Research Topics
Genomes and GenesSpecies | Xiaoyu ZhangSummaryAffiliation: University of Georgia Country: USA Publications
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Publications
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thalianaXiaoyu 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...- The epigenetic landscape of plantsXiaoyu Zhang
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
Science 320:489-92. 2008.... - The transposable element landscape of the model legume Lotus japonicusDawn 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... - SET DOMAIN GROUP2 is the major histone H3 lysine [corrected] 4 trimethyltransferase in ArabidopsisLin 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... - Pack-MULE transposable elements mediate gene evolution in plantsNing Jiang
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
Nature 431:569-73. 2004.... - BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleraceaXiaoyu 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... - Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleraceaXiaoyu 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... - 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... - PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elementsXiaoyu 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... - An active DNA transposon family in riceNing 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... - The SRA methyl-cytosine-binding domain links DNA and histone methylationLianna 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... - Whole-genome analysis of histone H3 lysine 27 trimethylation in ArabidopsisXiaoyu 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... - Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterningShawn 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.... - Role of RNA polymerase IV in plant small RNA metabolismXiaoyu 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... - The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylationXiaoyu 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... - Two-step recruitment of RNA-directed DNA methylation to tandem repeatsSimon 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... - RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsisSimon 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... - Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsisXiaoyu Zhang
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
Cell 126:1189-201. 2006.... - Inhibitory effect of Epimedium extract on S-adenosyl-L-homocysteine hydrolase and biomethylationXiaoyu 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... - Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2Mary 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... - 1alpha,25-Dihydroxyvitamin D(3) antiproliferative actions involve vitamin D receptor-mediated activation of MAPK pathways and AP-1/p21(waf1) upregulation in human osteosarcomaWei 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... - Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markersJean 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... - Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterningIan 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... - 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...