Nuclear-receptor interactions on DNA-response elements.

Nuclear receptors regulate transcription by binding to DNA-response elements using their conserved DNA-binding domains. These response elements contain conserved hexameric sequences that can be arranged in various bipartite configurations, including inverted and direct repeats. A series of structural studies on receptor--DNA binding complexes illustrate the strategies used by receptors to recognize the symmetry of their binding site as well as its sequence. These structures also indicate how cooperation between receptors enhances their joint affinity and selectivity for correctly configured sites.

[1]  S. Khorasanizadeh,et al.  Transcription factors: The right combination for the DNA lock , 1999, Current Biology.

[2]  V. Chatterjee,et al.  Functional analysis of a transactivation domain in the thyroid hormone beta receptor. , 1994, The Journal of biological chemistry.

[3]  R. Shukin,et al.  Determinants of DNA sequence specificity of the androgen, progesterone, and glucocorticoid receptors: evidence for differential steroid receptor response elements. , 1999, Molecular endocrinology.

[4]  P. Chambon,et al.  Activation function 2 (AF‐2) of retinoic acid receptor and 9‐cis retinoic acid receptor: presence of a conserved autonomous constitutive activating domain and influence of the nature of the response element on AF‐2 activity. , 1994, The EMBO journal.

[5]  K. Umesono,et al.  The nuclear receptor superfamily: The second decade , 1995, Cell.

[6]  P. Sigler,et al.  The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex , 1995, Nature Structural Biology.

[7]  B. O’Malley,et al.  Orphan receptors: in search of a unifying hypothesis for activation. , 1992, Molecular endocrinology.

[8]  C. Glass,et al.  Coactivator and corepressor complexes in nuclear receptor function. , 1999, Current opinion in genetics & development.

[9]  H. Gronemeyer,et al.  The nuclear receptor ligand-binding domain: structure and function. , 1998, Current opinion in cell biology.

[10]  R J Fletterick,et al.  Structure and specificity of nuclear receptor-coactivator interactions. , 1998, Genes & development.

[11]  M. Cleary,et al.  Structure of a HoxB1–Pbx1 Heterodimer Bound to DNA Role of the Hexapeptide and a Fourth Homeodomain Helix in Complex Formation , 1999, Cell.

[12]  L. Guarente,et al.  Structure of HAP1-18–DNA implicates direct allosteric effect of protein–DNA interactions on transcriptional activation , 1999, Nature Structural Biology.

[13]  Song Tan,et al.  Crystal structure of the yeast MATα2/MCM1/DNA ternary complex , 1998, Nature.

[14]  John W. R. Schwabe,et al.  The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements , 1993, Cell.

[15]  K. Umesono,et al.  Determinants for selective RAR and TR recognition of direct repeat HREs. , 1993, Genes & development.

[16]  D. Barettino,et al.  Characterization of the ligand‐dependent transactivation domain of thyroid hormone receptor. , 1994, The EMBO journal.

[17]  P. Sigler,et al.  Structural determinants of nuclear receptor assembly on DNA direct repeats , 1995, Nature.

[18]  C. Wolberger,et al.  Crystal Structure of the MATa1/MATα2 Homeodomain Heterodimer Bound to DNA , 1995, Science.

[19]  J. Gustafsson,et al.  Structural determinants of DNA-binding specificity by steroid receptors. , 1995, Molecular endocrinology.

[20]  M. Lazar,et al.  Interdomain communication regulating ligand binding by PPAR-γ , 1998, Nature.

[21]  M. Lazar,et al.  Structural elements of an orphan nuclear receptor-DNA complex. , 1998, Molecular cell.

[22]  R. Evans,et al.  The RXR heterodimers and orphan receptors , 1995, Cell.

[23]  S. Khorasanizadeh,et al.  Structure of the RXR–RAR DNA‐binding complex on the retinoic acid response element DR1 , 2000, The EMBO journal.

[24]  P. Sigler,et al.  DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B , 1999, Nature Structural Biology.

[25]  David A. Agard,et al.  The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of This Interaction by Tamoxifen , 1998, Cell.

[26]  Millard H. Lambert,et al.  Asymmetry in the PPARγ/RXRα Crystal Structure Reveals the Molecular Basis of Heterodimerization among Nuclear Receptors , 2000 .

[27]  M. Lazar,et al.  direct repeat . represses transcription as a dimer on a novel The monomer-binding orphan receptor RevErb , 1995 .

[28]  K. Yamamoto,et al.  Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA , 2003, Nature.

[29]  R. Kaptein,et al.  Millisecond to microsecond time scale dynamics of the retinoid X and retinoic acid receptor DNA-binding domains and dimeric complex formation. , 1999, Biochemistry.

[30]  P. Chambon,et al.  The patterns of binding of RAR, RXR and TR homo‐ and heterodimers to direct repeats are dictated by the binding specificites of the DNA binding domains. , 1993, The EMBO journal.

[31]  P. Chambon,et al.  Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. , 2000, Molecular cell.

[32]  F. Rastinejad Retinoid X receptor and its partners in the nuclear receptor family. , 2001, Current opinion in structural biology.

[33]  Myles Brown,et al.  Polarity-specific activities of retinoic acid receptors determined by a co-repressor , 1995, Nature.

[34]  S. Safe,et al.  Reciprocal Activation of Xenobiotic Response Genes by Nuclear Receptors Sxr/pxr and Car , 2000 .

[35]  J. Lees,et al.  Identification of a conserved region required for hormone dependent transcriptional activation by steroid hormone receptors. , 1992, The EMBO journal.

[36]  Li Zhang,et al.  Structure of a HAP1–DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein , 1999, Nature Structural Biology.

[37]  A. Vershon,et al.  A short, disordered protein region mediates interactions between the homeodomain of the yeast α2 protein and the MCM1 protein , 1993, Cell.

[38]  C. Glass,et al.  Regulation of retinoid signalling by receptor polarity and allosteric control of ligand binding , 1994, Nature.

[39]  L. Freedman,et al.  Nuclear receptor cofactors as chromatin remodelers. , 1999, Current opinion in genetics & development.

[40]  T. Shinoda,et al.  Characterization and DNA-binding properties of GRF, a novel monomeric binding orphan receptor related to GCNF and betaFTZ-F1. , 1999, European journal of biochemistry.

[41]  M. Sierk,et al.  Structural basis of RXR-DNA interactions. , 2000, Journal of molecular biology.

[42]  F. Claessens,et al.  Differences in DNA Binding Characteristics of the Androgen and Glucocorticoid Receptors Can Determine Hormone-specific Responses* , 2000, The Journal of Biological Chemistry.

[43]  A. Takeshita,et al.  Nuclear receptor coactivators facilitate vitamin D receptor homodimer action on direct repeat hormone response elements. , 2000, Endocrinology.

[44]  H. Dyson,et al.  DNA-induced conformational changes are the basis for cooperative dimerization by the DNA binding domain of the retinoid X receptor. , 1998, Journal of molecular biology.

[45]  S. Harrison,et al.  Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA , 1998, Nature.

[46]  Aneel K. Aggarwal,et al.  Structure of a DNA-bound Ultrabithorax–Extradenticle homeodomain complex , 1999, Nature.

[47]  V. Giguère,et al.  Determinants of target gene specificity for ROR alpha 1: monomeric DNA binding by an orphan nuclear receptor , 1995, Molecular and cellular biology.

[48]  K. Yamamoto,et al.  The function and structure of the metal coordination sites within the glucocorticoid receptor DNA binding domain , 1988, Nature.

[49]  A. Johnson,et al.  Molecular mechanisms of cell-type determination in budding yeast. , 1995, Current opinion in genetics & development.

[50]  P. Chambon,et al.  The dimerization interfaces formed between the DNA binding domains of RXR, RAR and TR determine the binding specificity and polarity of the full‐length receptors to direct repeats. , 1994, The EMBO journal.