Article abstract
Nature Structural & Molecular Biology 16, 847 - 852 (2009)
Published online: 20 July 2009 | doi:10.1038/nsmb.1636
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
Yong Zhang1, Zarmik Moqtaderi2, Barbara P Rattner3, Ghia Euskirchen4, Michael Snyder4, James T Kadonaga3, X Shirley Liu1 & Kevin Struhl2
Abstract
We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over Escherichia coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro show strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor have fewer nucleosome-free regions, reduced rotational positioning and less translational positioning than obtained by intrinsic histone-DNA interactions. Notably, nucleosomes assembled in vitro have only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
- Section of Molecular Biology, University of California, San Diego, La Jolla, California, USA.
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.
Correspondence to: Kevin Struhl2 e-mail: kevin@hms.harvard.edu
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