Xiaoyu Zhang

Summary

Affiliation: University of Georgia
Country: USA

Publications

  1. pmc Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Green Street, Athens, GA 30602, USA
    Genome Biol 10:R62. 2009
  2. doi request reprint The epigenetic landscape of plants
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Science 320:489-92. 2008
  3. pmc The transposable element landscape of the model legume Lotus japonicus
    Dawn Holligan
    Department of Plant Biology, University of Georgia, Athens 30602, USA
    Genetics 174:2215-28. 2006
  4. pmc SET DOMAIN GROUP2 is the major histone H3 lysine [corrected] 4 trimethyltransferase in Arabidopsis
    Lin Guo
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 107:18557-62. 2010
  5. ncbi request reprint Pack-MULE transposable elements mediate gene evolution in plants
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Nature 431:569-73. 2004
  6. ncbi request reprint BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, 30602, USA
    J Mol Evol 60:677-87. 2005
  7. pmc Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 101:5589-94. 2004
  8. ncbi request reprint Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs)
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Curr Opin Plant Biol 7:115-9. 2004
  9. pmc PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Genetics 166:971-86. 2004
  10. ncbi request reprint An active DNA transposon family in rice
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Nature 421:163-7. 2003

Collaborators

Detail Information

Publications24

  1. pmc Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Green Street, Athens, GA 30602, USA
    Genome Biol 10:R62. 2009
    ..In plants, methylation of histone H3 lysine 4 (H3K4me) is associated with genes and required for normal plant development...
  2. doi request reprint The epigenetic landscape of plants
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Science 320:489-92. 2008
    ....
  3. pmc The transposable element landscape of the model legume Lotus japonicus
    Dawn Holligan
    Department of Plant Biology, University of Georgia, Athens 30602, USA
    Genetics 174:2215-28. 2006
    ..japonicus genome contains many hundreds, perhaps thousands of Sireviruses: Ty1/copia-like elements with an extra ORF. Significantly, several of the L. japonicus Sireviruses have recently amplified and may still be actively transposing...
  4. pmc SET DOMAIN GROUP2 is the major histone H3 lysine [corrected] 4 trimethyltransferase in Arabidopsis
    Lin Guo
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 107:18557-62. 2010
    ..Taken together, these results suggest that SDG2 is the major enzyme responsible for H3K4me3 in Arabidopsis and that SDG2-dependent H3K4m3 is critical for regulating gene expression and plant development...
  5. ncbi request reprint Pack-MULE transposable elements mediate gene evolution in plants
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Nature 431:569-73. 2004
    ....
  6. ncbi request reprint BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, 30602, USA
    J Mol Evol 60:677-87. 2005
    ..As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family...
  7. pmc Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Proc Natl Acad Sci U S A 101:5589-94. 2004
    ..thaliana. In addition, the observation that B. oleracea and A. thaliana share virtually all TE lineages makes it unlikely that wholesale removal of TEs is responsible for the compact genome of A. thaliana...
  8. ncbi request reprint Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs)
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Curr Opin Plant Biol 7:115-9. 2004
    ..Although many questions remain about MITE origins and mode of amplification, data accumulated over the past two years have led to the formulation of testable models...
  9. pmc PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements
    Xiaoyu Zhang
    Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
    Genetics 166:971-86. 2004
    ..Taken together, our results indicate that PIF and Pong are founding members of a large eukaryotic transposon superfamily and that members of this superfamily are responsible for the origin and amplification of Tourist-like MITEs...
  10. ncbi request reprint An active DNA transposon family in rice
    Ning Jiang
    Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
    Nature 421:163-7. 2003
    ..Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation...
  11. pmc The SRA methyl-cytosine-binding domain links DNA and histone methylation
    Lianna M Johnson
    Life Science Core Curriculum, University of California, Los Angeles, Los Angeles, California 90095, USA
    Curr Biol 17:379-84. 2007
    ..Hence, unlike the methyl-binding domain (MBD), which binds only methylated-CpG sequences, the SRA domain is a versatile new methyl-DNA-binding motif...
  12. pmc Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Biol 5:e129. 2007
    ..The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals...
  13. pmc Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    Shawn J Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
    Nature 452:215-9. 2008
    ....
  14. pmc Role of RNA polymerase IV in plant small RNA metabolism
    Xiaoyu Zhang
    Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 104:4536-41. 2007
    ..We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors...
  15. ncbi request reprint The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095, USA
    Nat Struct Mol Biol 14:869-71. 2007
    ..The LHP1 chromodomain also binds H3K27me3 with high affinity, suggesting that LHP1 has functions similar to those of Polycomb...
  16. pmc Two-step recruitment of RNA-directed DNA methylation to tandem repeats
    Simon W L Chan
    Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Biol 4:e363. 2006
    ..Tandem repeats throughout the Arabidopsis genome produce siRNAs, suggesting that repeat acquisition may be a general mechanism for the evolution of gene silencing...
  17. pmc RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis
    Simon W L Chan
    Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
    PLoS Genet 2:e83. 2006
    ..Our results suggest that non-CG DNA methylation that is inherited via a network of persistent targeting signals has been co-opted to regulate developmentally important genes...
  18. ncbi request reprint Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    Xiaoyu Zhang
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
    Cell 126:1189-201. 2006
    ....
  19. ncbi request reprint Inhibitory effect of Epimedium extract on S-adenosyl-L-homocysteine hydrolase and biomethylation
    Xiaoyu Zhang
    Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Graduate School of Chinese Academy of Sciences, Changchun 130022, China
    Life Sci 78:180-6. 2005
    ..These results will provide new clues to the mechanisms of Epimedium in curing of cardiovascular disease and regulating tumor cell growth...
  20. ncbi request reprint Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2
    Mary Grace Goll
    Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
    Science 311:395-8. 2006
    ..Indirect sequence recognition is also a feature of eukaryotic DNA methyltransferases, which may have arisen from a Dnmt2-like RNA methyltransferase...
  21. pmc 1alpha,25-Dihydroxyvitamin D(3) antiproliferative actions involve vitamin D receptor-mediated activation of MAPK pathways and AP-1/p21(waf1) upregulation in human osteosarcoma
    Wei Wu
    Department of Biochemistry, University of California, 5436 Boyce Hall, Riverside, CA 92521, USA
    Cancer Lett 254:75-86. 2007
    ..Our results demonstrate a cross-talk between 1,25D/VDR nongenomic and genomic signaling at the level of MAP kinase activation that leads to reduction of cell proliferation in human osteosarcoma cells...
  22. ncbi request reprint Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers
    Jean Marc Deragon
    CNRS UMR6547, GDR2157 Biomove, Universite Blaise Pascal, 24 avenue des Landais, 63177, Aubiere, France
    Syst Biol 55:949-56. 2006
    ..The importance of these new data for the use of Brassicaceae SINEs as molecular markers in future applications is discussed...
  23. ncbi request reprint Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning
    Ian R Henderson
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095, USA
    Nat Genet 38:721-5. 2006
    ..Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs...
  24. pmc cDNA microarrays as a tool for identification of biomineralization proteins in the coccolithophorid Emiliania huxleyi (Haptophyta)
    Patrick Quinn
    Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
    Appl Environ Microbiol 72:5512-26. 2006
    ..Nonetheless, the data described herein represent profiles of the transcription changes associated with biomineralization-related pathways in E. huxleyi and have identified novel and potentially useful targets for more detailed analysis...