Determinants of nucleosome organization in primary human cells.

Anton Valouev, Steven M Johnson, Scott D Boyd, Cheryl L Smith, Andrew Z Fire, Arend Sidow

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA.

Nature 2011 Jun 23

filter terms:

Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.

Citation

Anton Valouev, Steven M Johnson, Scott D Boyd, Cheryl L Smith, Andrew Z Fire, Arend Sidow. Determinants of nucleosome organization in primary human cells. Nature. 2011 Jun 23;474(7352):516-20