title: Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.
abstract: The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the TH1 response, and in gene regulation in plasma B-cells and dendritic cells. T-bet is a member of the Tbox family of transcription factors; however, T-bet coordinately regulates the expression of many more genes than other Tbox proteins. A central unresolved question is how T-bet is able to simultaneously recognize distant Tbox binding sites, which may be located thousands of base pairs away. We have determined the crystal structure of the Tbox DNA binding domain (DBD) of T-bet in complex with a palindromic DNA. The structure shows a quaternary structure in which the T-bet dimer has its DNA binding regions splayed far apart, making it impossible for a single dimer to bind both sites of the DNA palindrome. In contrast to most other Tbox proteins, a single T-bet DBD dimer binds simultaneously to identical half-sites on two independent DNA. A fluorescence-based assay confirms that T-bet dimers are able to bring two independent DNA molecules into close juxtaposition. Furthermore, chromosome conformation capture assays confirm that T-bet functions in the direct formation of chromatin loops in vitro and in vivo. The data are consistent with a looping/synapsing model for transcriptional regulation by T-bet in which a single dimer of the transcription factor can recognize and coalesce distinct genetic elements, either a promoter plus a distant regulatory element, or promoters on two different genes.
authors: Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10021; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; cel2010@med.cornell.edu gpetsko@med.cornell.edu.
authors: Ce Feng
authors: CF
authors: Liu
authors: Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; Department of Chemistry, Franklin and Marshall College, Lancaster, PA 17604.
authors: Gabriel S
authors: GS
authors: Brandt
authors: Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202.
authors: Quyen Q
authors: QQ
authors: Hoang
authors: Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
authors: Natalia
authors: N
authors: Naumova
authors: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115.
authors: Vanja
authors: V
authors: Lazarevic
authors: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115; Division of Life and Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Korea.
authors: Eun Sook
authors: ES
authors: Hwang
authors: Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
authors: Job
authors: J
authors: Dekker
authors: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115; Division of Rheumatology, Allergy, and Immunology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; Ragon Institute of Massachusetts Institute of Technology, Massachusetts General Hospital, and Harvard University, Charlestown, MA 02129.
authors: Laurie H
authors: LH
authors: Glimcher
authors: Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.
authors: Dagmar
authors: D
authors: Ringe
authors: Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10021; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; cel2010@med.cornell.edu gpetsko@med.cornell.edu.
authors: Gregory A
authors: GA
authors: Petsko
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D016678:Genome; D055029:Inverted Repeat Sequences; D051379:Mice; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D020825:T-Box Domain Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014982:Xenopus laevis; D000098815:T-bet Transcription Factor
chemical_list: D002843:Chromatin; D011994:Recombinant Proteins; D020825:T-Box Domain Proteins; D000098815:T-bet Transcription Factor; D004247:DNA
keywords: DNA looping; T-bet; crystal structure; master regulator; transcriptional regulation