In this amazing Cell paper, Keji Zhao and his colleagues used Solexa sequencing to create genome-wide maps of nucleosome positions in resting and activated human T cells. They digested DNA with micrococcal nuclease, then gel-purified ~150bp fragments (DNA fragments wrapped around nucleosomes are ~147bp-long) and ran their sample through the Solexa pipeline. The Solexa technology allows the 5′ and 3′ ends (~25bp) of these fragments to be sequenced, and these reads are then mapped onto the human genome.
The resolution of the results they got provides some fascinating insights into chromatin structure and regulation, and the link with gene expression. They detected 8 phased nucleosomes surrounding the TSS of expressed genes, but only right upstream (+1) of the TSS of non-expressed genes. The 5′ end of +1 nucleosomes peaked at +40bp for expressed genes, but +10bp for non-expressed genes. Nucleosome levels at -1 were lower than -2 and +1 for both expressed and non-expressed genes, suggesting that all core promoters are nucleosome-depleted. -1 levels of induced genes do not appear to change upon T cell activation, however increases in -1 levels were observed for repressed genes (-1 nucleosome levels appear inversely correlated to RNA Pol occupancy, also measured by ChIP-seq). The lists goes on and on.
While the authors focus their paper on nucleosome patterns surrounding the TSS, to me, nucleosome patterns in the rest of the genome would be more intriguing. What kind of nucleosome patterns are found in gene deserts ? in recombination hotspots ? in ultra-conserved sequenced ? they present anecdotal evidence that enhancer regions need to be nucleosome-free, in order for regulatory elements to be able to recruit transcription factors. It would be interesting to see if this is a general feature of enhancers (which would then allow to predict where they are in the genome).
