DYNAMICS AND FUNCTION OF G4 DNA

Summary

Principal Investigator: N Maizels
Abstract: G-rich DNA can form structures stabilized by interactions between guanines, referred to as G4 DNA. These structures have been widely studied in vitro, but until recently had not been shown to form in vivo. My laboratory has very recently directly identified G4 DNA formed in vivo. Building upon and extending this result, we now propose to study in detail how G4 DNA forms, how it is eliminated from living cells, and whether G4 DNA contributes to genomic instability. To that end we will pursue the following specific aims: (1) We will ask if G4 DNA forms at two G-rich genes, c-myc and the rDNA repeats; (2) we will ask whether G4 DNA formation contributes to genomic instability in yeast; (3) we will study instability of G-rich repeats in human cells, and the functions of BLM helicase in their maintenance; (4) we will identify the conserved motif(s) within RecQ family helicases that specify G4 DNA interaction, and create the corresponding mutants to study functions of enzymes in this family in vivo;, and (5) we will ask how mismatch repair factors participate in elimination of G4 DNA. Results from experiments in this proposal will extend our understanding of G4 DNA formation in living cells, characterize pathways that promote its elimination, and establish its contribution to genomic instability that leads to genetic disease and development of malignancy.
Funding Period: 2002-08-01 - 2009-07-31
more information: NIH RePORT

Top Publications

  1. pmc G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD
    Lucas T Gray
    Department of Immunology, University of Washington, Seattle, Washington, USA
    Nat Chem Biol 10:313-8. 2014
  2. pmc G4 motifs correlate with promoter-proximal transcriptional pausing in human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Nucleic Acids Res 39:4975-83. 2011
  3. pmc Distinct activities of exonuclease 1 and flap endonuclease 1 at telomeric g4 DNA
    Aarthy C Vallur
    Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS ONE 5:e8908. 2010
  4. pmc Selection for the G4 DNA motif at the 5' end of human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, 1959 N E Pacific Street, Seattle, WA 98195 7650, USA
    Mol Carcinog 48:319-25. 2009
  5. pmc Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions
    Aarthy C Vallur
    Departments of Immunology and Biochemistry, University of Washington Medical School, Seattle, WA 98195 7650, USA
    Proc Natl Acad Sci U S A 105:16508-12. 2008
  6. pmc Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195 7650, USA
    Nucleic Acids Res 36:1321-33. 2008
  7. ncbi G-rich proto-oncogenes are targeted for genomic instability in B-cell lymphomas
    Michelle L Duquette
    Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Cancer Res 67:2586-94. 2007
  8. ncbi Dynamic roles for G4 DNA in the biology of eukaryotic cells
    Nancy Maizels
    Department of Immunology, University of Washington School of Medicine, 1959 N E Pacific Street, Seattle, Washington 98195 7650, USA
    Nat Struct Mol Biol 13:1055-9. 2006
  9. pmc Gene function correlates with potential for G4 DNA formation in the human genome
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, 1959 NE Pacific Street, Seattle, WA 98195 7650, USA
    Nucleic Acids Res 34:3887-96. 2006
  10. ncbi A conserved G4 DNA binding domain in RecQ family helicases
    Michael D Huber
    Department of Biochemistry, University of Washington Medical School, Seattle, WA 98195, USA
    J Mol Biol 358:1071-80. 2006

Scientific Experts

  • N Maizels
  • Erik D Larson
  • Johanna Eddy
  • Aarthy C Vallur
  • Michelle L Duquette
  • Michael D Huber
  • Lucas T Gray
  • Yves Pommier
  • Sudir Varma
  • William C Reinhold
  • Hongfang Liu
  • Jerome C Shiels
  • Myron F Goodman
  • Phuong Pham

Detail Information

Publications12

  1. pmc G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD
    Lucas T Gray
    Department of Immunology, University of Washington, Seattle, Washington, USA
    Nat Chem Biol 10:313-8. 2014
    ..XPB and XPD enrichment at G4 motifs characterizes specific signaling pathways and regulatory pathways associated with specific cancers. These results identify new candidate pathways for therapies targeted to quadruplexes. ..
  2. pmc G4 motifs correlate with promoter-proximal transcriptional pausing in human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Nucleic Acids Res 39:4975-83. 2011
    ..These results suggest potential roles for dynamic G4 DNA and G4 RNA structures in cis-regulation of pausing, and thus genome-wide regulation of gene expression, in human cells...
  3. pmc Distinct activities of exonuclease 1 and flap endonuclease 1 at telomeric g4 DNA
    Aarthy C Vallur
    Department of Immunology, University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS ONE 5:e8908. 2010
    ..Telomeres are composed of G-rich repeats that readily form G4 DNA. We recently showed that human EXO1 and FEN1 exhibit distinct activities on G4 DNA substrates representative of intermediates in immunoglobulin class switch recombination...
  4. pmc Selection for the G4 DNA motif at the 5' end of human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, 1959 N E Pacific Street, Seattle, WA 98195 7650, USA
    Mol Carcinog 48:319-25. 2009
    ..They further show that for tumor suppressor genes and proto-oncogenes, independent selection determines potential for G4 DNA formation of 5' regulatory regions of transcripts and downstream coding regions...
  5. pmc Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions
    Aarthy C Vallur
    Departments of Immunology and Biochemistry, University of Washington Medical School, Seattle, WA 98195 7650, USA
    Proc Natl Acad Sci U S A 105:16508-12. 2008
    ....
  6. pmc Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195 7650, USA
    Nucleic Acids Res 36:1321-33. 2008
    ..These elements could in principle be recognized either as DNA or as RNA, providing structural targets for regulation at the level of transcription or RNA processing...
  7. ncbi G-rich proto-oncogenes are targeted for genomic instability in B-cell lymphomas
    Michelle L Duquette
    Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Cancer Res 67:2586-94. 2007
    ..These results identify G-richness as one feature of genomic structure that can contribute to genomic instability in AID-positive B-cell malignancies...
  8. ncbi Dynamic roles for G4 DNA in the biology of eukaryotic cells
    Nancy Maizels
    Department of Immunology, University of Washington School of Medicine, 1959 N E Pacific Street, Seattle, Washington 98195 7650, USA
    Nat Struct Mol Biol 13:1055-9. 2006
    ..This Perspective highlights those advances and identifies some key open questions...
  9. pmc Gene function correlates with potential for G4 DNA formation in the human genome
    Johanna Eddy
    Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, 1959 NE Pacific Street, Seattle, WA 98195 7650, USA
    Nucleic Acids Res 34:3887-96. 2006
    ..Selection based on G4P could promote genomic stability (or instability) of specific classes of genes; or reflect mechanisms for global regulation of gene expression...
  10. ncbi A conserved G4 DNA binding domain in RecQ family helicases
    Michael D Huber
    Department of Biochemistry, University of Washington Medical School, Seattle, WA 98195, USA
    J Mol Biol 358:1071-80. 2006
    ....
  11. ncbi AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation
    Michelle L Duquette
    Department of Biochemistry, University of Washington Medical School, Seattle, 98195 7650, USA
    Oncogene 24:5791-8. 2005
    ..Aberrant targeting of AID to DNA structures formed upon c-MYC transcription may therefore contribute to the genetic instability of c-MYC in B-cell malignancies...
  12. ncbi MutSalpha binds to and promotes synapsis of transcriptionally activated immunoglobulin switch regions
    Erik D Larson
    Department of Immunology, Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, 1959 N E Pacific Street, Box 357650, Seattle, WA 98195, USA
    Curr Biol 15:470-4. 2005
    ..G mismatches, initial products of DNA deamination by AID. These results suggest that MutSalpha interacts with the S regions in switching B cells to promote DNA synapsis and recombination...