Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome-DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.Eukaryotic genomic DNA exists as highly compacted nucleosome arrays called chromatin. Each nucleosome contains a 147-base-pair (bp) stretch of DNA, which is sharply bent and tightly wrapped around a histone protein octamer 1 . This sharp bending occurs at every DNA helical repeat (∼10 bp), when the major groove of the DNA faces inwards towards the histone octamer, and again ∼5 bp away, with opposite direction, when the major groove faces outward. Bends of each direction are facilitated by specific dinucleotides 2,3 . Neighbouring nucleosomes are separated from each other by 10-50-bp-long stretches of unwrapped linker DNA 4 ; thus, 75-90% of genomic DNA is wrapped in nucleosomes. Access to DNA wrapped in a nucleosome is occluded 1 for polymerase, regulatory, repair and recombination complexes, yet nucleosomes also recruit other proteins through interactions with their histone tail domains 5 . Thus, the detailed locations of nucleosomes along the DNA may have important inhibitory or facilitatory roles 6,7 in regulating gene expression.DNA sequences differ greatly in their ability to bend sharply 2,3,8 . Consequently, the ability of the histone octamer to wrap differing DNA sequences into nucleosomes is highly dependent on the specific DNA sequence 9,10 . In vitro studies show this range of affinities to be 1,000-fold or greater 11 . Thus, nucleosomes have substantial DNA sequence preferences. A key One view is that the sequence preferences of nucleosomes might not be meaningful. Nucleosome positions might be regulated in cells in trans by the abundant 12 ATP-dependent nucleosome remodelling complexes 13 , which might over-ride the sequence preferences of nucleosomes and move them to new locations whenever needed. Another view, however, is that remodelling factors do not themselves determine the destinations of the nucleosomes that they mobilize. Rather, the remodelling complexes may allow nucleosomes to sample alternative positi...

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Intrinsic nucleosome dynamics termed "site exposure" provides spontaneous and cooperative access to buried regions of nucleosomal DNA in vitro. Two different mechanisms for site exposure have been proposed, one based on nucleosome translocation, the other on dynamic nucleosome conformational changes in which a stretch of the nucleosomal DNA is transiently released off the histone surface. Here we report on three experiments that distinguish between these mechanisms. One experiment investigates the effects on the accessibilities of restriction enzyme target sites inside nucleosomes when extra DNA (onto which the nucleosome may move at low energetic cost) is appended onto one end. The other two experiments test directly for nucleosome mobility under the conditions used to probe accessibility to restriction enzymes: one on a selected nonnatural nucleosome positioning sequence, the other on the well-studied 5S rRNA gene nucleosome positioning sequence. We find from all three assays that restriction enzymes gain access to sites throughout the entire length of the nucleosomal DNA without contribution from nucleosome translocation. We conclude that site exposure in nucleosomes in vitro occurs via a nucleosome conformational change that leads to transient release of a stretch of DNA from the histone surface, most likely involving progressive uncoiling from an end. Recapture at a distal site along DNA that has partially uncoiled would result in looped structures which are believed to contribute to RNA polymerase elongation and may contribute to spontaneous or ATP-driven nucleosome mobility. Transient open states may facilitate the initial entry of transcription factors and enzymes in vivo.DNA target sites for gene regulatory proteins may be sterically occluded by packaging in nucleosomes in vivo, yet the cognate proteins are nevertheless still able to bind to them (11,13,36,40,50). How this is accomplished is not known. Entry of site-specific factors into chromatin may be facilitated in vivo by the action of nucleosome remodeling enzymes (14,25,26,42,45,49), including histone acetylases and ATP-dependent machines that promote nucleosome translocation or conformational changes. A question inherent in this idea is how such factors would know which nucleosomes to remodel. Recent discoveries (6,12,26) suggest that in some cases remodeling factors are recruited to specific DNA target sites by other sequence-specific DNA binding proteins that bind first-raising the question of how those proteins gain access to their target sites.We and others (8, 28) have suggested that spontaneous partial uncoiling or breathing motions of nucleosomal DNA could allow for the progressive invasion of a nucleosome starting from an end. Such conformational dynamics would allow for passive binding of proteins to target sites that, in the time average, are buried inside nucleosomes. This could also represent an initial step of entry into chromatin, with subsequent recruitment of remodeling factors acting to move or destabilize that histone octamer, ...