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

Yongheng Chen, Darren L. Bates, Raja Dey, Po Han Chen, Ana Carolina Dantas Machado, Ite A. Laird-Offringa, Remo Rohs, Lin Chen

Research output: Contribution to journalArticlepeer-review

60 Scopus citations

Abstract

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. 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, thereby bridging two separate DNA fragments. This was confirmed in solution by an in-gel fluorescence resonance energy transfer analysis. These findings not only provide insights into the structure and function of GATA proteins but also shed light on the molecular basis of long-range gene regulation.

Original languageEnglish (US)
Pages (from-to)1197-1206
Number of pages10
JournalCell reports
Volume2
Issue number5
DOIs
StatePublished - Nov 29 2012
Externally publishedYes

Bibliographical note

Funding Information:
The authors thank Dr. Liang Guo, Dr. Aidong Han, and Grace Kim for experimental assistance and discussion, and staff members Corie Ralston, Peter Zwart, and Kevin Royal of the Advanced Light Source, Berkeley Center for Structural Biology, for help with data collection. L.C. is supported by National Institutes of Health (NIH) grants GM064642 and GM077320. R.R. is supported in part by grant IRG-58-007-51 from the American Cancer Society. Y.C. is partly supported by an NIH postdoctoral fellowship. Y.C., D.L.B., and L.C. designed the research; Y.C. and D.L.B. purified the protein and DNA; Y.C. and D.L.B. grew the crystals and collected diffraction data; Y.C., D.L.B., and R.D. solved and refined the structures; P.C. and I.A.L. conducted the Biacore experiments; D.L.B performed the in-gel FRET; A.C.D.M. and R.R. performed the computational work; and Y.C., D.L.B., and L.C. wrote the manuscript. All authors commented on and revised the manuscript.

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