Xiaoyu Zhang's Lab - Publications

22. Zhang X. (2008) The Epigenetic Landscape of Plants. Science 320:489 - 492. [PDF]

21. Cokus S.J., Feng S., Zhang X. Chen Z ., Merriman B., Haudenschild C.D., Pradhan S., Nelson S.F., Pellegrini M. and Jacobsen S.E. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-219 [PDF] [Suppl. Data]

20. Zhang X. Germann S., Blus J.B., Khorasanizadeh S., Gaudin V. and Jacobsen S.E. (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nature Structural & Molecular Biology 14:869 - 871. [PDF] [Suppl. Data]

19. Zhang X., Leroy O., Cokus S, Bernatavichute Y.V., Pellegrini M., Goodrich, J. and Jacobsen S.E. (2007) Whole-genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis. PLoS Biology 5(5): e129. [PDF] [Suppl. Data]

18. Zhang X., Henderson I.R., Lu C., Green P.J. and Jacobsen S.E. (2007) Role of RNA Polymerase IV in Small RNA Metabolism. Proc. Natl. Acad. Sci. USA. 104: 4536-4541. [PDF] [Suppl. Figs. Tables] [Suppl. Fig. Legends] [Suppl. Data]

17. Johnson L.M., Bostick M., Zhang X., Kraft E., Henderson I.R., Callis J. Jacobsen S.E. (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation. Current Biology 17: 379-384. [PDF] [Suppl. Data]

16. Zhang X. and Jacobsen S.E. (2006) Genetic Analyses of DNA Methyltransferases in Arabidopsis thaliana. Cold Spring Harbor Symposia on Quantitative Biology 71:439-447. [PDF]

15. Zhang X., Yazaki J., Sundaresan A., Cokus S, Chan S.W-L., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E. and Ecker J.R. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201. [PDF] [Suppl. Data 1] [Suppl. Data 2] [Commentary in Cell] [Commentary in Nature Review Genetics]

14. Goll M.G., Kirpekar F., Maggert K.A., Yoder J.A., Hsieh C.L., Zhang X., Golic K.G., Jacobsen S.E. and Bestor T.H. (2006) Methylation of tRNAAsp by the DNA Methyltransferase Homolog Dnmt2. Science 311: 395 - 398. [PDF] [Suppl. Data]

13. Chan S. W-L., Zhang X., Bernatavichute Y.V and Jacobsen S.E. (2006) Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats. PLoS Biology 4(11): e363. [PDF] [Suppl. Data]

12. Henderson I.R., Zhang X., Lu C., Johnson L., Meyers B.C., Green P.J. and Jacobsen S.E. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nature Genetics 38: 721-725. [PDF] [Suppl. Data]

11. Chan S.W-L., Henderson I.R., Zhang X., Shah G., Chien J.SC., and Jacobsen S.E. (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genetics 2(6):e83. [PDF] [Suppl. Data]

10. Deragon J-M. and Zhang X. (2006) Short Interspersed Elements (SINEs) in Plants: Origin, Classification and Use as Phylogenetic Markers. Systematic Biology 55(6):949-956. [PDF]

9. Holligan D., Zhang X., Jiang N., Pritham E. and Wessler S.R. (2006) Transposable elements in the model legume Lotus japonicus: abundance, diversity and intraspecific insertion polymorphism. Genetics 174: 2215 - 2228. [PDF] [Suppl. Figs.] [Suppl. Fig Legends] [Suppl. Tables]

8. Zhang X. and Wessler S.R. (2005) BoS: A Large and Diverse Family of Short Interspersed Elements (SINEs) in Brassica oleracea. J. Mol. Evol. 60: 677-87. [PDF]

7. Jiang N., Bao Z., Zhang X., Eddy, S.R., and Wessler, S.R. (2004). Pack-MULE Transposable Elements Mediate Gene Evolution in Plants. Nature 431: 569-573. [PDF] [Suppl. Data]

6. Zhang X. and Wessler S.R. (2004) Genome-wide comparative analysis of transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc. Natl. Acad. Sci. USA. 101: 5589-5594. [PDF] [Suppl. Data]

5. Zhang X., Jiang N., Feshotte C. and Wessler S.R. (2004) PIF- and Pong-like transposable elements: distribution, evolution and relationships with Tourist-like miniature inverted-repeat transposable elements. Genetics 166: 971-986. [PDF]

4. Jiang N., Feschotte, C., Zhang X. and Wessler S.R. (2004) Using rice to understand the origin and amplification of miniature inverted-repeat transposable elements (MITEs). Current Opinion in Plant Biology. 7:115-119. [PDF]

3. Jiang N., Bao Z., Zhang X., Hirochika H., Eddy S.R., McCouch S.R., and Wessler S.R. (2003). An active DNA transposon family in rice. Nature 421: 163-167. [PDF] [Suppl. Data]

2. Feschotte C., Zhang X. and Wessler S.R. (2002). Miniature Inverted-repeat Transposable Elements (MITEs) and their relationship with established DNA transposons. In Mobile DNA II (Craig N, Craigie R, Gellert M & Lambowitz A, eds.). American Society of Microbiology. [PDF]

1. Zhang X., Feshotte C., Zhang Q., Jiang N., Eggelston W.B. and Wessler S.R. (2001) P Instability Factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc. Natl. Acad. Sci. USA 98:12572-12577. [PDF] [Suppl. Data] [Commentary in PNAS]