Philipp Korber from the University of Munich considers the view that there is a universal genomic code that determines nucleosome positioning a prominent hypothesis; one that he, together with colleagues and collaborators Karl Ekwall from the Karolinska Institute and Guo-Cheng Yuan from Harvard University, recently helped call into question.

Genomic DNA does not exist in random coils in the nucleus but is wrapped around octamers of histone proteins, the nucleosomes, which in turn can form higher-order structures. The positioning of the nucleosomes determines the accessibility of DNA to other proteins such as polymerases and thereby influences transcription. Knowing where along a DNA molecule the nucleosomes are positioned allows one to better understand how genes are turned on or off.

Histones are among the most conserved proteins across all eukaryotes, and their higher affinity for certain DNA sequences has led scientists to postulate a positioning code. Korber calls this idea that eukaryotic DNA has evolved information that is sufficient to determine the positioning of the nucleosomes 'intellectually pleasing', but he says: “we and others had indications from in vitro reconstruction work (in [Saccharomyces] cerevisiae) that DNA sequence alone does not sufficiently determine positioning.”

Among researchers working in the chromatin field, S. pombe is emerging as a preferred model organism because it has many features in common with multicellular organisms. Yet when Alexandra Lantermann, a doctorate student in Korber's group, set out to determine genome-wide nucleosome positioning in vivo, she found published nucleosome maps for only 3 loci—a negligible number given the approximately 5,000 genes in the S. pombe genome—and no reliable information on transcription start and termination sites (TSSs and TTSs). So Lantermann first used a laborious method to determine nucleosome positioning with locus-specific probes to obtain a gold-standard set of positions. Then, in what Korber calls a herculean effort, Lantermann annotated TSSs and TTSs of all S. pombe genes by hand.

To get a genome-wide positioning map, Lantermann digested chromatin with micrococcal nuclease and hybridized the DNA protected by the nucleosomes to a tiling array at 20-base-pair resolution. When she aligned the hybridization signals of all genes at their TSS, several interesting findings emerged. Downstream of the TSS Lantermann saw regular arrays, that is, similar average spacing between nucleosomes across all genes. To Korber, this suggests that the passage of the polymerase sets up the array. Upstream of the TSS, the researchers saw a nucleosome-depleted region (NDR). Similar NDRs have been reported in S. cerevisiae, and there, poly(A+T) stretches had been shown to be crucial in keeping the DNA nucleosome free. However, in S. pombe such sequences are not enriched in NDRs. Apparently, S. pombe uses a different, yet to be determined, mechanism to keep NDRs free of nucleosomes. In general, the correlation between DNA sequence and nucleosome positioning was very different between both yeast, arguing against universally conserved DNA sequence rules.

Interestingly, promoter regions enriched for the histone variant H2A.Z, which is considered an epigenetic mark for silent chromatin, also had arrays upstream of the TSS, indicating that histone H2A.Z has a role in positioning as well, again in contrast to S. cerevisiae.

Although much remains to be done to elucidate mechanisms, the value of this map is obvious. As Korber describes it, “everyone can turn to this map and find out where in their gene of interest is an NDR or a regular array and how high the nucleosome occupancy is.” And in addition every gene is annotated with a TSS and a TTS.

Elucidating the mechanism of positioning will give important clues as to the intricate interplay between chromatin packaging and all DNA-related processes such as transcription, replication or DNA repair.