Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites

Ce Feng Liu, Gabriel S. Brandt, Quyen Hoang, Natalia Naumova, Vanja Lazarevic, Eun Sook Hwang, Job Dekker, Laurie H. Glimcher, Dagmar Ringe, Gregory A. Petsko

Research output: Contribution to journalArticle

3 Citations (Scopus)

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 fluorescencebased 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.

Original languageEnglish (US)
Pages (from-to)E6572-E6581
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number43
DOIs
StatePublished - Oct 25 2016

Fingerprint

Genome
DNA
Transcription Factors
Genes
T-Lymphocytes
Proteins
Adaptive Immunity
Cell Lineage
Plasma Cells
Innate Immunity
Base Pairing
Dendritic Cells
Chromatin
T-box transcription factor TBX21
B-Lymphocytes
Chromosomes
Binding Sites

Keywords

  • Crystal structure
  • DNA looping
  • Master regulator
  • T-bet
  • Transcriptional regulation

ASJC Scopus subject areas

  • General

Cite this

Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites. / Liu, Ce Feng; Brandt, Gabriel S.; Hoang, Quyen; Naumova, Natalia; Lazarevic, Vanja; Hwang, Eun Sook; Dekker, Job; Glimcher, Laurie H.; Ringe, Dagmar; Petsko, Gregory A.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, No. 43, 25.10.2016, p. E6572-E6581.

Research output: Contribution to journalArticle

Liu, Ce Feng ; Brandt, Gabriel S. ; Hoang, Quyen ; Naumova, Natalia ; Lazarevic, Vanja ; Hwang, Eun Sook ; Dekker, Job ; Glimcher, Laurie H. ; Ringe, Dagmar ; Petsko, Gregory A. / Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites. In: Proceedings of the National Academy of Sciences of the United States of America. 2016 ; Vol. 113, No. 43. pp. E6572-E6581.
@article{194fcc5efd35402f961c2ad26fe7112d,
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 fluorescencebased 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.",
keywords = "Crystal structure, DNA looping, Master regulator, T-bet, Transcriptional regulation",
author = "Liu, {Ce Feng} and Brandt, {Gabriel S.} and Quyen Hoang and Natalia Naumova and Vanja Lazarevic and Hwang, {Eun Sook} and Job Dekker and Glimcher, {Laurie H.} and Dagmar Ringe and Petsko, {Gregory A.}",
year = "2016",
month = "10",
day = "25",
doi = "10.1073/pnas.1613914113",
language = "English (US)",
volume = "113",
pages = "E6572--E6581",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "43",

}

TY - JOUR

T1 - Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites

AU - Liu, Ce Feng

AU - Brandt, Gabriel S.

AU - Hoang, Quyen

AU - Naumova, Natalia

AU - Lazarevic, Vanja

AU - Hwang, Eun Sook

AU - Dekker, Job

AU - Glimcher, Laurie H.

AU - Ringe, Dagmar

AU - Petsko, Gregory A.

PY - 2016/10/25

Y1 - 2016/10/25

N2 - 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 fluorescencebased 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.

AB - 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 fluorescencebased 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.

KW - Crystal structure

KW - DNA looping

KW - Master regulator

KW - T-bet

KW - Transcriptional regulation

UR - http://www.scopus.com/inward/record.url?scp=84992422455&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84992422455&partnerID=8YFLogxK

U2 - 10.1073/pnas.1613914113

DO - 10.1073/pnas.1613914113

M3 - Article

C2 - 27791029

AN - SCOPUS:84992422455

VL - 113

SP - E6572-E6581

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 43

ER -