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Molecular and Cellular Biology, January 2004, p. 697-707, Vol. 24, No. 2
0270-7306/04/$08.00+0     DOI: 10.1128/MCB.24.2.697-707.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Structural Features of Transcription Factor IIIA Bound to a Nucleosome in Solution

Joseph M. Vitolo ,^, Zungyoon Yang, Ravi Basavappa, and Jeffrey J. Hayes^*

Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14625

Received 16 July 2003/ Returned for modification 23 September 2003/ Accepted 14 October 2003

Assembly of a DNA fragment containing a Xenopus borealis somatic-type 5S RNA gene into a nucleosome greatly restricts binding of the 5S gene-specific transcription factor IIIA (TFIIIA) to the 5S internal promoter. However, TFIIIA binds with high affinity to 5S nucleosomes lacking the N-terminal tail domains of the core histones or to nucleosomes in which these domains are hyperacetylated. The degree to which tail acetylation or removal improves TFIIIA binding cannot be simply explained by a commensurate change in the general accessibility of nucleosomal DNA. In order to investigate the molecular basis of how TFIIIA binds to the nucleosome and to ascertain if binding involves all nine zinc fingers and/or displacement of histone-DNA interactions, we examined the TFIIIA-nucleosome complex by hydroxyl radical footprinting and site-directed protein-DNA cross-linking. Our data reveal that the first six fingers of TFIIIA bind and displace approximately 20 bp of histone-DNA interactions at the periphery of the nucleosome, while binding of fingers 7 to 9 appears to overlap with histone-DNA interactions. Molecular modeling based on these results and the crystal structures of a nucleosome core and a TFIIIA-DNA cocomplex yields a precise picture of the ternary complex and a potentially important intermediate in the transition from naïve chromatin structure to productive polymerase III transcription complex.

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* Corresponding author. Mailing address: Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14625. Phone: (585) 273-4887. Fax: (585) 271-2683. E-mail: jjhs{at}mai.rochester.edu.

J.M.V. and Z.Y. contributed equally to this work.

Present address: NIH, NIDCR, GTTB, Bethesda, MD 20892.

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Molecular and Cellular Biology, January 2004, p. 697-707, Vol. 24, No. 2
0022-538X/04/$08.00+0     DOI: 10.1128/MCB.24.2.697-707.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

This article has been cited by other articles:

• Yang, Z., Zheng, C., Thiriet, C., Hayes, J. J. (2005). The Core Histone N-Terminal Tail Domains Negatively Regulate Binding of Transcription Factor IIIA to a Nucleosome Containing a 5S RNA Gene via a Novel Mechanism. Mol. Cell. Biol. 25: 241-249 [Abstract] [Full Text]