DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation

Abstract

Summary GATA transcription factors regulate transcription during development and differentiation by recognizing distinct GATA sites with a tandem of two conserved zinc fingers and by mediating long-range DNA looping. However, the molecular basis of these processes is not well understood yet. Here, we determined three crystal structures of the full DNA binding domain (DBD) of human GATA3 protein, which contains both zinc fingers, in complex with different DNA sites. In one structure, both zinc fingers wrap around a palindromic GATA site, cooperatively enhancing the binding affinity and kinetic stability. Strikingly, in the other two structures, the two fingers of GATA DBD bind GATA sites on different DNA molecules, thus bridging two separate DNA fragments, which is confirmed in solution by an in-gel FRET analysis. These findings not only provide new insights into the structure and function of GATA proteins, but also shed light on the molecular basis of long-range gene regulation.

GATA1 Binding Kinetics on Conformation-Specific Binding Sites Elicit Differential Transcriptional Regulation

“…The N and C fingers in a single GATA1 molecule individually bind to two GATA motifs aligned in a palindromic orientation, indicating that the N finger contributes to the specific bivalent binding of GATA1 to Pal-GATA. In this regard, structural analysis of GATA3 revealed that N finger binds the opposite face of DNA that is bound by C finger and the N finger interacts with the C-terminal basic tail of the C finger inserted into the minor groove (39). This model nicely supports the notion that N finger does not contribute to GATA1 binding to rPal-GATA, in which two GATA motifs are aligned in a reverse palindromic orientation.…”

GATA2 is required for lymphatic vessel valve development and maintenance

“…However, the zinc finger domains of GATA1-3 are highly conserved, with all mutated residues being identical (Supplemental Figure 5). A homology model of the GATA2 C-terminal zinc finger (Supplemental Figure 5), based on GATA3 bound to DNA (52) indicates that the Emberger R361L and R396Q mutations likely disrupt binding to DNA by mutation of key residues that interact with the major and minor grooves, respectively ( Figure 2D). R362 makes some minor interactions with phosphates on the backbone ure 2A).…”

Methylation of Gata3 Protein at Arg-261 Regulates Transactivation of the Il5 Gene in T Helper 2 Cells

“…Each GATA family member possesses two highly conserved type IV zinc fingers, referred to as the N-terminal zinc finger (N-finger) and C-terminal zinc finger (C-finger), both of which are involved in DNA binding and protein-protein interactions (2). Among the six vertebrate homologues, Gata1-3 play key roles in the development and maintenance of hematopoietic and immune cells.…”