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, Kluyveromyces waltii and Debaryomyces hansenii). 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 nucleosome-remodelling 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.
This is a preview of subscription content, access via your institution