Ban T, Guo Z, Kim C, Zhang H, Duan C, Zhang H, Zhu J-K, Du J*, Lang Z* (2021) A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation. Nature Communications, 12(1):3367. [PMID: 34099688][Citations]
  11. Wang Y#, Zhou X#, Luo J, Lv S, Liu R, Du X, Jia B, Yuan F, Zhang H, and Du J* (2021) Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2. J Integr Plant Biol, 63(6):1091-1096. [PMID: 33913587][Citations]
  12. 2020

  13. Zhang H*, Zhao Y, Zhu, J-K* (2020) Thriving under Stress: How Plants Balance Growth and the Stress Response. Dev Cell, 55(5):P525-543. [PMID: 33290694][Citations]
  14. Zhu Z, Zhang H* (2020) It Takes NSUN2 to Beat the Heat in Rice. Dev Cell, 53:253-254. [PMID: 32369737][Citations]
  15. Yang R, He L, Huang H, Zhu JK, Lozano-Duran R, Zhang H* (2020) RNA-directed DNA methylation has an important developmental function in Arabidopsis that is masked by the chromatin remodeler PICKLE. J Integr Plant Biol, 62(11):1647-1652. [PMID: 32515549][Citations]
  16. Shu WJ, Chen R, Yin ZH, Li F, Zhang H, Du HN* (2020) Rph1 coordinates transcription of ribosomal protein genes and ribosomal RNAs to control cell growth under nutrient stress conditions. Nucleic Acids Res, 48(15):8360-8373. [PMID: 32619236][Citations]
  17. Zhao C*, Zhang H, Song C, Zhu J-K*, Shabala S* (2020) Mechanisms of plant responses and adaptation to soil salinity. The Innovation, 1(1):100017. [PMID: 34557705][Citations]
  18. Rasouli F, Kiani-Pouya A, Li L, Zhang H, Chen Z, Hedrich R, Wilson R*, Shabala S* (2020) Sugar Beet (Beta vulgaris) Guard Cells Responses to Salinity Stress: A Proteomic Analysis. International Journal of Molecular Sciences, 21(7):2331. [PMID: 32230932][Citations]
  19. Rasouli F, Kiani-Pouya A, Zhang H, Shabala S* (2020) Developing and validating protocols for mechanical isolation of guard-cell enriched epidermal peels for omics studies. Functional Plant Biology, 47(9):803-814. [PMID: 32513383][Citations]
  20. 2019

  21. Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK*, Zhang H* (2019) The genome of broomcorn millet. Nature Communications, 10:436. [PMID: 30683860][Citations]
  22. Cao M#, Chen R#, Li P#, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T* (2019) TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature, 568:240–243. [PMID: 30944466][Citations]
  23. Huang H, Liu R, Niu Q, Tang K, Zhang B, Zhang H, Chen K, Zhu JK*, Lang Z* (2019) Global increase in DNA methylation during orange fruit development and ripening. Proc Natl Acad Sci U S A, 116(4):1430-1436. [PMID: 30635417][Citations]
  24. Kiani-Pouya A, Rasouli F, Bazihizina N, Zhang H, Hedrich R, Shabala S* (2019) A large-scale screening of quinoa accessions reveals an important role of epidermal bladder cells and stomatal patterning in salinity tolerance. Environmental and Experimental Botany, 168:103885. [PMID: ][Citations]
  25. Tang T, Zhang Y, Wang Y, Cai Z, Lu Z, Li L, Huang R, Hagelkruys A, Matthias P, Zhang H, Seiser C, Xie Y* (2019) HDAC1 and HDAC2 Regulate Intermediate Progenitor Positioning to Safeguard Neocortical Development. Neuron, 101(6):1117-1133. [PMID: 30709655][Citations]
  26. Wang X, Liu B, Ma J, Zhang Y, Hu T, Zhang H, Feng Y, Pan H, Xu Z, Liu G, Lin X, Zhu J, Bei Q*, Xie Z* (2019) Soil aluminum oxides determine biological nitrogen fixation and diazotrophic communities across major types of paddy soils in China. Soil Biological and Biochemistry, 131:81-89. [PMID: ][Citations]
  27. 2018

  28. Zhang H*, Li Y, Zhu JK* (2018) Developing naturally stress-resistant crops for a sustainable agriculture. Nat Plants, 4(12):989-996. [PMID: 30478360][Citations]
  29. Zhang C#, Du X#, Tang K#, Yang Z, Pan L, Zhu P, Luo J, Jiang Y, Zhang H, Wan H, Wang X, Wu F, Tao WA, He XJ, Zhang H, Bressan RA, Du J*, Zhu JK* (2018) Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin. Nat Commun, 9(1):4547. [PMID: 30382101][Citations]
  30. Böhm J#, Messerer M#, Müller HM#, Scholz-Starke J, Gradogna A, Scherzer S, Maierhofer T, Bazihizina N, Zhang H, Stigloher C, Ache P, Al-Rasheid KAS, Mayer KFX, Shabala S, Carpaneto A, Haberer G*, Zhu JK*, Hedrich R* (2018) Understanding the Molecular Basis of Salt Sequestration in Epidermal Bladder Cells of Chenopodium quinoa. Curr Biol, 28(19):3075-3085.e7. [PMID: 30245105][Citations]
  31. Vílchez JI, Tang Q, Kaushal R, Wang W, Lv S, He D, Chu Z, Zhang H, Liu R, Zhang H* (2018) Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a High-Salinity Environment. Genome Announcements, 6(25). [PMID: 29930045][Citations]
  32. Carter B, Bishop B, Ho KK, Huang R, Jia W, Zhang H, Pascuzzi PE, Deal RB, Ogas J* (2018) The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis. Plant Cell, 30(6):1337-1352. [PMID: 29802212][Citations]
  33. Rosas-Diaz T, Zhang D, Fan P, Wang L, Ding X, Jiang Y, Jimenez-Gongora T, Medina-Puche L, Zhao X, Feng Z, Zhang G, Liu X, Bejarano ER, Tan L, Zhang H, Zhu JK, Xing W, Faulkner C, Nagawa S, Lozano-Duran R* (2018) A virus-targeted plant receptor-like kinase promotes cell-to-cell spread of RNAi. Proc Natl Acad Sci U S A, 115(6):1388-1393. [PMID: 29363594][Citations]
  34. 2017

  35. Xu RH, Wei W, Krawczyk M, Wang W, Luo H, Flagg K, Yi S, Shi W, Quan Q, Li K, Zheng L, Zhang H, Caughey BA, Zhao Q, Hou J, Zhang R, Xu Y, Cai H, Li G, Hou R, Zhong Z, Lin D, et al (2017) Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma. Nat Mater, 16(11):1155-1161. [PMID: 29035356][Citations]
  36. Zou C, Chen A, Xiao L, Muller HM, Ache P, Haberer G, Zhang M, Jia W, Deng P, Huang R, Lang D, Li F, Zhan D, Wu X, Zhang H, Bohm J, Liu R, Shabala S, Hedrich R, Zhu JK, Zhang H (2017) A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value. Cell Res, 27(11):1327-1340. [PMID: 28994416][Citations]
  37. Duan CG, Wang X, Zhang L, Xiong X, Zhang Z, Tang K, Pan L, Hsu CC, Xu H, Tao WA, Zhang H, Zhu JK (2017) A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis. Proc Natl Acad Sci U S A, 114(35):E7377-E7384. [PMID: 28808009][Citations]
  38. Hao X, Luo H, Krawczyk M, Wei W, Wang W, Wang J, Flagg K, Hou J, Zhang H, Yi S, Jafari M, Lin D, Chung C, Caughey BA, Li G, Dhar D, Shi W, Zheng L, Hou R, Zhu J, Zhao L, Fu X, et al (2017) DNA methylation markers for diagnosis and prognosis of common cancers. Proc Natl Acad Sci U S A, 114(28):7414-7419. [PMID: 28652331][Citations]
  39. Yang R, Zheng Z, Chen Q, Yang L, Huang H, Miki D, Wu W, Zeng L, Liu J, Zhou JX, Ogas J, Zhu JK, He XJ, Zhang H (2017) The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci. Genome Biol, 18(1):103. [PMID: 28569170][Citations]
  40. Sun Y, Wang K, Caceres-Moreno C, Jia W, Chen A, Zhang H, Liu R, Macho AP (2017) Genome sequencing and analysis of Ralstonia solanacearum phylotype I strains FJAT-91, FJAT-452 and FJAT-462 isolated from tomato, eggplant, and chili pepper in China. Stand Genomic Sci, 749.0. [PMID: 28428834][Citations]
  41. Duan CG, Wang X, Xie S, Pan L, Miki D, Tang K, Hsu CC, Lei M, Zhong Y, Hou YJ, Wang Z, Zhang Z, Mangrauthia SK, Xu H, Zhang H, Dilkes B, Tao WA, Zhu JK (2017) A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation. Cell Res, 27(2):226-240. [PMID: 27934869][Citations]
  42. 2016

  43. Tang K, Lang Z, Zhang H, Zhu JK (2016) The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nat Plants, 2(11):16169. [PMID: 27797352][Citations]
  44. Zhang Q, Li Y, Xu T, Srivastava AK, Wang D, Zeng L, Yang L, He L, Zhang H, Zheng Z, Yang DL, Zhao C, Dong J, Gong Z, Liu R, Zhu JK (2016) The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism. Cell Discov, 2:16027. [PMID: 27551435][Citations]
  45. Zhang Q, Wang D, Lang Z, He L, Yang L, Zeng L, Li Y, Zhao C, Huang H, Zhang H, Zhang H, Zhu JK (2016) Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation. Proc Natl Acad Sci U S A, 113(29):E4248-56. [PMID: 27382183][Citations]
  46. Carter B, Henderson JT, Svedin E, Fiers M, McCarthy K, Smith A, Guo C, Bishop B, Zhang H, Riksen T, Shockley A, Dilkes BP, Boutilier K, Ogas J (2016) Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana. Genetics, 203(2):817-29. [PMID: 27075727][Citations]
  47. Yang DL, Zhang G, Tang K, Li J, Yang L, Huang H, Zhang H, Zhu JK (2016) Dicer-independent RNA-directed DNA methylation in Arabidopsis. Cell Res, 26(11):1264. [PMID: 26642813][Citations]
  48. Before 2016

  49. Zhang H, Zhu J (2015) Protecting genes from RNA silencing by destroying aberrant transcripts. Sci China Life Sci, 58(6):613-5. [PMID: 25994414][Citations]
  50. Zheng Z, Yu H, Miki D, Jin D, Zhang Q, Ren Z, Gong Z, Zhang H, Zhu JK (2015) Involvement of Multiple Gene-Silencing Pathways in a Paramutation-like Phenomenon in Arabidopsis. Cell Rep, 11(8):1160-7. [PMID: 25981044][Citations]
  51. Shi H, Jiang C, Ye T, Tan DX, Reiter RJ, Zhang H, Liu R, Chan Z (2015) Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin. J Exp Bot, 66(3):681-94. [PMID: 25225478][Citations]
  52. Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N, Zhu JK (2014) The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J, 12(6):797-807. [PMID: 24854982][Citations]
  53. Zhang H, Tang K, Qian W, Duan CG, Wang B, Zhang H, Wang P, Zhu X, Lang Z, Yang Y, Zhu JK (2014) An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis. Mol Cell, 54(3):418-30. [PMID: 24726328][Citations]
  54. Lei M, La H, Lu K, Wang P, Miki D, Ren Z, Duan CG, Wang X, Tang K, Zeng L, Yang L, Zhang H, Nie W, Liu P, Zhou J, Liu R, Zhong Y, Liu D, Zhu JK (2014) Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns. Proc Natl Acad Sci U S A, 111(1):527-32. [PMID: 24248388][Citations]
  55. Zhang H, He X, Zhu JK (2013) RNA-directed DNA methylation in plants: Where to start?. RNA Biol, 10(10):1593-6. [PMID: 25003825][Citations]
  56. Huang CF, Miki D, Tang K, Zhou HR, Zheng Z, Chen W, Ma ZY, Yang L, Zhang H, Liu R, He XJ, Zhu JK (2013) A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet, 9(9):e1003779. [PMID: 24068953][Citations]
  57. Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, Cai T, Tang K, Liu R, Shi X, He XJ, Zhu JK (2013) DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A, 110(20):8290-5. [PMID: 23637343][Citations]
  58. Ho KK, Zhang H, Golden BL, Ogas J (2013) PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor. Biochim Biophys Acta, 1829(2):199-210. [PMID: 23128324][Citations]
  59. Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S, Zhu X, Shi X, Zhang K, Pontes O, Chen X, Liu R, Gong Z, Zhu JK (2012) A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science, 336(6087):1445-8. [PMID: 22700931][Citations]
  60. Zhang H, Bishop B, Ringenberg W, Muir WM, Ogas J (2012) The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27. Plant Physiol, 159(1):418-32. [PMID: 22452853][Citations]
  61. Zhang H, Ogas J (2009) An epigenetic perspective on developmental regulation of seed genes. Mol Plant, 2(4):610-627. [PMID: 19825643][Citations]
  62. Zhang H, Rider SD Jr, Henderson JT, Fountain M, Chuang K, Kandachar V, Simons A, Edenberg HJ, Romero-Severson J, Muir WM, Ogas J (2008) The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27. J Biol Chem, 283(33):22637-48. [PMID: 18539592][Citations]
  63. Li HC, Chuang K, Henderson JT, Rider SD Jr, Bai Y, Zhang H, Fountain M, Gerber J, Ogas J (2005) PICKLE acts during germination to repress expression of embryonic traits. Plant J, 44(6):1010-22. [PMID: 16359393][Citations]