Publications

(# for equal contribution; * for corresponding authors)

    2022


  1. Liquid-liquid phase separation of RBGD2/4 is required for heat stress resistance in Arabidopsis
    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)
    Developmental Cell, 57(5):583-597.e6. [PMID: 35231447] [Citations]
  2. Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response
    Guo J, Chai X, Mei Y, Du J, Du H, Shi H, Zhu JK, Zhang H* (2022)
    Stress Biology, 2:1. [Citations]
  3. Transcriptome analyses of quinoa leaves revealed critical function of epidermal bladder cells in salt stress acclimation
    Kiani-Pouya A#, Li L#, Rasouli F, Zhang Z, Chen J, Yu M, Tahir A, Hedrich R, Shabala S*, Zhang H* (2022)
    Plant Stress, 100061. [Citations]
  4. Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia
    Richards SM*,#, Li, L#, Breen J, Hovhannisyan N, Estrada O, Gasparyan B, Gilliham M, Smith A, Cooper A, Zhang H* (2022)
    Scientific Reports, 12, 15164. [PMID: 36071150] [Citations]
  5. Stalk cell polar ion transport provide for bladder-based salinity tolerance in Chenopodium quinoa
    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)
    New Phytologist, 05 May 2022. [PMID: 35510810] [Citations]
  6. Genome-wide analysis of CqCrRLK1L and CqRALF gene families in Chenopodium quinoa and their roles in salt stress response
    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)
    Frontiers in Plant Science, 21 June 2022. [PMID: 35873972] [Citations]
  7. A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds
    Li L, Song J, Zhang M, Iqbal S, Li Y, Zhang H*, Zhang H* (2022)
    bioRxiv, 2022.08.15.504044. [Citations]
  8. 2021


  9. Salinity Effects on Guard Cell Proteome in Chenopodium quinoa
    Rasouli F, Kiani-Pouya A, Shabala L, Li L, Tahir A, Yu M, Hedrich R, Chen Z, Wilson R, Zhang H*, Shabala S* (2021)
    Int J Mol Sci, 22(1):428. [PMID: 33406687] [Citations]
  10. Alleviating the effect of quinoa and the underlying mechanism on hepatic steatosis in high-fat diet-fed rats
    Song C#, Lv W#, Li Y#, Nie P, Lu J, Geng Y*, Zhang H*, Song L* (2021)
    Nutrition & Metabolism, 18(1):106. [PMID: 34922572] [Citations]
  11. The receptor-like kinases BAM1 and BAM2 are required for root xylem patterning
    Fan P#, Aguilar E#, Bradai M, Xue H, Wang H, Rosas-Diaz T, Tang W, Wolf S, Zhang H, Xu L, Lozano-Durán R* (2021)
    Proc Natl Acad Sci U S A, 118(12):e2022547118. [PMID: 33723062] [Citations]
  12. 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
    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)
    Nature Communications, 12(1):3367. [PMID: 34099688] [Citations]
  13. Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2
    Wang Y#, Zhou X#, Luo J, Lv S, Liu R, Du X, Jia B, Yuan F, Zhang H, and Du J* (2021)
    J Integr Plant Biol, 63(6):1091-1096. [PMID: 33913587] [Citations]
  14. 2020


  15. Thriving under Stress: How Plants Balance Growth and the Stress Response
    Zhang H*, Zhao Y, Zhu, J-K* (2020)
    Dev Cell, 55(5):P525-543. [PMID: 33290694] [Citations]
  16. It Takes NSUN2 to Beat the Heat in Rice
    Zhu Z, Zhang H* (2020)
    Dev Cell, 53:253-254. [PMID: 32369737] [Citations]
  17. RNA-directed DNA methylation has an important developmental function in Arabidopsis that is masked by the chromatin remodeler PICKLE
    Yang R, He L, Huang H, Zhu JK, Lozano-Duran R, Zhang H* (2020)
    J Integr Plant Biol, 62(11):1647-1652. [PMID: 32515549] [Citations]
  18. Rph1 coordinates transcription of ribosomal protein genes and ribosomal RNAs to control cell growth under nutrient stress conditions
    Shu WJ, Chen R, Yin ZH, Li F, Zhang H, Du HN* (2020)
    Nucleic Acids Res, 48(15):8360-8373. [PMID: 32619236] [Citations]
  19. Mechanisms of plant responses and adaptation to soil salinity
    Zhao C*, Zhang H, Song C, Zhu J-K*, Shabala S* (2020)
    The Innovation, 1(1):100017. [PMID: 34557705] [Citations]
  20. Sugar Beet (Beta vulgaris) Guard Cells Responses to Salinity Stress: A Proteomic Analysis
    Rasouli F, Kiani-Pouya A, Li L, Zhang H, Chen Z, Hedrich R, Wilson R*, Shabala S* (2020)
    International Journal of Molecular Sciences, 21(7):2331. [PMID: 32230932] [Citations]
  21. Developing and validating protocols for mechanical isolation of guard-cell enriched epidermal peels for omics studies
    Rasouli F, Kiani-Pouya A, Zhang H, Shabala S* (2020)
    Functional Plant Biology, 47(9):803-814. [PMID: 32513383] [Citations]
  22. 2019


  23. The genome of broomcorn millet
    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)
    Nature Communications, 10:436. [PMID: 30683860] [Citations]
  24. TMK1-mediated auxin signalling regulates differential growth of the apical hook
    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)
    Nature, 568:240–243. [PMID: 30944466] [Citations]
  25. Global increase in DNA methylation during orange fruit development and ripening
    Huang H, Liu R, Niu Q, Tang K, Zhang B, Zhang H, Chen K, Zhu JK*, Lang Z* (2019)
    Proc Natl Acad Sci U S A, 116(4):1430-1436. [PMID: 30635417] [Citations]
  26. A large-scale screening of quinoa accessions reveals an important role of epidermal bladder cells and stomatal patterning in salinity tolerance
    Kiani-Pouya A, Rasouli F, Bazihizina N, Zhang H, Hedrich R, Shabala S* (2019)
    Environmental and Experimental Botany, 168:103885. [Citations]
  27. HDAC1 and HDAC2 Regulate Intermediate Progenitor Positioning to Safeguard Neocortical Development
    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)
    Neuron, 101(6):1117-1133. [PMID: 30709655] [Citations]
  28. Soil aluminum oxides determine biological nitrogen fixation and diazotrophic communities across major types of paddy soils in China
    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 Biological and Biochemistry, 131:81-89. [Citations]
  29. The receptor-like kinases BAM1 and BAM2 promote the cell-to-cell movement of miRNA in the root stele to regulate xylem patterning
    Fan P, Wang H, Xue H, Rosas-Diaz T, Tang W, Zhang H, Xu L, Lozano-Durán R* (2019)
    bioRxiv, 603415. [Citations]
  30. 2018


  31. Developing naturally stress-resistant crops for a sustainable agriculture
    Zhang H*, Li Y, Zhu JK* (2018)
    Nat Plants, 4(12):989-996. [PMID: 30478360] [Citations]
  32. Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
    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)
    Nat Commun, 9(1):4547. [PMID: 30382101] [Citations]
  33. Understanding the Molecular Basis of Salt Sequestration in Epidermal Bladder Cells of Chenopodium quinoa
    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)
    Curr Biol, 28(19):3075-3085.e7. [PMID: 30245105] [Citations]
  34. Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a High-Salinity Environment
    Vílchez JI, Tang Q, Kaushal R, Wang W, Lv S, He D, Chu Z, Zhang H, Liu R, Zhang H* (2018)
    Genome Announcements, 6(25). [PMID: 29930045] [Citations]
  35. The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis
    Carter B, Bishop B, Ho KK, Huang R, Jia W, Zhang H, Pascuzzi PE, Deal RB, Ogas J* (2018)
    Plant Cell, 30(6):1337-1352. [PMID: 29802212] [Citations]
  36. A virus-targeted plant receptor-like kinase promotes cell-to-cell spread of RNAi
    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)
    Proc Natl Acad Sci U S A, 115(6):1388-1393. [PMID: 29363594] [Citations]
  37. 2017


  38. Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma
    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)
    Nat Mater, 16(11):1155-1161. [PMID: 29035356] [Citations]
  39. A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value
    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)
    Cell Res, 27(11):1327-1340. [PMID: 28994416] [Citations]
  40. A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis
    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)
    Proc Natl Acad Sci U S A, 114(35):E7377-E7384. [PMID: 28808009] [Citations]
  41. DNA methylation markers for diagnosis and prognosis of common cancers
    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)
    Proc Natl Acad Sci U S A, 114(28):7414-7419. [PMID: 28652331] [Citations]
  42. The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci
    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)
    Genome Biol, 18(1):103. [PMID: 28569170] [Citations]
  43. 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
    Sun Y, Wang K, Caceres-Moreno C, Jia W, Chen A, Zhang H, Liu R, Macho AP (2017)
    Stand Genomic Sci, 749.0. [PMID: 28428834] [Citations]
  44. A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation
    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)
    Cell Res, 27(2):226-240. [PMID: 27934869] [Citations]
  45. 2016


  46. The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications
    Tang K, Lang Z, Zhang H, Zhu JK (2016)
    Nat Plants, 2(11):16169. [PMID: 27797352] [Citations]
  47. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism
    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)
    Cell Discov, 2:16027. [PMID: 27551435] [Citations]
  48. Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation
    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)
    Proc Natl Acad Sci U S A, 113(29):E4248-56. [PMID: 27382183] [Citations]
  49. Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana
    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)
    Genetics, 203(2):817-29. [PMID: 27075727] [Citations]
  50. Dicer-independent RNA-directed DNA methylation in Arabidopsis
    Yang DL, Zhang G, Tang K, Li J, Yang L, Huang H, Zhang H, Zhu JK (2016)
    Cell Res, 26(11):1264. [PMID: 26642813] [Citations]
  51. Before 2016


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