Eukaryotic genomes are packaged into regularly spaced arrays of nucleosomes, although the spacing between nucleosomes varies among species and cell types1
. Despite this regularity, high-resolution, genome-wide analyses reveal a common nucleosomal pattern2-8
. Nucleosomes are depleted at many (but not all) enhancer, promoter, and terminator regions, and they typically occupy preferred positions within mRNA coding regions and just upstream of the promoter. In yeast, the -1 and +1 nucleosomes flanking the promoter are strongly positioned, and the degree of nucleosome positioning gradually decreases from the 5′ to 3′ end of the coding region6,8
There are three distinct mechanisms for nucleosome depletion in vivo
. First, specific DNA-binding activator proteins can generate nucleosome-depleted regions by recruiting ATP-dependent remodeling complexes and histone acetylases9-11
; this mechanism is independent of transcriptional activity12
. Second, the process of transcriptional elongation by RNA polymerase II involves cycles of histone eviction and reassembly, and continuous high levels of Pol II elongation reduce histone density within coding regions13-15
. Third, certain DNA sequences, notably poly(dA:dT) tracts, intrinsically disfavor nucleosome formation in vitro
, increase chromatin accessibility in vivo
, and are strongly over-represented in nucleosome-free regions16,17,18
, indicating a role of intrinsic histone-DNA interactions.
The positioning of nucleosomes along the DNA is related to, but distinct from, the issue of nucleosome occupancy. Nucleosome occupancy or density reflects the average histone levels on a given region of DNA in a population of cells, but it does not address where an individual nucleosome is positioned with respect to a certain DNA sequence. Indeed, differently positioned nucleosomes within a given genomic region will all contribute to nucleosome density. Nucleosome positioning refers to two fundamental relationships between the histone octamer and the DNA wrapped around it. Rotational positioning defines the orientation of the DNA helix on the histone surface. Nucleosomes are rotationally positioned with a 10 bp helical periodicity, reflecting preferences for dinucleotides that face inwards or outwards with respect to the histones and optimize DNA bending19-21
. The translational position of a nucleosome refers to the specific 146 bp sequence covered by the histone octamer, and it is often defined as the midpoint of this sequence. The degree of translational positioning can vary from perfect positioning, in which a nucleosome occupies a given 146 bp stretch in all DNA molecules in a population, to random positioning, in which nucleosomes occupy all possible genomic positions equally. In vivo
, translational positioning is strongly influenced by relatively constant spacing between nucleosomes, which is presumably due to the action of nucleosome-remodeling complexes.
Nucleosomes can also be statistically positioned from a fixed barrier such as a DNA-binding protein22
. Nucleosomes near the barrier are highly positioned, and the degree of positioning decreases in accord with the distance from the barrier due to variations in spacing between nucleosomes. A barrier model for statistical positioning can explain the location of nucleosomes in yeast genes8
, but the molecular nature of the barrier is unknown.
Nucleosomes exhibit intrinsic DNA sequence preferences19,20,23
, and many yeast promoter regions are nucleosome-depleted because the DNA sequence intrinsically disfavors nucleosome formation16,17
. More generally, it has been proposed that there is a nucleosome code in which the pattern of nucleosome positioning in vivo
is determined primarily by genomic DNA sequence and hence can be predicted16,24
. Here, we use S. cerevisiae
and E. coli
DNA to examine the role of intrinsic histone-DNA interactions for establishing the nucleosomal pattern in vivo
on a genome-wide basis.