*co-first authors, ^#corresponding author, members of our group are underlined. 

2024

1. Liu Q^#, Ton J, Manavella PA, Komiya R, Zhai J. (2024) Focus on epigenetics. Plant Physiology. 194(4): 1925-1928.

   
   

2. Zhang Y, Zhang X, Tang Q, Li L, Jiang T, Fang Y, Zhang H, Zhai J, Ren G, Zheng B^#. (2024) A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants. Science China Life Sciences. 67(6): 1280–1291.

   
   

3. Huang G^#, Bao Z, Feng L, Zhai J, Wendel JF, Cao X, Zhu Y^#. (2024) A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development. Nature Genetics. 56(9): 1953-1963.

   
   

4. Fan Q, Zhao X, Li J, Liu R, Liu M, Feng Q, Long Y, Fu Y, Zhai J, Pan Q^#, Li Y^#. (2024) DeepSME: De Novo Nanopore Basecalling of Motif-insensitive DNA Methylation and Alignment-free Digital Information Decryptions at Single-Molecule Level. bioRxiv. 10.1101/2024.08.15.606762.

   
   

5. Zhao X, Li J, Fan Q, Dai J, Long Y, Liu R, Zhai, J, Pan Q^#, Y Li^#. (2024) Composite Hedges Nanopores codec system for rapid and portable DNA data readout with high INDEL-Correction. Nature Communications. 15 (1), 9395.

   
   

6. Li Z*, Zheng L, Zhai J^#, Long Y^#. (2024) Analysis of DNA 5-methylcytosine Using Nanopore Sequencing. Bio-protocol. 14(3): e4943.

   
   

7. Yan Y*, Luo H*, Qin Y*, Yan T, Jia J, Hou Y, Liu Z, Zhai J, Long Y^#, Deng X^#, Cao X^#. (2024) Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5. PNAS. 121 (6) e2317408121.

   
   

2023

8. Li T*, Tang S*, Li W*, Zhang S, Wang J, Pan D, Lin Z, Ma X, Chang Y, Liu B, Sun J, Wang X, Zhao M, You C, Luo H, Wang M, Ye X, Zhai J, Shen Z, Du H^#, Song X^#, Huang G^#, Cao X^#. (2023) Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe. PNAS. 120 (44) e2308984120.

   
   

9. Zhang K*, Zhao X*, Zhao Y*, Zhang Z*, Liu Z, Liu Z, Yu Y, Li J, Ma Y, Dong Y, Pang X, Jin X, Li N, Liu B,  Wendel JF, Zhai J, Long Y^#, Wang T^#, Gong L^#. (2023) Cell type–specific cytonuclear coevolution in three allopolyploid plant species. PNAS. 120 (40) e2310881120.

   
   

10. Liu Z*, Yang J*, Long Y*, Zhang C*, Wang D, Zhang X, Dong W, Zhao L, Liu C, Zhai J^#, Wang E^#.  (2023) Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago. Nature Plants. 10.1038/s41477-023-01524-8.

    
    

11. Mo W*, Shu Y*, Liu B, Long Y, Li T, Cao X, Deng X^#, Zhai J^#. (2023) Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis. Nature Plants. 10.1038/s41477-023-01498-7.

    
    

12. Liu Z*, Kong X*, Long Y*, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J^#, Yan Z^#. (2023) Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. Nature Plants. 10.1038/s41477-023-01387-z.

    
    

2022 

13. Tian S^#, Li G, Ning D, Jing K, Xu Y, Yang Y, Fullwood MJ, Yin P, Huang G, Plewczynski D, Wang W, Zhai J, Wang Z, Dai Z, Lin Y, Chen W^#, Zheng M^#. (2022) MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification. Briefings in Bioinformatics. 23(6):bbac380.

    
    

14. Zhang H*, Jia J, Zhai J^#. (2022) Plant Intron-Splicing Efficiency Database (PISE): exploring splicing of ~1,650,000 introns in Arabidopsis, maize, rice, and soybean from ~57,000 public RNA-seq libraries. Science China Life Sciences.10.1007/s11427-022-2193-3.

    
    

15. Jiang K*^#, Guo H, Zhai J^#. (2022) Interplay of phytohormones and epigenetic regulation: a recipe for plant development and plasticity. Journal of Integrative Plant Biology. 65(2):381-398.

    
    

16. Qin Y, Long Y, Zhai J^#. (2022) Genome-wide characterization of nascent RNA processing in plants. Current Opinion in Plant Biology. 69:102294.

    
    

17. Jia J*, Lu W*, Liu B, Fang H, Yu Y, Mo W, Zhang H, Jin X, Shu Y, Long Y, Pei Y, Zhai J^#. (2022) An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length. Nature Plants. 8(9):1118-1126.

    
    

18. Lu D*, Feng L*, Zhai J, Li B^#, Xi M^#. (2022) Safeguard DCL2-Dependent 22-nt siRNA generation by DCL1. Biochemical and Biophysical Research Communications. 605, 97-103.

    
    

19. Ji R*, Xu X*, Liu J, Zhao T, Li H, Zhai J, Liu B^#. (2022) Induced Mutation in GmCOP1b Enhances the Performance of Soybean under Dense Planting Conditions. International Journal of Molecular Sciences. 23(10):5394.

    
    

20. Wang Q*, Xue Y*, Zhang L*, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S^#, Jacobsen SE^#, Du J^#.(2022) A SYBR Gold-based Label-free in vitro Dicing Assay. Bio-protocol. 12(07): e4382.
    

    
    

21. Li Z*, Long Y*, Yu Y, Zhang F, Zhang H, Liu Z, Jia J, Mo W, Tian SZ, Zheng M, Zhai J^#. (2022) Pore-C Simultaneously Captures Genome-wide Multi-way Chromatin Interaction and Associated DNA Methylation Status in Arabidopsis. Plant Biotechnology Journal. 20(6):1009-1011.

    
    

22. Yu Y*, Zhang H*, Long Y, Shu Y, Zhai J^# (2022) Plant Public RNA-seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA-Seq libraries. Plant Biotechnology Journal. 20, 806-808.

    
    

23. Lu D, Zhai J^#, Xi M^# (2022) Regulation of DNA Methylation During Plant Endosperm Development. Frontiers in Genetics. 13:760690.

    
    

2021 

24. Mo W*, Liu B*, Zhang H, Jin X, Lu D, Yu Y, Liu Y, Jia J, Long Y, Deng X, Cao X, Guo H, Zhai J^# (2021) Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing. Genome Biology. 22(1):322.
    

    
    

25. Zhang Y*, Waseem M*, Zeng Z, Xu J, Chen C, Liu Y, Zhai J, Xia R^#. (2021) MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development. New Phytologist. doi: 10.1111/nph.17853.

    
    

26. Wang Q*, Xue Y*, Zhang L*, Zhong Z, Feng S, Wang S, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S^#, Jacobsen SE^#, Du J^#. (2021) Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science. 374(6571):1152-1157.
    

    
    

27. Long Y*, Jia J*, Mo W, Jin X, Zhai J^#. (2021) FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing. Nature Protocols. 16:4355–4381.

    
    

28. Hu D*, Yu Y*, Wang C*, Long Y, Liu Y, Feng L, Lu D, Liu B, Jia J, Xia R, Du J, Zhong X, Gong L, Wang K^#, Zhai J^#. (2021) Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions. Plant Cell. 33(9):2950-2964.

    
    

29. Fang J*, Leichter SM*, Jiang J*, Biswal M, Lu J, Zhang Z, Ren W, Zhai J, Cui Q, Zhong X^#, Song J^#. (2021) Substrate deformation regulates DRM2-mediated DNA methylation in plants. Science Advances. 7(23):eabd9224.

    
    

30. Qiao Y*^#, Xia R, Zhai J, Hou Y, Feng L, Zhai Y, Ma W^#. (2021) Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens. Annual Review of Phytopathology. doi.org/10.1146/annurev-phyto-121520-023514.

    
    

31. Chen C*, Li J*, Feng J, Liu B, Feng L, Yu X, Li G, Zhai J, Meyers BC, Xia R^#. (2021) sRNAanno—a database repository of uniformly annotated small RNAs in plants. Horticulture Research. 8:45.

    
    

32. Long Y*, Liu Z*, Jia J*, Mo W, Fang L, Lu D, Liu B, Zhang H, Chen W, Zhai J^#. (2021) FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants. Genome Biology. doi.org/10.1186/s13059-021-02288-0.

    
    

2020

33. Yu Y, Zhai J^#. (2020) The chromatin will never forget. Nature Plants. doi.org/10.1038/s41477-020-00803-y.

    
    

34. Wang C*, Ji W*, Liu Y, Zhou P, Meng Y, Zhang P, Wen J, Mysore KS, Zhai J, Young ND, Tian Z, Niu L, Lin H^#. (2020) The antagonistic MYB paralogs RH1 and RH2 govern anthocyanin leaf markings in Medicago truncatula. New Phytologist. doi.org/10.1111/nph.17097.

    
    

35. Jia J*, Ji R*, Li Z, Yu Y, Nakano M, Long Y, Feng L, Qin C, Lu D, Zhan J, Xia R, Meyers BC, Liu B^#, Zhai J^#. (2020) Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats. Plant Cell. 32(12):3662-3673.

    
    

36. Zhang H*, Zhang F*, Yu Y*, Feng L, Jia J, Liu B, Li B, Guo H, Zhai J^#.(2020) A comprehensive online database for exploring ∼20,000 public Arabidopsis RNA-Seq libraries. Molecular Plant. 13(9):1231-1233.

    
    

37. Jia J*, Long Y*, Zhang H, Li Z, Liu Z, Zhao Y, Lu D, Jin X, Deng X, Xia R, Cao X, Zhai J^#. (2020) Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. Nature Plants. 6(7):780-788.

    
    

38. Liu Q*^#, Bischof S*, Harris CJ Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE^#. (2020) The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis. Nature Communications. 11(1):2798.

    
    

39. Wu H*, Li B*, Iwakawa HO, Pan Y, Tang X, Ling-Hu Q, Liu Y, Sheng S, Feng L, Zhang H, Zhang X, Tang Z, Xia X, Zhai J, Guo H^#. (2020) Plant 22-nt siRNAs mediate translational repression and stress adaptation. Nature. 581(7806):89-93.

    
    

40. Bailey-Serres J*^#, Zhai J, Seki M. (2020) The Dynamic Kaleidoscope of RNA Biology in Plants. Plant Physiology. 182(1):1-9.

    
    

41. Feng L*, Zhang F*, Zhang H, Zhao Y, Meyers BC, Zhai J^#. (2020) An online database for exploring over 2,000 Arabidopsis small RNA libraries. Plant Physiology. 182(2):685-691. 

     

2019 

42. Ricci W. A., Lu Z., Ji L., Marand A. P., Ethridge C. L., Murphy N. G., Noshay J.M., Galli M., Guerra M.K.M, Tatché M.C., Johannes F., Rowley M.J, Corce V.G., Zhai J, Scanlon M.J., Buckler E.S., Gallavotti A., Springer N.M., Schmitz R.J.^#, Zhang X^#. (2019) Widespread long-range cis-regulatory elements in the maize genome. Nature Plants, 1-13

    
    

43. Hou Y*, Zhai Y*, Feng L, Karimi HZ, Rutter BD, Zeng L, Choi DS, Zhang B, Gu W, Chen X, Ye W, Innes RW, Zhai J, Ma W^#. (2019) A Phytophthora Effector Suppresses Trans-Kingdom RNAi to Promote Disease Susceptibility. Cell Host & Microbe. 25(1):153-165.

    
    

2018 


44. Tamim S.*, Cai Z*, Mathioni S.M., Zhai J, Teng C, Zhang Q, Meyers B.C.^# (2018) Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses. New Phytologist. doi:doi.org/10.1101/243907




45. Wanlu Liu*, Sascha Duttke*, Jonathan Hetzel, Martin Groth, Suhua Feng, Javier Gallego-Bartolome, Zhenhui Zhong, Hsuan Yu Kuo, Zhai J, Joanne Chory, and Steve Jacobsen^#. (2018) RNA-directed DNA methylation involves co-transcriptional small RNA-guided slicing of Pol V transcripts in Arabidopsis. Nature Plants. 4, p181–188.




46. Yu Zhang*, Jake Harris*, Qikun Liu*, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie, Xinyuan Chen, Lingyu Zhan, Suhua Feng, Jingyi Jessica Li, Haifeng Wang^#, Zhai J^#, and Steven E. Jacobsen^#. (2018) Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. PNAS. .115 (5) E1069-E1074.

    
    

2017 


47. Yu Yu*, Lijuan Ji*, Brandon H Le*, Zhai J, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C Meyers, Xuemei Chen^# ( 2017 ) ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis. PLoS biology.. 15(2): e2001272.




48. Kuo HY*, Jacobsen EL*, Long Y, Chen X, Zhai J^#. ( 2017 ) Characteristics and processing of Pol IV-dependent transcripts in Arabidopsis. Journal of Genetics and Genomics 20;44(1):3-6. doi: 10.1016/j.jgg.2016.10.009.




49. Fang H*, Liu Z, Long Y, Liang Y, Jin Z, Zhang L, Liu D, Li H, Zhai J^#, Pei Y^#. ( 2017 ) The Ca²⁺ /calmodulin2-binding transcription factor TGA3 elevates LCD expression and H₂S production to bolster Cr⁶⁺ tolerance in Arabidopsis. Plant Journal. Jul 3. doi: 10.1111/tpj.13627.




50. Nan GL^#, Zhai J, Arikit S, Morrow D, Fernandes J, Mai L, Nguyen N, Meyers BC, Walbot V^#.(2017) MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize. Development  144(1):163-172.


2016 


51. Groth M^#, Moissiard G, Wirtz M, Wang H, GarciaSalinas G, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Garza RID, Jacobsen SE^# (2016) MTHFD1 controls DNA methylation in Arabidopsis. Nature Communication Jun 13;7:11640




52. Israel Ausin, Suhua Feng, Chaowei Yu, Wanlu Liu, Hsuan Yu Kuo, Elise L. Jacobsen, Zhai J, Javier Gallego-Bartolome, Lin Wang, Ulrika Egertsdotter, Nathaniel R. Street, Steven E. Jacobsen^#, Haifeng Wang^#(2016) DNA methylome of the 20-gigabase Norway spruce genome. PNAS. 113(50):E8106-E8113.


2015 


53. Zhai J*, Bischof S*, Wang H, Feng S, Lee T, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson I, Meyers BC, Ausin I^#, Jacobsen SE^#(2015) A 'One precursor, One siRNA' model for PolIV-dependent siRNA Biogenesis. Cell 163, 445–455




54. Zhai J*, Zhang H*, Arikit S, Huang K, Nan G, Walbot V^#, Meyers BC^# (2015) Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction. PNAS 112(10): 3146-51




55. Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor N, Bart R, Carrington JC, Jacobsen SE^#, Ausin I^# (2015) CG gene body DNA methylation changes and evolution of duplicated genes in cassava. PNAS 112(44):13729-34




56. Yan Z*, Hossain MS*, Valdés-López O, Hoang NT, Zhai J, Wang J, Libault M, Joshi T, Brechenmacher L, Findley S, Qiu L, Sherrier DJ, Meyers BC, Xu D, Stacey G^# (2015) Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Plant Biotechnology Journal 10.1111/pbi.12387




57. Tu B*, Xu C*, Liu L*, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ren G, Yu B, Li S, Meyers BC, Mo B^#, Chen X^# (2015) Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genetics 11(4): e1005119




58. Yan Z*, Hossain MS*, Arikit S, Valdé O, Zhai J, Wang J, Libault M, Ji T, Qiu L, Meyers BC, Stacey G^# (2015) Identification of MicroRNAs and their mRNA targets during soybean nodule development: Functional analysis of the role of miR393* in soybean nodulation. New Phytologist 10.1111/nph.13365




59. Zhao M, Cai C, Zhai J, Lin F, Zhao M, Baumann DD, Ping J, Sun L, Liu Y, Zhang B, Tang Z, Hughes E, Doerge RW, Hughes TJ, Ma J^#.(2015) Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Immune Responses: Insights from analyses of Soybean Rps Gene Near-Isogenic Lines. The Plant Genome 10.3835




60. Cantó-Pastor A, Mollá-Morales A, Ernst E, Dahl W, Zhai J, Yan Y, Meyers BC, Shanklin J, Martienssen RA (2015) Efficient transformation and artificial miRNA gene silencing in Lemna minor. Plant Biology 10.1111/plb.12215


2014 


61. Arikit S, Xia R, Kakrana A, Huang K, Zhai J, Yan Z, Valdés-López O, Prince S, Musket TA, Nguyen HT, Stacey G, Meyers BC^#(2014) An atlas of soybean small RNAs demonstrates regulation by phased siRNAs of hundreds of coding genes. The Plant Cell26: 4584-4601




62. Feng S*, Cokus SJ*, Schubert V, Zhai J, Pellegrini M, Jacobsen SE^# (2014) Genome-wide Hi-C analyses in wild type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Molecular Cell 55(5):694-707




63. Wong J, Gao L, Yang Y, Zhai J, Arikit S, Yu Y, Duan S, Xiong Q, Yan J, Li S, Liu R, Wang Y, Tang G, Meyers BC, Chen X, Ma W^#(2014) Roles of Small RNAs in Soybean Defense against Phytophthora sojae Infection. The Plant Journal 10.1111/tpj.12590




64. Zhai J*, S Arikit*, SA Simon, BF Kingham, BC Meyers^# (2014) Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods. 67(1),84-90

    
    

65. Schapire AL*, Bologna NG*, Moro B, Zhai J, Meyers BC, Palatnik JF^#. (2014) Reprint of: Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. Methods. 67(1):36-44 
    




66. Creasey KM, Zhai J, Borges F, Van EF, Meyers BC, Martienssen RA^# (2014) miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis. Nature 508 (7496):411-5




67. Wei L*, Gu L*, Song X*, Cui X, Lua Z, Zhou M, Wang L, Hu F, Zhai J, Meyers BC, Cao X^# (2014) Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. PNAS 111(10):3877-82


2013 


68. Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay L, Ji L, Xie M, Cao X, Yu B, Timmermans M, Yang B, Chen X, Meyers BC^#. (2013) Plant microRNAs display differential 3'-truncation and tailing, modifications which are ARGONAUTE1-dependent and conserved across species. The Plant Cell 25(7):2417-28




69. Zhai J and Meyers BC^# (2013). Deep Sequencing from hen1 Mutants to Identify Small RNA 3′ Modifications. Cold Spring Harb Symp Quant Biol 1943-4456




70. Schapire A*, Bologna NG*, Moro B, Zhai J, Meyers BC, Palatnik JF^# (2013) Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. Methods. doi:10.1016/j.ymeth.2013.08.032




71. Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Paoli ED, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC, and Green PJ^# (2013) Parallel Analysis of RNA Ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biology 14(12):R145




72. Amborella Genome Project. (2013) The Amborella Genome and the Evolution of Flowering Plants. Science 342(6165):1241089




73. Jeong DH*, Thatcher SR*, Brown RS, Zhai J, Park S, Meyers BC, Green PJ^# (2013) Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage. Plant Physiology 162(3):1225




74. Raman V*, Simon SA*, Romag A, Demirci F, Mathioni SM, Zhai J, Meyers BC, Donofrio NM^# (2013) Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus Magnaporthe oryzae. BMC Genomics 14:326




75. Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik J^# (2013) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Research (10):1675-89




76. Arikit S,Zhai J, Meyers BC^# (2013) Biogenesis and function of rice small RNAs from non-coding RNA precursors. Current Opinion in Plant Biology 16(2):170-9.


2012 


77. Lee TF, Gurazada SG, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC^# (2012) RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 7(7):781-95




78. Zhao Y*, Yu Y*, Zhai J, Ramachandran V, Dinh T, Meyers BC, Mo B^#, Chen X^# (2012) HESO1, a nucleotidyl transferase in Arabidopsis, uridylates unmethylated miRNAs and siRNAs to trigger their degradation. Current Biology 22(8):689-94


2011 


79. Zhai J, Jeong D-H, Paoli ED, Park S, Rosen BD, Li Y, González AJ, Yan Z, Kitto Sherry L, Grusak Michael A, Jackson Scott A, Stacey Gary, Cook Douglas R, Green Pamela J, Sherrier D Janine, Meyers Blake C^#. (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes & Development 25(23):2540-53.




80. Song X*, Li P*, Zhai J*, Zhou M*, Ma L, Liu B, Jeong DH, Nakano M, Cao S, Liu C, Chu C, Wang X, Green P,Meyers BC, Cao X^#. (2011) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. The Plant Journal 69, 462-474.




81. The_International_Medicago_Initiative (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520-524.




82. Jeong D-H, Park S, Zhai J, Gurazada SGR, Paoli ED, Meyers BC, Green PJ^#. (2011) Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage. The Plant Cell 23(12):4185-207.


2010 


83. Yu B, Bi L, Zhai J, Agarwal M, Li S, Wu Q, Ding SW, Meyers BC, Vaucheret H, Chen X^#. (2010) siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Research 38(17):5844-5850.




84. The International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763-768.




85. Meyers BC, Simon SA, Zhai J. (2010) MicroRNA processing: battle of the bulge. Current Biology 20(2):R68-70. (review)




86. Lee TF, Zhai J, Meyers BC^#. (2010) Conservation and divergence in eukaryotic DNA methylation. PNAS 107(20):9027-9028. (review)


2009 


87. Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC^#. (2009) Short-read sequencing technologies for transcriptional analyses. Annual Review Plant Biology 60:305-333. (review)




88. Park W, Zhai J, Lee JY^#. (2009) Highly efficient gene silencing using perfect complementary artificial miRNA targeting AP1 or heteromeric artificial miRNA targeting AP1 and CAL genes. Plant Cell Rep 28(3):469-480.




89. De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, Meyers BC, Jorgensen RA, Green PJ. (2009) Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA 15(11):1965-1970.


2008 


90. Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X, Cao X^#. (2008) Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genetics 4, e1000056.




91. Simon SA, Zhai J, Zeng J, Meyers BC^#. (2008) The cornucopia of small RNAs in plant genomes. Rice 1(1):52-62. (review)


2007 


92. Pei Y*, Niu L*, Lu F*, Liu C*, Zhai J, Kong X, Cao X^#. (2007) Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis. Plant Physiology 144, 1913-1923.




93. Ding Y, Wang X, Su L, Zhai J, Cao S, Zhang D, Liu C, Bi Y, Qian Q, Cheng Z, Chu C^#, Cao X^#. (2007) SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. The Plant Cell 19, 9-22.


2006 


94. Xia R*, Wang J*, Liu C, Wang Y, Zhai J, Liu J, Hong X, Cao X, Zhu JK, Gong Z^#. (2006) ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. The Plant Cell 18, 85-103. 1(1):52-62.