58. Liu J and Zhong X (2024) Epiallelic variation of non-coding RNA genes and their phenotypic consequences. Nature Communications (Accepted)

57. Liu J and Zhong X (2024) Population epigenetics: DNA methylation in the plant omics era. Plant Physiology, (Accepted)

56. Chen J, Lu J, Liu J, Fang J, Zhong X, Song J. (2023) DNA conformational dynamics in the context-dependent non-CG CHH methylation by plant methyltransferase DRM2. JBC DOI:https://doi.org/10.1016/j.jbc.2023.105433 PDF

55. Liu ZW, Liu J, Liu F, Zhong X. (2023) Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis. Nucleic Acids Research doi.org/10.1093/nar/gkad306 PDF

54. Yang F, Sun Y, Du X, Chu Z, Zhong X, Chen X. (2023) Plant-specific histone deacetylases associate with ARGONAUTE4 to promote heterochromatin stabilization and plant heat tolerance. New Phytol. 238(1):252-269. doi: 10.1111/nph.18729. Epub 2023 Feb 1 PDF

53. Scheid R, Dowell JA, Sanders D, Jiang J, Denu JM, Zhong X. (2022) Histone Acid Extraction and High Throughput Mass Spectrometry to Profile Histone Modifications in Arabidopsis thaliana. Curr Protoc 2(8):e527. doi: 10.1002/cpz1.527. PDF

52. Fang J*, Jiang J*, Leichter SM*, Liu J, Biswal M, Khudaverdyan N, Zhong X#, Song J#  (2022) Mechanistic basis for maintenance of CHG DNA methylation in plants. Nature Communications 13(1):3877. (*Equal contribution,  #Corresponding authors) PDF

51. Liu ZW, Simmons CH, Zhong X (2022) Linking transcriptional silencing with chromatin remodeling, folding, and positioning in the nucleus. Current Opinion in Plant Biology 69:102261. PDF

50. Leichter SM, Du J, Zhong X (2022) Structure and mechanism of  plant DNA methyltransferases.DNA Methyltransferase – Role and Function pp 137–157 Adv Exp Med Biol doi: 10.1007/978-3-031-11454-0_6. PDF

49. Kim E, Liu P, Zhang S, Wang Y, Schehr J, Wolfe S, Dickerson A, Donahue K, Lu L, Rui L, Zhong X, Wisinski KB, Yu M, Suzuki A, Lang J, Ong IM, Xu W (2021) BAF155 methylation drives triple-negative breast cancer metastasis by hijacking super-enhancers and subverting anti-tumor Immunity. Nucleic Acids Res 49(21): 12211-12233 PDF

48. Schmitz RJ, Marand AP, Zhang X, Mosher RA, Turck F, Chen X, Axtell MJ, Zhong X, Brady SM, Meyers BC (2021) Commentary: Quality control and evaluation of plant epigenomics data. Plant Cell 34(1):503-513  PDF

47. Nozawa K*, Chen J*, Jiang J*, Leichter SM, Yamada M, Suzuki T, Liu F, Ito H#, Zhong X# (2021) DNA methyltransferase CHROMOMETHYLASE3 is required for full ONSEN transposon activation in heat stress. PLOS Genetics 17(8): e1009710. https://doi.org/10.1371/journal.pgen.1009710 (*Equal contribution,  #Corresponding authors) PDF

46. Hu D, Yu Y, Wang C, Long Y, Liu Y, Feng Li, 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  DOI: 10.1093/plcell/koab162  PDF

45. Fang J*, Leichter SM*, Jiang J*, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X#, Song J# (2021) Substrate deformation regulates DRM2-mediated DNA methylation in plants. Science Advances 2021 7(23):1-13 (*Equal contribution,  #Corresponding authors) PDF

44. Jiang J, Liu J, Sanders D, Qian S, Ren W, Song J, Liu F#, Zhong X# (2021) UVR8 interacts with de novo DNA methyltransferase and suppresses DNA methylation in Arabidopsis. Nature Plants 7(2):184-197. doi: 10.1038/s41477-020-00843-4 (#Corresponding authors). PDF

43. Scheid R, Chen J, Zhong X (2021) Biological role and mechanism of chromatin readers in plants. Current Opinion in Plant Biology 10;61:102008. doi: 10.1016/j.pbi.2021.102008 PDF

42. Chen J, Liu J, Jiang J, Qian S, Song J, Kabara R, Delo I, Serino G, Liu F, Hua Z, Zhong X (2021) F-box protein CFK1 interacts with and degrades de novo DNA methyltransferase in Arabidopsis. New Phytologist 229(6):3303-3317. doi: 10.1111/nph.17103 PDF

41. Joly-Lopez Z, Platts AE, Gulko B, Choi J, Groen SC, Zhong X, Siepel A, Purugganan MD (2020) A fitness consequence map of the rice genome. Nature Plants 6(2):119-130. doi: 10.1038/s41477-019-0589-3 PDF.

40. Jiang J, Ding A, Liu F#, Zhong X# (2020) Linking signaling pathways to chromatin dynamics. Journal of Experimental Botany 71(17):5179-5190. doi: 10.1093/jxb/eraa202 (#Corresponding authors) PDF

39. Yang L*, Chen X*, Wang Z, Sun Q, Hong A, Zhang A, Zhong X#, Hua J# (2020) HOS15 and HDA9 negatively regulates immunity through histone deacetylation on intracellular immune receptor NLR genes in Arabidopsis. New Phytologist doi.org/10.1111/nph.16380 (*Equal contribution,  #Corresponding authors) PDF

38. Chen X#, Ding A, Zhong X# (2020) Functions and mechanisms of plant histone deacetylases. Science China Life Sciences, doi.org/10.1007/s11427-019-1587-x. #Corresponding author PDF

37. Mayer KS*, Chen X*, Sanders D, Chen J, Jiang J, Nguyen P, Scalf M, Smith LM, Zhong X (2019) HOS15 acts with the histone deacetylase to modulate transcription and development. Plant Physiology doi: 10.1104/pp.18.01156 (*Equal contribution). PDF

36. Stoddart CI, Feng S, Campbell MG, Liu W, Wang H, Zhong X, Bernatavichute Y, Cheng Y, Jacobsen SE, Narlikar, GJ. (2019) A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase. Molecular Cell, 73(1), 73-83.e6. PDF

35. Kong G, You X, Wen Z, Chang YI, Qian S, Ranheim E, Letson C, Zhang X, Zhou Y, Liu Y,  Rajagopalan A, Zhang J, Stieglitz E, Loh M, Hofmann I, Yang D, Zhong X, Padron E, Zhou L, Pear WS, and  Zhang J (2018) Downregulating Notch counteracts KrasG12D-induced ERK activation and oxidative phosphorylation in myeloproliferative neoplasm. Leukemia doi: 10.1038/s41375-018-0248-0  PDF

34. Yang Z*, Qian S*,  Scheid R, Lu L,  Chen X, Liu R, Du X,  Lv X, Boersma M, Scalf M,  Smith L, Denu J, Du J#, Zhong X# (2018) EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nature Genetics 50(9) 1247-1253 doi: 10.1038/s41588-018-0187-8 (*Equal contribution, #Corresponding authors) PDF  Nature Genetics News & Views   UW News

33. Qian S*, Lv X*, Scheid R*,  Lu L,  Yang Z, Chen W,Liu R, Boersma M, Denu J, Zhong X#,  Du J# (2018) Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nature Communications 9(1):2425  DOI: 10.1038/s41467-018-04836-y (*Equal contribution, #Corresponding authors) PDF

32. Chen X, Lu L, Qian S, Scalf M, Smith L,  Zhong X (2018) Canonical and non-canonical actions of Arabidopsis histone deacetylases in ribosomal RNA processing. Plant Cell    30(1):134-152.  PDFFeatured by: In the Histone Zone: The Mighty Eraser.    WID News    Ribosomes Meet Epigenetics.

31. Lu L*, Chen X*, Qian S, Zhong X (2018) The plant-specific histone residue Phe41 is important for genome-wide H3.1 distribution.  Nature Communications 9(1):630 doi:10.1038/s41467-018-02976-9. (*Equal contributionPDF

30. Lomax A, Woods DP, Dong Y, Bouche F, Rong Y, Mayer KS, Zhong X, Amasino RM (2018) An ortholog of CURLY LEAF/ENHANCER OF ZESTE like-1 is required for proper flowering in Brachypodium distachyonPlant Journal 93(5):871-882 doi: 10.1111/tpj.13815. PDF

29. Sanders D, Qian S, Fieweger R, Lu L, Dowell JA, Denu JM, Zhong X (2017) Histone lysine-to-methionine mutations reduce histone methylation and cause developmental pleiotropy. Plant Physiology 73(4):2243-2252. PDF

28. Kim Y, Wang R, Gao L, Li D, Xu C, Mang H, Jeon J, Chen X, Zhong X, Kwak J, Mo B, Xiao L, Chen X (2016) POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. PNAS 131 (51): 14858-63. PDF

27. Chen X, Lu L, Meyer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X (2016) POWERDRESS interacts with histone deacetylase 9 to promote aging in Arabidopsis. eLife DOI: http://dx.doi.org/10.7554/eLife.17214  PDF

26. Zeng H*, Lu L*, Chan N, Horswill M, Ahlquist P, Zhong X#, Xu W# (2016) Systematic identification of Ctr9 regulome in ERα-positive breast cancer. BMC Genomics 17(1): 902 (*Equal contribution, #Corresponding authors)  PDF

25. Zhang J, Kong G, Rajagopalan A, Lu L, Song J, Hussaini M, Zhang X, Ranheim EA, Liu Y, Wang J, Gao X, Chang Y, Johnson K, Zhou Y, Yang D, Bhatnagar B, Lucas DM, Bresnick E, Zhong X, Padron E, Zhang J (2016) p53-/- synergizes withZhang enhanced NrasG12D signaling to transform megakaryocyte-erythroid progenitors in acute myeloid leukemia. Blood 129(3):358-370 PDF          

24. Li Y, Bouchlaka MN, Wolff J, Grindle KM, Lu L, Qian S, Zhong X, Pflum N, Jobin P, Kahl BS, Eickhoff JC, Wuerzberger-Davis SM, Miyamoto S, Thomas CJ, Yang DT, Capitini CM, Rui L(2016)  FBXO10 deficiency and BTK activation upregulate BCL2 expression in mantle cell lymphoma. Oncogene 35(48):6223-6234 PDF

23. Zhong X (2016) Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation. New Phytologist 210: 76–80  PDF

22. Lu L, Chen X, Sanders D, Qian S, Zhong X (2015) High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns in Arabidopsis and rice. Epigenetics 10(11): 1044-1053 PDF

21. Zhong X*#, Hale CJ*, Nguyen M, Ausin I, Groth M, Hetzel J, Vashisht AA, Henderson IR, Wohlschlegel JA, Jacobsen SE# (2015) DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis.PNAS112 (3): 911-916. (*Equal contribution, #Corresponding authors) PDF 

20. Yelagandula R, Stroud H, Holec S, Zhou K, Feng S, Zhong X,  Muthurajan UM, Nie X, Kawashima T, Groth M, Luger K, Jacobsen SE, Berger F (2014) The histone variant H2A.W marks heterochromatin and promotes chromatin condensation in Arabidopsis. Cell 158: 98-109. PDF

19. Zhong X*, Du J*, Hale CJ, Gallego-Bartolome J, Feng S, Vashisht AA, Chory J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell 157: 1050-1060. (*Equal contributionPDF

18. Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE (2014) SRA- and SET-domain-containing proteins link RNA Polymerase V occupancy to DNA methylation. Nature  507:124-128. PDF

17. Stroud H, Do T, Du J, Zhong X, Feng S, Johnson LM, Patel DJ, Jacobsen SE (2014) Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nature Structural & Molecular Biology 21: 64-72. PDF

16. Du J*, Zhong X*, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE. (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. (*Equal contribution) Cell 151: 167-180.  PDF

15. Zhong X*, Hale CJ*, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE. (2012) DDR complex facilitates genome-wide association of RNA polymerase V to promoters and evolutionarily young transposons. Nature Structural & Molecular Biology 19(9): 870-875. (*Equal contributionPDF

14. Wang Y, Itaya A, Zhong X, Wu Y, Zhang J, van der Knaap E, Olmstead R, Qi Y, Ding B.  (2011) Function and evolution of a microRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. Plant Cell 23: 3185-203. PDF

13. Henderson IR, Deleris A, Wong W, Zhong X, Chin HG, Horwitz G, Kelly KA, Pradhan S, Jacobsen SE. (2010) The DRM2 cytosine methyltransferase requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thalianaPLoS Genetics 6(10): e1001182. PDF

12. Qian S, Zhong X, Yu L, Ding B, Haan PD, Boris-Lawrie K(2009) HIV-1 Tat RNA silencing suppressor activity is conserved across kingdoms and counteracts translational repression of HIV-1. PNAS 106(2): 605-10. PDF

11. Ding B and Zhong X. (2009) Viroids/Virusoids. In Encyclopedia of Microbiology Third Edition. Elsevier publisher. pp 535-545.

10. Zhong Xand Ding B. (2008) Distinct RNA motifs mediate systemic RNA trafficking. Plant Signaling & Behavior 3(1): 58-59. PDF

9. Zhong X, Archual A, Amin A, Tao X and Ding B. (2008) A genomic map of viroid RNA motifs critical for replication and systemic trafficking. Plant Cell 20: 35-47.  PDF

8. Zhong X*, Tao X*, Stombaugh J, Leontis N, Ding B. (2007) Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic traffickingEMBO J 26: 3836-3846. (*Equal contribution)  PDF

7. Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, Takeda R, Harris AR, Molina C, Nelson RS, Ding B. (2007) A structured viroid RNA serves as a substrate for Dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. J Virol 81(6): 2980-2994. PDF

6. Wang Y, Zhong X, Itaya A, Ding B. (2007) Evidence for the existence of the loop E motif of Potato spindle tuber viroid in vivo. J Virol 81(4): 2074-2077. PDF

5. Zhong X, Leontis N, Qian S, Itaya A, Qi Y, Boris-Lawrie K, Ding B. (2006) Tertiary structural and functional analyses of a viroid RNA motif by isostericity matrix and mutagenesis reveal its essential role in replication. J Virol 80(17): 8566-8581. PDF

4. Zhong X, Itaya A, Ding B. (2005) Transfecting protoplasts by electroporation to study viroid replication. Curr Protoc Microbiol 2005 Jul; Chapter 16: Unit 16D.4. doi: 10.1002/ 9780471729259.mc16d04s00. PDF

3. Cao X, Zhou P, Zhang X, Zhu S, Zhong X, Xiao Q, Ding B, Li Y. (2005) Identification of an RNA silencing suppressor from a plant double-stranded RNA virus. J Virol 79(20): 13018-13027. PDF

2. Ding B, Itaya A, Zhong X. (2005) Viroid trafficking: a small RNA makes a big move. Curr Opin Plant Biol 8(6): 606-612. PDF

1. Qi Y, Zhong X, Itaya A, Ding B. (2004) Dissecting RNA silencing in protoplasts uncovers novel interactions of viral suppressors with the silencing pathway at the cellular level. Nucleic Acids Res 32(22): e179. PDF