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Biophys. J. BioFAST: First Published April 13, 2007. doi:10.1529/biophysj.106.099929
© 2007 by the Biophysical Society.

A more recent version of this article appeared on July 1, 2007.
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NUCLEIC ACIDS

DNA compaction by the nuclear factor Y (NF-Y)

Rosalinda F Guerra 1, Laura Imperadori 1, Roberto Mantovani 1, David D Dunalp 2 and Laura Finzi 2*

1 University of Milano
2 Emory University

* To whom correspondence should be addressed. E-mail: lfinzi{at}emory.edu.

Submitted on October 23, 2006
Revised on January 7, 2007
Accepted on 9 March 2007


  Abstract
The nuclear factor Y (NF-Y), a trimeric, CCAAT-binding transcriptional activator with histone-like subunits, was until recently considered a prototypical promoter transcription factor. However, recent in vivo chromatin immuno-precipitation assays associated with microarray methodologies (ChIP-on-chip experiments), have indicated that a large portion of target sites (40-50%) are located outside of core promoters. We applied the tethered particle motion technique (TPM) to the major histocompatibility complex (MHC) Class II enhancer-promoter region, to characterize: i) the progressive compaction of DNA due to increasing concentrations of NF-Y, ii) the role of specific subunits and domains of NF-Y in the process, and iii) the interplay between NF-Y and the Regulatory Factor-X (RFX), which cooperatively binds to the X-box, adjacent to the CCAAT box. Our study shows that NFY has histone-like activity, since it binds DNA non-specifically with high affinity to compact it. This activity, which depends on the presence of all trimer subunits and of their glutamine-rich domains, seems to be attenuated by the transcriptional cofactor RFX. Most importantly NF-Y-induced DNA compaction may facilitate promoter-enhancer interactions, which are known to be critical for expression regulation.

Key Words: DNA looping, Single molecule microscopy, Tethered Particle Motion (TPM), transcriptional factors




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Copyright © 2007 by the Biophysical Society.