D J Clark

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Nucleosome positioning, nucleosome spacing and the nucleosome code
    David J Clark
    Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Building 6A, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892, USA
    J Biomol Struct Dyn 27:781-93. 2010
  2. pmc Remodeling of yeast CUP1 chromatin involves activator-dependent repositioning of nucleosomes over the entire gene and flanking sequences
    C H Shen
    Laboratory of Cellular and Developmental Biology (NIDDK, National Institutes of Health, Bethesda, Maryland 20892-2715, USA
    Mol Cell Biol 21:534-47. 2001
  3. ncbi request reprint DNA sequence plays a major role in determining nucleosome positions in yeast CUP1 chromatin
    C H Shen
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 276:35209-16. 2001
  4. pmc Activation of Saccharomyces cerevisiae HIS3 results in Gcn4p-dependent, SWI/SNF-dependent mobilization of nucleosomes over the entire gene
    Yeonjung Kim
    Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Biol 26:8607-22. 2006
  5. pmc An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled
    B P Leblanc
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 6, Room B1 12, Bethesda, MD 20892 2715, USA
    Proc Natl Acad Sci U S A 97:10745-50. 2000
  6. ncbi request reprint Mapping histone modifications by nucleosome immunoprecipitation
    David J Clark
    Laboratory of Molecular Growth Regulation, NICHD, National Institutes of Health, Bethesda, Maryland, USA
    Methods Enzymol 410:416-30. 2006
  7. ncbi request reprint The DNA-binding domain of the yeast Spt10p activator includes a zinc finger that is homologous to foamy virus integrase
    Geetu Mendiratta
    Laboratory of Molecular Growth Regulation, NICHD National Institutes of Health, 6 Center Drive, Bethesda, MD 20892 2426, USA
    J Biol Chem 281:7040-8. 2006
  8. pmc Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements
    Peter R Eriksson
    Laboratory of Molecular Growth Regulation, National Instistute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Biol 25:9127-37. 2005
  9. ncbi request reprint Purification and nucleosome mapping analysis of native yeast plasmid chromatin
    Yeonjung Kim
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Building 50 Room 3148, 50 South Drive MSC 8028, Bethesda, MD 20892 8028, USA
    Methods 33:59-67. 2004
  10. pmc SWI/SNF-dependent long-range remodeling of yeast HIS3 chromatin
    Yeonjung Kim
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Building 50, Room 3148, National Institutes of Health, Bethesda, MD 20892 8028, USA
    Proc Natl Acad Sci U S A 99:15381-6. 2002

Collaborators

  • C J Benham
  • T Tsukiyama
  • Leonardo Mariño-Ramírez
  • Peter R Eriksson
  • Yeonjung Kim
  • Geetu Mendiratta
  • Chang Hui Shen
  • C H Shen
  • B P Leblanc
  • Dwaipayan Ganguli
  • Neil McLaughlin
  • Kim Lindstrom
  • Tiffany A Pompa
  • Neil B McLaughlin
  • Tyra G Wolfsberg
  • David Landsman
  • Mohendra Jainerin
  • Carolyn Neal
  • Benoit P Leblanc
  • Ramin Akhavan
  • J A Alfieri

Detail Information

Publications13

  1. pmc Nucleosome positioning, nucleosome spacing and the nucleosome code
    David J Clark
    Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Building 6A, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892, USA
    J Biomol Struct Dyn 27:781-93. 2010
    ..Such a code might facilitate the shunting of nucleosomes from one array to another by ATP-dependent chromatin remodelling machines...
  2. pmc Remodeling of yeast CUP1 chromatin involves activator-dependent repositioning of nucleosomes over the entire gene and flanking sequences
    C H Shen
    Laboratory of Cellular and Developmental Biology (NIDDK, National Institutes of Health, Bethesda, Maryland 20892-2715, USA
    Mol Cell Biol 21:534-47. 2001
    ....
  3. ncbi request reprint DNA sequence plays a major role in determining nucleosome positions in yeast CUP1 chromatin
    C H Shen
    Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 276:35209-16. 2001
    ..We suggest that events occurring in yeast CUP1 chromatin determine which positions are occupied in vivo and when they are occupied...
  4. pmc Activation of Saccharomyces cerevisiae HIS3 results in Gcn4p-dependent, SWI/SNF-dependent mobilization of nucleosomes over the entire gene
    Yeonjung Kim
    Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Biol 26:8607-22. 2006
    ..We propose that Gcn4p stimulates nucleosome mobilization over the entire HIS3 gene by the SWI/SNF complex. We suggest that the net effect of interplay among remodeling machines at HIS3 is to create a highly dynamic chromatin structure...
  5. pmc An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled
    B P Leblanc
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 6, Room B1 12, Bethesda, MD 20892 2715, USA
    Proc Natl Acad Sci U S A 97:10745-50. 2000
    ..The role of transcription factors might be to mark the promoter and to regulate specific melting of promoter DNA...
  6. ncbi request reprint Mapping histone modifications by nucleosome immunoprecipitation
    David J Clark
    Laboratory of Molecular Growth Regulation, NICHD, National Institutes of Health, Bethesda, Maryland, USA
    Methods Enzymol 410:416-30. 2006
    ..This method is sensitive, provides maximal resolution, and is inexpensive. The approach described here may serve as a paradigm for the study of histone-modifying patterns...
  7. ncbi request reprint The DNA-binding domain of the yeast Spt10p activator includes a zinc finger that is homologous to foamy virus integrase
    Geetu Mendiratta
    Laboratory of Molecular Growth Regulation, NICHD National Institutes of Health, 6 Center Drive, Bethesda, MD 20892 2426, USA
    J Biol Chem 281:7040-8. 2006
    ..The zinc finger of Spt10p is homologous to that of foamy virus integrase, perhaps suggesting that this integrase is also a sequence-specific DNA-binding protein...
  8. pmc Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements
    Peter R Eriksson
    Laboratory of Molecular Growth Regulation, National Instistute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Biol 25:9127-37. 2005
    ..No other high-affinity sites are predicted in the yeast genome. Thus, Spt10p is a sequence-specific activator of the histone genes, possessing a DNA-binding domain fused to a likely HAT domain...
  9. ncbi request reprint Purification and nucleosome mapping analysis of native yeast plasmid chromatin
    Yeonjung Kim
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Building 50 Room 3148, 50 South Drive MSC 8028, Bethesda, MD 20892 8028, USA
    Methods 33:59-67. 2004
    ..This method requires purified chromatin, but is capable of mapping relatively long stretches of chromatin in great detail. Typically, it reveals very complex chromatin structures...
  10. pmc SWI/SNF-dependent long-range remodeling of yeast HIS3 chromatin
    Yeonjung Kim
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Building 50, Room 3148, National Institutes of Health, Bethesda, MD 20892 8028, USA
    Proc Natl Acad Sci U S A 99:15381-6. 2002
    ..We propose that the SWISNF complex is recruited to the HIS3 promoter by Gcn4p and then directs remodeling of a chromatin domain, with important implications for transcription...
  11. pmc Spt10 and Swi4 control the timing of histone H2A/H2B gene activation in budding yeast
    Peter R Eriksson
    Program in Genomics of Differentiation, NICHD, National Institutes of Health, Building 6A, Room 2A14, 6 Center Drive, Bethesda, MD 20892 2426, USA
    Mol Cell Biol 31:557-72. 2011
    ..Both activators dissociate from the HTA1-HTB1 promoter after expression has been activated. Thus, SBF and Spt10 cooperate to control the timing of HTA1-HTB1 expression...
  12. pmc Cooperative binding of the yeast Spt10p activator to the histone upstream activating sequences is mediated through an N-terminal dimerization domain
    Geetu Mendiratta
    Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Building 6A Room 2A14, 6 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 35:812-21. 2007
    ..Residues 1-396 are sufficient for normal growth, indicating that the critical functions of Spt10p reside in the N-terminal domains...
  13. pmc Targeted histone acetylation at the yeast CUP1 promoter requires the transcriptional activator, the TATA boxes, and the putative histone acetylase encoded by SPT10
    Chang Hui Shen
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 8028, USA
    Mol Cell Biol 22:6406-16. 2002
    ..These observations constitute evidence for a novel mechanism of chromatin activation at CUP1, with a major role for the TATA box...