DNA-binding specificity of GATA family transcription factors

GATA-binding proteins constitute a family of transcription factors that recognize a target site conforming to the consensus WGATAR (W = A or T and R = A or G). Here we have used the method of polymerase chain reaction-mediated random site selection to assess in an unbiased manner the DNA-binding specificity of GATA proteins. Contrary to our expectations, we show that GATA proteins bind a variety of motifs that deviate from the previously assigned consensus. Many of the nonconsensus sequences bind protein with high affinity, equivalent to that of conventional GATA motifs. By using the selected sequences as probes in the electrophoretic mobility shift assay, we demonstrate overlapping, but distinct, sequence preferences for GATA family members, specified by their respective DNA-binding domains. Furthermore, we provide additional evidence for interaction of amino and carboxy fingers of GATA-1 in defining its binding site. By performing cotransfection experiments, we also show that transactivation parallels DNA binding. A chimeric protein containing the finger domain of areA and the activation domains of GATA-1 is capable of activating transcription in mammalian cells through GATA motifs. Our findings suggest a mechanism by which GATA proteins might selectively regulate gene expression in cells in which they are coexpressed.

[1]  Roy Po.  Human SRF-related proteins : DNA-binding properties and potential regulatory targets , 2007 .

[2]  Simon,et al.  Mouse GATA-4: a retinoic acid-inducible GATA-binding transcription factor expressed in endodermally derived tissues and heart , 1993, Molecular and cellular biology.

[3]  H. Yang,et al.  Distinct roles for the two cGATA-1 finger domains , 1992, Molecular and cellular biology.

[4]  H. Yang,et al.  Distinct roles for the two cGATA-1 finger domains , 1992, Molecular and cellular biology.

[5]  S. Ruben,et al.  Selection of optimal kappa B/Rel DNA-binding motifs: interaction of both subunits of NF-kappa B with DNA is required for transcriptional activation , 1992, Molecular and cellular biology.

[6]  L. Zon,et al.  Cell cycle-dependent initiation and lineage-dependent abrogation of GATA-1 expression in pure differentiating hematopoietic progenitors. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[7]  B. Graves,et al.  Interaction of murine ets-1 with GGA-binding sites establishes the ETS domain as a new DNA-binding motif. , 1992, Genes & development.

[8]  B. Graves,et al.  Interaction of murine ets-1 with GGA-binding sites establishes the ETS domain as a new DNA-binding motif. , 1992, Genes & development.

[9]  S. Orkin,et al.  In vivo footprinting of the human alpha-globin locus upstream regulatory element by guanine and adenine ligation-mediated polymerase chain reaction , 1992, Molecular and cellular biology.

[10]  S. Orkin,et al.  In vivo footprinting of the human alpha-globin locus upstream regulatory element by guanine and adenine ligation-mediated polymerase chain reaction , 1992, Molecular and cellular biology.

[11]  S. Orkin,et al.  Human transcription factor GATA-2. Evidence for regulation of preproendothelin-1 gene expression in endothelial cells. , 1992, The Journal of biological chemistry.

[12]  T. Cooper,et al.  Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression , 1991, Molecular and cellular biology.

[13]  S. Orkin,et al.  GATA-binding transcription factors in hematopoietic cells. , 1992, Blood.

[14]  S. Orkin,et al.  GATA-binding transcription factors in hematopoietic cells. , 1992, Blood.

[15]  L. Zon,et al.  GATA-binding transcription factors in mast cells regulate the promoter of the mast cell carboxypeptidase A gene. , 1991, The Journal of biological chemistry.

[16]  L. Zon,et al.  GATA-binding transcription factors in mast cells regulate the promoter of the mast cell carboxypeptidase A gene. , 1991, The Journal of biological chemistry.

[17]  B. Magasanik,et al.  Sequence and expression of GLN3, a positive nitrogen regulatory gene of Saccharomyces cerevisiae encoding a protein with a putative zinc finger DNA-binding domain , 1991, Molecular and cellular biology.

[18]  R. Treisman,et al.  Human SRF-related proteins: DNA-binding properties and potential regulatory targets. , 1991, Genes & development.

[19]  T. Cooper,et al.  Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression , 1991, Molecular and cellular biology.

[20]  L. Zon,et al.  Expression of GATA-binding proteins during embryonic development in Xenopus laevis. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[21]  L. Zon,et al.  Expression of GATA-binding proteins during embryonic development in Xenopus laevis. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[22]  G. Marzluf,et al.  nit-4, a pathway-specific regulatory gene of Neurospora crassa, encodes a protein with a putative binuclear zinc DNA-binding domain , 1991, Molecular and cellular biology.

[23]  G. Marzluf,et al.  nit-4, a pathway-specific regulatory gene of Neurospora crassa, encodes a protein with a putative binuclear zinc DNA-binding domain , 1991, Molecular and cellular biology.

[24]  J. Spieth,et al.  elt-1, an embryonically expressed Caenorhabditis elegans gene homologous to the GATA transcription factor family , 1991, Molecular and cellular biology.

[25]  J. Spieth,et al.  elt-1, an embryonically expressed Caenorhabditis elegans gene homologous to the GATA transcription factor family , 1991, Molecular and cellular biology.

[26]  T. Quertermous,et al.  Cloning of the GATA-binding protein that regulates endothelin-1 gene expression in endothelial cells. , 1991, The Journal of biological chemistry.

[27]  T. Quertermous,et al.  Cloning of the GATA-binding protein that regulates endothelin-1 gene expression in endothelial cells. , 1991, The Journal of biological chemistry.

[28]  M. Mattei,et al.  A T‐cell specific TCR delta DNA binding protein is a member of the human GATA family. , 1991, The EMBO journal.

[29]  S. Tsai,et al.  Human GATA‐3: a lineage‐restricted transcription factor that regulates the expression of the T cell receptor alpha gene. , 1991, The EMBO journal.

[30]  J. D. Engel,et al.  Murine and human T-lymphocyte GATA-3 factors mediate transcription through a cis-regulatory element within the human T-cell receptor delta gene enhancer , 1991, Molecular and cellular biology.

[31]  J. D. Engel,et al.  Murine and human T-lymphocyte GATA-3 factors mediate transcription through a cis-regulatory element within the human T-cell receptor delta gene enhancer , 1991, Molecular and cellular biology.

[32]  S. Tsai,et al.  Human GATA‐3: a lineage‐restricted transcription factor that regulates the expression of the T cell receptor alpha gene. , 1991, The EMBO journal.

[33]  S. Ekker,et al.  Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosophila. , 1991, The EMBO journal.

[34]  G. Felsenfeld,et al.  trans-Activation of a globin promoter in nonerythroid cells , 1991, Molecular and cellular biology.

[35]  G. Felsenfeld,et al.  trans-Activation of a globin promoter in nonerythroid cells , 1991, Molecular and cellular biology.

[36]  D. Baltimore,et al.  An inhibitory domain of E12 transcription factor prevents DNA binding in E12 homodimers but not in E12 heterodimers , 1991, Cell.

[37]  D. Baltimore,et al.  An inhibitory domain of E12 transcription factor prevents DNA binding in E12 homodimers but not in E12 heterodimers , 1991, Cell.

[38]  S. Orkin,et al.  Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor GATA-1 , 1991, Nature.

[39]  S. Orkin,et al.  Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor GATA-1 , 1991, Nature.

[40]  H. Weintraub,et al.  Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. , 1990, Science.

[41]  H. Weintraub,et al.  Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. , 1990, Science.

[42]  S. Orkin,et al.  Transcriptional activation and DNA binding by the erythroid factor GF-1/NF-E1/Eryf 1. , 1990, Genes & development.

[43]  J. D. Engel,et al.  Activity and tissue-specific expression of the transcription factor NF-E1 multigene family. , 1990, Genes & development.

[44]  J. D. Engel,et al.  Activity and tissue-specific expression of the transcription factor NF-E1 multigene family. , 1990, Genes & development.

[45]  S. Orkin,et al.  A nonerythroid GATA-binding protein is required for function of the human preproendothelin-1 promoter in endothelial cells , 1990, Molecular and cellular biology.

[46]  Y. Fu,et al.  cys-3, the positive-acting sulfur regulatory gene of Neurospora crassa, encodes a sequence-specific DNA-binding protein. , 1990, The Journal of biological chemistry.

[47]  L. Zon,et al.  Structure and transcription of the mouse erythropoietin receptor gene , 1990, Molecular and cellular biology.

[48]  G. Marzluf,et al.  nit-2, the major positive-acting nitrogen regulatory gene of Neurospora crassa, encodes a sequence-specific DNA-binding protein. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[49]  F. Grosveld,et al.  The beta‐globin dominant control region: hypersensitive site 2. , 1990, The EMBO journal.

[50]  F. Grosveld,et al.  The beta‐globin dominant control region: hypersensitive site 2. , 1990, The EMBO journal.

[51]  L. Zon,et al.  Structure and transcription of the mouse erythropoietin receptor gene , 1990, Molecular and cellular biology.

[52]  R. Davies,et al.  The regulatory gene areA mediating nitrogen metabolite repression in Aspergillus nidulans. Mutations affecting specificity of gene activation alter a loop residue of a putative zinc finger. , 1990, The EMBO journal.

[53]  W. Vainchenker,et al.  Megakaryocytic and erythrocytic lineages share specific transcription factors , 1990, Nature.

[54]  W. Vainchenker,et al.  Megakaryocytic and erythrocytic lineages share specific transcription factors , 1990, Nature.

[55]  Stuart H. Orkin,et al.  Expression of an erythroid transcription factor in megakaryocytic and mast cell lineages , 1990, Nature.

[56]  Stuart H. Orkin,et al.  Expression of an erythroid transcription factor in megakaryocytic and mast cell lineages , 1990, Nature.

[57]  Y. Fu,et al.  nit-2, the major nitrogen regulatory gene of Neurospora crassa, encodes a protein with a putative zinc finger DNA-binding domain , 1990, Molecular and cellular biology.

[58]  Y. Fu,et al.  nit-2, the major nitrogen regulatory gene of Neurospora crassa, encodes a protein with a putative zinc finger DNA-binding domain , 1990, Molecular and cellular biology.

[59]  A. Migliaccio,et al.  Progressive inactivation of the expression of an erythroid transcriptional factor in GM- and G-CSF-dependent myeloid cell lines. , 1990, Nucleic acids research.

[60]  F. Studier,et al.  Use of T7 RNA polymerase to direct expression of cloned genes. , 1990, Methods in enzymology.

[61]  F. Studier,et al.  Use of T7 RNA polymerase to direct expression of cloned genes. , 1990, Methods in enzymology.

[62]  A. Migliaccio,et al.  Progressive inactivation of the expression of an erythroid transcriptional factor in GM- and G-CSF-dependent myeloid cell lines. , 1990, Nucleic acids research.

[63]  G. Felsenfeld,et al.  The erythroid-specific transcription factor eryf1: A new finger protein , 1989, Cell.

[64]  Shih-Feng Tsai,et al.  Cloning of cDNA for the major DNA-binding protein of the erythroid lineage through expression in mammalian cells , 1989, Nature.

[65]  Shih-Feng Tsai,et al.  Cloning of cDNA for the major DNA-binding protein of the erythroid lineage through expression in mammalian cells , 1989, Nature.

[66]  S. Orkin,et al.  Increased γ-globin expression in a nondeletion HPFH mediated by an erythroid-specif ic DNA-binding factor , 1989, Nature.

[67]  S. Orkin,et al.  Increased γ-globin expression in a nondeletion HPFH mediated by an erythroid-specif ic DNA-binding factor , 1989, Nature.

[68]  C. Caskey,et al.  Construction of plasmids that express E. coli beta-galactosidase in mammalian cells. , 1989, Nucleic acids research.

[69]  C. Caskey,et al.  Construction of plasmids that express E. coli beta-galactosidase in mammalian cells. , 1989, Nucleic acids research.

[70]  F. Grosveld,et al.  The human beta‐globin promoter; nuclear protein factors and erythroid specific induction of transcription. , 1988, The EMBO journal.

[71]  F. Grosveld,et al.  The human beta‐globin promoter; nuclear protein factors and erythroid specific induction of transcription. , 1988, The EMBO journal.

[72]  F. Grosveld,et al.  The human beta-globin gene 3' enhancer contains multiple binding sites for an erythroid-specific protein. , 1988, Genes & development.

[73]  F. Grosveld,et al.  The human beta-globin gene 3' enhancer contains multiple binding sites for an erythroid-specific protein. , 1988, Genes & development.

[74]  M. Reitman,et al.  An erythrocyte-specific DNA-binding factor recognizes a regulatory sequence common to all chicken globin genes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[75]  M. Reitman,et al.  An erythrocyte-specific DNA-binding factor recognizes a regulatory sequence common to all chicken globin genes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[76]  H. Okayama,et al.  Calcium phosphate-mediated gene transfer: a highly efficient transfection system for stably transforming cells with plasmid DNA. , 1988, BioTechniques.

[77]  H. Okayama,et al.  Calcium phosphate-mediated gene transfer: a highly efficient transfection system for stably transforming cells with plasmid DNA. , 1988, BioTechniques.

[78]  F. Studier,et al.  Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. , 1986, Journal of molecular biology.

[79]  F. Studier,et al.  Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. , 1986, Journal of molecular biology.

[80]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .