RESEARCH HIGHLIGHTS

Nature Reviews Genetics | AOP, published online 29 August 2012; doi:10.1038/nrg3331

C H R O M AT I N

A model for nucleosome positioning

Nucleosome positioning is influenced by DNA sequence preferences and by various protein complexes, but the relative contribution of these influences has been under debate. This paper describes a functional evolutionary approach to assess the contribution of DNA sequence and proteins further, and the authors propose a model for the establishment of nucleosome positioning invivo. Hughes and colleagues generated seven strains of Saccharomyces cerevisiae that contained yeast artificial chromosomes (YACs) with large segments of foreign DNA from three yeast species (Kluyveromyces lactis, Kluyveromyceswaltii and Debaryomyceshansenii). By crosslinking the chromatin with formaldehyde and then digesting the chromatin using miccrococcal nuclease, mononucelosomal DNA could be analysed by deep sequencing. The authors were then able to compare nucleosome-mapping data between the endogenous genome and the modified S.cerevisiae strains to describe the contribution of DNA sequence (cis) and protein factors (trans) in nucleosome positioning

further. The principle of their functional evolutionary approach is as follows: features that change when a genomic region is placed in the context of S.cerevisiae are influenced by protein factors that differ between the two species, whereas features that are maintained when the foreign DNA is present in the S.cerevisiae must be due either to intrinsic DNA sequence or to conserved trans-acting regulators. Promoter nucleosome-depleted regions (NDRs) were largely maintained in the YACs and were usually located close to their endogenous position, which is consistent with the idea that nucleosome depletion at fungal promoters is largely influenced by DNA sequence. However, nucleosome positions were generally found to change across the YAC strains, and thus the authors suggest that these differences must be due to a trans-acting factor (or factors). They propose that nucleosomeremodelling complexes recognize the NDRs and position nucleosomes flanking the NDR, and the RNA polymerase II preinitiation complex fine-tunes the position of the

+1 nucleosome. This idea is supported by the observation that the locations of the +1 nucleosome and RNA start sites shift in concert. The third step of their model involves the positioning of downstream nucleosomes. The authors propose that this may depend on transcriptional elongation through the recruitment of nucleosomeremodelling activites and histone chaperones by the elongating RNA polymerase II machinery. This model is supported by previous work showing that yeast mutant strains lacking nucleosome-remodelling complexes have drastically reduced positioning of downstream nucleo somes but fairly normal positioning of the +1 and +2 nucleosomes. In summary, this model suggests that determining nucleosome positioning invivo is a three-step process that involves DNA sequence, nucleosome remodellers, transcription factors and transcriptional elongation machinery. The authors state that this model can explain why the general pattern of nucleosome positioning is conserved across eukaryotes but shows species-specific differences regarding chromatin structure.
BryonyJones
ORIGINAL RESEARCH PAPER Hughes, A.L. etal. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol. Cell 9Aug 2012 (doi:10.1016/ j.molcel.2012.07.003)

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VOLUME 13 | O CTOBER 2012