Xinjian He, Ph.D. - Postgraduate - 北京生命科学研究所

Xinjian He, Ph.D.

Associate Investigator, NIBS, Beijing，China

Phone：010-80726688-8555

Fax： 010-80707715

E-mail：hexinjian@nibs.ac.cn

Education

1997	B.S. Biology, Department of Biology, Nanjing Normal University,Nanjing, China
2000	M.S. Crop Genetics and Breeding, Department of Agronomy,Nanjing Agricultural University, Nanjing, China
2004	Ph.D. Biochemistry and Molecular Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences,Beijing, China

Professional Experience

2010-present	Associate Investigator, National Institute of Biological Sciences,Beijing, China
2006-2009	Postdoctoral Research Associate, Department of Botany and Plant Sciences, University of California, Riverside, USA
2004-2006	Postdoctoral Researcher, Department of Biology, University of Iowa, USA

Research Description

Chromatin changes caused by DNA methylation and histone modifications play crucial roles in genome stability, gene regulation, genomic imprinting and transgene silencing. DNA methylation refers to addition of a methyl group to 5’-cytosine of DNA, which extensively exists from prokaryotes to eukaryotes. In plants, the methylated genomic DNA loci are frequently accompanied by the occurrence of siRNAs and noncoding RNAs, which cause de novo DNA methylation through RNA-directed DNA methylation. The histone modifications include methylation, acetylation, phosphorylation and ubiquitination, which coordinate with DNA methylation and regulate chromatin status. We will study the RNA-directed DNA methylation and histone modification mechanisms by applying genetic, molecular biological and biochemical approaches. We attempt to identify new components in the pathway and study their functions in genome stability, development and transcriptional gene silencing. These studies will help to understand the dynamic regulation of epigenomes during plant development and adaptation to environments.

Publications

1. Zhao N, Su XM, Liu ZW, Zhou JX, Su YN, Cai XW, Chen L, Wu Z, He XJ. The RNA recognition motif-containing protein UBA2c prevents early flowering by promoting transcription of the flowering repressor FLM in Arabidopsis. New Phytol., 2022, 233, 751-765.

2. Shang JY, Lu YJ, Cai XW, Su YN, Feng C, Li L, Chen S, He XJ. COMPASS functions as a module of the INO80 chromatin remodeling complex to mediate histone H3K4 methylation in Arabidopsis. Plant Cell, 2021, 33, 3250-3271.

3. Feng C, Cai XW, Su YN, Li L, Chen S, He XJ. rabidopsis RPD3-like histone deacetylases form multiple complexes involved in stress response. J Genet Genomics., 2021, 48, 369-383.

4. Zhou JX, Du P, Liu ZW, Feng C, Cai XW, He XJ. FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin. Plant J., 2021, 107, 467-479.

5. Wu CJ, Liu ZZ, Wei L, Zhou JX, Cai XW, Su YN, Li L, Chen S, He XJ. Three functionally redundant plant-specific paralogs are core subunits of the SAGA histone acetyltransferase complex in Arabidopsis. Mol Plant, 2021, 14, 1071-1087.

6. Qian F, Zhao QY, Zhang TN, Li YL, Su YN, Li L, Sui JH, Chen S, He XJ. The histone H3K27me3 reader cooperates with a family of PHD finger-containing proteins to regulate flowering time in Arabidopsis. J Integr Plant Biol., 2021, 63, 787-802.

7. Guo J, Wei L, Chen SS, Cai XW, Su YN, Li L, Chen S, He XJ. The CBP/p300 histone acetyltransferases function as plant-specific MEDIATOR subunits in Arabidopsis. J Integr Plant Biol., 2021, 63, 755-771.

8. Ning YQ, Liu N, Lan KK, Su YN, Li L, Chen S, He XJ. DREAM complex suppresses DNA methylation maintenance genes and precludes DNA hypermethylation. Nat Plants, 2020, 6, 942-956.

9. Zhou HR, Lin RN, Huang HW, Li L, Cai T, Zhu JK, Chen S, He XJ. The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production. Plant J., 2020, 103, 1503-1515.

10. Luo YX, Hou XM, Zhang CJ, Tan LM, Shao CR, Lin RN, Su YN, Cai XW, Li L, ChenS, He XJ. A plant-specific SWR1 chromatin-remodeling complex couples histone H2A.Z deposition with nucleosome sliding. EMBO J., 2020, 39, e102008.

11. Tan LM, Liu R, Gu BW, Zhang CJ, Luo J, Guo J, Wang Y, Chen L, Du X, Li S, Shao CR, Su YN, Lin RN, Li L, Chen S, Du J*, He XJ*. Dual recognition of H3K4me3 and DNA by the ISWI component ARID5 regulates the floral transition in Arabidopsis. Plant Cell, 2020, in press. (*co-corresponding authors).

12. Liu ZW, Zhao N, Su YN, Chen SS, He XJ. Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis. Sci Rep., 2020, 10, 3094.

13. Ning YQ, Chen Q, Lin RN, Li YQ, Li L, Chen S, He XJ. The HDA19 histone deacetylase complex is involved in the regulation of flowering time in a photoperiod-dependent manner. Plant J., 2019, 98, 448-464.

14. Zhao QQ, Lin RN, Li L, Chen S, He XJ. A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes. J Integr Plant Biol., 2019, 61, 120-139.

15. 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. Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin. Nat Commun., 2018, 9, 4547.

16. Tan LM, Zhang CJ, Hou XM, Shao CR, Lu YJ, Zhou JX, Li YQ, Li L, Chen S, He XJ. The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing. EMBO J., 2018, 37, pii: e98770.

17. Zhao QY, He XJ. Exploring potential roles for the interaction of MOM1 with SUMO and the SUMO E3 ligase-like protein PIAL2 in transcriptional silencing. PLoS One, 2018, 13, e0202137.

18. Zhou JX, Liu ZW, Li YQ, Li L, Wang B, Chen S, He XJ. Arabidopsis PWWP domain proteins mediate H3K27 trimethylation on FLC and regulate flowering time. J Integr Plant Biol., 2018, 60, 362-368.

19. Luo YX, Han YF, Zhao QY, Du JL, Dou K, Li L, Chen S, He XJ. Sumoylation of SUVR2 contributes to its role in transcriptional gene silencing. Sci China Life Sci. 2018, 61, 235-243.

20. 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. The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci. Genome Biol. 2017, 18, 103.

21. Wang L, Kong D, Lv Q, Niu G, Han T, Zhao X, Meng S, Cheng Q, Guo S, Du J, Wu Z, Wang J, Bao F, Hu Y, Pan X, Xia J, Yuan D, Han L, Lian T, Zhang C, Wang H, He XJ, He YK. Tetrahydrofolate Modulates Floral Transition through Epigenetic Silencing. Plant Physiol., 2017, 174, 1274-1284.

22. Zhang CJ, Hou XM, Tan LM, Shao CR, Huang HW, Li YQ, Li L, Cai T, Chen S, He XJ. The Arabidopsis acetylated histone-binding protein BRAT1 forms a complex with BRP1 and prevents transcriptional silencing. Nat Commun., 2016, 7, 11715.

23. Liu ZW, Zhou JX, Huang HW, Li YQ, Shao CR, Li L, Cai T, Chen S, He XJ. Two Components of the RNA-Directed DNA Methylation Pathway Associate with MORC6 and Silence Loci Targeted by MORC6 in Arabidopsis. PLoS Genet., 2016, 12, e1006026.

24. Han YF, Zhao QY, Dang LL, Luo YX, Chen SS, Shao CR, Huang HW, Li YQ, Li L, Cai T, Chen S, He XJ. The SUMO E3 Ligase-Like Proteins PIAL1 and PIAL2 Interact with MOM1 and Form a Novel Complex Required for Transcriptional Silencing. Plant Cell, 2016, 28, 1215-1229.

25. Ye R, Chen Z, Lian B, Rowley MJ, Xia N, Chai J, Li Y, He XJ, Wierzbicki AT, Qi Y. A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis. Mol Cell, 2016, 61, 222-235.

26. Chan Z, Wang Y, Cao M, Gong Y, Mu Z, Wang H, Hu Y, Deng X, He XJ, Zhu JK. RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway. New Phytol., 2016, 209, 1527-1539.

27. Han YF, Huang HW, Li L, Cai T, Chen S, He XJ. The Cytosolic Iron-Sulfur Cluster Assembly Protein MMS19 Regulates Transcriptional Gene Silencing, DNA Repair, and Flowering Time in Arabidopsis. PLoS One, 2015, 10, e0129137.

28. Du JL, Zhang SW, Huang HW, Cai T, Li L, Chen S, He XJ. The Splicing Factor PRP31 Is Involved in Transcriptional Gene Silencing and Stress Response in Arabidopsis. Mol Plant, 2015, 8, 1053-1068.

29. Wang C, Dong X, Jin D, Zhao Y, Xie S, Li X, He X, Lang Z, Lai J, Zhu JK, Gong Z. Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol., 2015, 167, 905-914.

30. Ning YQ, Ma ZY, Huang HW, Mo H, Zhao TT, Li L, Cai T, Chen S, Ma L, He XJ. Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14. Nucleic Acids Res., 2015, 43, 1469-1484.

31. Han YF, Dou K, Ma ZY, Zhang SW, Huang HW, Li L, Cai T, Chen S, Zhu JK, He XJ. SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis. Cell Res., 2014, 24, 1445-1465.

32. He XJ*, Ma ZY, Liu ZW. Non-coding RNA transcription and RNA-directed DNA methylation in Arabidopsis. Mol Plant, 2014, 7, 1406-1414. (*corresponding author).

33. Liu ZW, Shao CR, Zhang CJ, Zhou JX, Zhang SW, Li L, Chen S, Huang HW, Cai T, He XJ. The SET Domain Proteins SUVH2 and SUVH9 Are Required for Pol V Occupancy at RNA-Directed DNA Methylation Loci. PLoS Genet., 2014, 10, e1003948.

34. Huang CF, Miki D, Tang K, Zhou HR, Zheng Z, Chen W, Ma ZY, Yang L, Zhang H, Liu R, He XJ, Zhu JK. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet., 2013, 9, e1003779.

35. Zhou HR, Zhang FF, Ma ZY, Huang HW, Jiang L, Cai T, Zhu JK, Zhang C, He XJ. Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis. Plant Cell, 2013, 25, 2545-2559.

36. Dou K, Huang CF, Ma ZY, Zhang CJ, Zhou JX, Huang HW, Cai T, Tang K, Zhu JK, He XJ. The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs. Nucleic Acids Res., 2013, 41, 8489-8502.

37. 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*. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc. Natl. Acad. Sci. USA, 2013, 110, 8290-8295. (*co-corresponding authors).

38. Zhang CJ, Zhou JX, Liu J, Ma ZY, Zhang SW, Dou K, Huang HW, Cai T, Liu R, Zhu JK, He XJ. The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis. EMBO J., 2013, 32, 1128-1140.

39. Zhang H, He X, Zhu JK. RNA-directed DNA methylation in plants: Where to start? RNA Biol., 2013, 10, 1593-1596.

40. Zhang CJ, Ning YQ, Zhang SW, Chen Q, Shao CR, Guo YW, Zhou JX, Li L, Chen S, He XJ. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. PLoS Genet., 2012, 8, e1002693.

41. Liu J, Bai G, Zhang C, Chen W, Zhou J, Zhang S, Chen Q, Deng X, He XJ*, Zhu JK. An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing. Cell Res., 2012, 21, 1691-1700. (*corresponding author).

42. He XJ*, Chen T*, Zhu JK. Regulation and function of DNA methylation in plants and animals. Cell Res., 2011, 21, 442-465. (*co-corresponding authors).

43. Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature, 2010, 465, 106-109.

44. Zheng Z*, Xing Y*, He XJ*, Li W, Hu Y, Yadav SK, Oh J, Zhu JK. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. Plant J., 2010, 62, 92-99. (*co-first authors)

45. He XJ, Hsu YF, Zhu S, Liu HL, Pontes O, Zhu J, Cui X, Wang CS, Zhu JK. A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes & Dev., 2009, 23, 2717-2722.

46. He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell, 2009, 137, 498-508.

47. He XJ, Hsu YF, Pontes O, Zhu J, Lu J, Bressan RA, Pikaard CS, Wang CS, Zhu JK. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes & Dev., 2009, 23, 318-330.

48. He XJ, Mulford KE, Fassler JS. Oxitative stress function of the S. cerevisiae Skn7 receiver domain. Eukaryot. Cell, 2009, 8, 768-778.

49. Li WX, Oono Y, Zhu J, He XJ, Wu J, Iida K, Lu XY, Cui X, Jin H, Zhu JK. The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell, 2008, 20, 2238-2251.

50. Cao WH, Liu J, He XJ, Mu RL, Zhou HL, Chen SY, Zhang JS. Modulation of ethylene responses affects plant salt-stress responses. Plant Physiol., 2007, 143, 707-19.

51. He XJ, Fassler JS. Identification of novel Yap1p and Skn7p binding sites involved in the oxidative stress response of Saccharomyces cerevisiae. Mol. Microbiol., 2005, 58, 1454-1467.

52. He XJ, Mu RL, Cao WH, Zhang ZG, Zhang JS, Chen SY. AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J., 2005, 44, 903-916.

53. Zhang WK, Shen YG, He XJ, Du BX, Xie ZM, Luo GZ, Zhang JS, Chen SY. Characterization of a novel cell cycle-related gene from Arabidopsis. J Exp. Bot., 2005, 56, 807-816.

54. He XJ, Zhang ZG, Yan DQ, Zhang JS, Chen SY. A salt-responsive receptor-like kinase gene regulated by the ethylene signaling pathway encodes a plasma membrane serine/threonine kinase. Theor. Appl. Genet., 2004, 09, 377-383.

55. Wang YJ, Zhang ZG, He XJ, Zhou HL, Wen YX, Dai JX, Zhang JS, Chen SY. A rice transcription factor OsbHLH1 is involved in cold stress response. Theor. Appl. Genet., 2003, 107, 1402-1409.

56. He X, Chen J, Zhang Z, Zhang J, Chen S. Identification of salt-stress responsive genes in rice (Oryza sativa L.) by cDNA array. Sci China C Life Sci., 2002, 45, 477-484.

57. Wang JF, He XJ, Zhang HS, Chen ZY. [Genetic analysis of blast resistance in japonica rice landrace heikezijing from Taihu region]. Yi Chuan Xue Bao, 2002, 29, 803-807.

58. Xie C, Zhang ZG, Zhang JS, He XJ, Cao WH, He SJ, Chen SY. Spatial expression and characterization of a putative ethylene receptor protein NTHK1 in tobacco. Plant Cell Physiol., 2002, 43, 810-815.