Crystal Structures of REF6 and Its Complex with DNA Reveal Diverse Recognition Mechanisms

[1]  Daoxiu Zhou,et al.  Dynamic and spatial restriction of Polycomb activity by plant histone demethylases , 2018, Nature Plants.

[2]  Xuemei Chen,et al.  Verification of DNA motifs in Arabidopsis using CRISPR/Cas9‐mediated mutagenesis , 2018, Plant biotechnology journal.

[3]  P. Slama.  Two‐domain analysis of JmjN‐JmjC and PHD‐JmjC lysine demethylases: Detecting an inter‐domain evolutionary stress , 2018, Proteins.

[4]  R. Blumenthal,et al.  Role for first zinc finger of WT1 in DNA sequence specificity: Denys–Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites , 2017, Nucleic acids research.

[5]  R. Mann,et al.  Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding , 2017, Nucleic acids research.

[6]  Wei Wu,et al.  Human apo-SRP72 and SRP68/72 complex structures reveal the molecular basis of protein translocation , 2017, Journal of molecular cell biology.

[7]  Masahiro Nakagawa,et al.  Structure of the SHR–SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD , 2017, Nature Plants.

[8]  Seung Jae Lee,et al.  Structural Analyses of Zinc Finger Domains for Specific Interactions with DNA. , 2016, Journal of microbiology and biotechnology.

[9]  C. Köhler,et al.  DNA-sequence-specific erasers of epigenetic memory , 2016, Nature Genetics.

[10]  C. Vincent,et al.  Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. , 2016, Developmental cell.

[11]  Bing Zhou,et al.  REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis , 2016, Nature Genetics.

[12]  A. Burlingame,et al.  Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis , 2016, Nature Genetics.

[13]  M. Goshe,et al.  Performing protein crosslinking using gas-phase cleavable chemical crosslinkers and liquid chromatography-tandem mass spectrometry. , 2015, Methods.

[14]  Remo Rohs,et al.  Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator , 2015, Nature Communications.

[15]  Yanhui Xu,et al.  Histone demethylase LSD2 acts as an E3 ubiquitin ligase and inhibits cancer cell growth through promoting proteasomal degradation of OGT. , 2015, Molecular cell.

[16]  Zhenhang Chen,et al.  The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers , 2015, Nature Communications.

[17]  Benjamin L. Oakes,et al.  A systematic survey of the Cys2His2 zinc finger DNA-binding landscape , 2015, Nucleic acids research.

[18]  Xiaodong Cheng,et al.  Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence , 2014, Genes & development.

[19]  Xingliang Hou,et al.  Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis , 2014, Nature Communications.

[20]  C. Dean,et al.  Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state , 2014, Nature.

[21]  M. Romero,et al.  NBCe1A dimer assemble visualized by bimolecular fluorescence complementation. , 2014, American journal of physiology. Renal physiology.

[22]  Jiahai Zhang,et al.  Structural and Functional Insights into the Human Börjeson-Forssman-Lehmann Syndrome-associated Protein PHF6* , 2014, The Journal of Biological Chemistry.

[23]  Lin Yang,et al.  DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale , 2013, Nucleic Acids Res..

[24]  Remo Rohs,et al.  Control of DNA minor groove width and Fis protein binding by the purine 2-amino group , 2013, Nucleic acids research.

[25]  S. Jacobsen,et al.  Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome , 2013, Cell.

[26]  J. Wong,et al.  Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b , 2012, Cell Research.

[27]  Zhongzhou Chen,et al.  Complex structures of the abscisic acid receptor PYL3/RCAR13 reveal a unique regulatory mechanism. , 2012, Structure.

[28]  Shujing Liu,et al.  Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development , 2012, Proceedings of the National Academy of Sciences.

[29]  T. Jenuwein,et al.  Arabidopsis REF6 is a histone H3 lysine 27 demethylase , 2011, Nature Genetics.

[30]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[31]  Jens Meiler,et al.  Bcl::Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System , 2011, 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

[32]  Aaron Klug,et al.  The discovery of zinc fingers and their applications in gene regulation and genome manipulation. , 2010, Annual review of biochemistry.

[33]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[34]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[35]  Detlef Snakenborg,et al.  BioXTAS RAW, a software program for high‐throughput automated small‐angle X‐ray scattering data reduction and preliminary analysis , 2009 .

[36]  R. Mann,et al.  The role of DNA shape in protein-DNA recognition , 2009, Nature.

[37]  J. H. Maddocks,et al.  Conformational analysis of nucleic acids revisited: Curves+ , 2009, Nucleic acids research.

[38]  T. Haran,et al.  The unique structure of A-tracts and intrinsic DNA bending , 2009, Quarterly Reviews of Biophysics.

[39]  Guanglin Li,et al.  Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. , 2008, Journal of integrative plant biology.

[40]  Lei Li,et al.  Modulation of brassinosteroid-regulated gene expression by jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis , 2008, Proceedings of the National Academy of Sciences.

[41]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[42]  Yi Zhang,et al.  JmjC-domain-containing proteins and histone demethylation , 2006, Nature Reviews Genetics.

[43]  Kevin Cowtan,et al.  The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.

[44]  S. Sugano,et al.  Solution structure of the zinc finger HIT domain in protein FON , 2005, Protein science : a publication of the Protein Society.

[45]  Klaus Harter,et al.  Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. , 2004, The Plant journal : for cell and molecular biology.

[46]  R. Amasino,et al.  Divergent Roles of a Pair of Homologous Jumonji/Zinc-Finger–Class Transcription Factor Proteins in the Regulation of Arabidopsis Flowering Time , 2004, The Plant Cell Online.

[47]  Jonathan G. Lees,et al.  CDtool-an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving. , 2004, Analytical biochemistry.

[48]  P. Schuck.  On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. , 2003, Analytical biochemistry.

[49]  K. Hibara,et al.  The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. , 2001, Development.

[50]  P. Schuck,et al.  Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. , 2000, Biophysical journal.

[51]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[52]  C. Pabo,et al.  High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. , 1998, Structure.

[53]  S. Harrison,et al.  Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[54]  S. Brown,et al.  NMR structure of a protein kinase C-gamma phorbol-binding domain and study of protein-lipid micelle interactions. , 1997, Biochemistry.

[55]  H Fujisawa,et al.  Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. , 1997, The Plant cell.

[56]  G. Sheldrick.  A short history of SHELX. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[57]  C. Pabo,et al.  DNA recognition by Cys2His2 zinc finger proteins. , 2000, Annual review of biophysics and biomolecular structure.