It has become evident that nucleosome sequence preferences and other factors regulate nucleosomal organization in vivo. However, how nucleosome positioning is regulated locally remains unclear. Using multiple sources of data generated in YPD medium, we identified four typical promoter classes characterized by distinct regulatory modes of nucleosome positioning. Insights into the four modes of nucleosomal regulation reveal that DNA encodes closed nucleosome organization to occlude cryptic sites between some divergent gene pairs, and high intrinsic TF-DNA binding affinity is associated with nucleosome displacement that overrides the underlying nucleosome sequence preferences. We also found that the four modes differ in Pol II occupancy around TSS and coexpression of TF target genes.
A key finding of this study is that Pol II occupancy is correlated with nucleosome occupancy around TSS. A recent study has found that nucleosome occupancy around TSS is correlated with transcriptional plasticity [9
], which quantifies the dynamic range of expression level in various conditions (see Materials and methods section for details). However, we found that there is no significant link between transcriptional plasticity and Pol II occupancy around TSS (see Additional file 7
). The correspondence between Pol II occupancy and nucleosome occupancy around TSS suggests two distinct modes of recruitment of Pol II. As DNA may be transiently accessible at promoters with high nucleosome occupancy around TSS, Pol II should be pre-engaged around TSS for transcription activation. On the other hand, pre-engaged Pol II seems unnecessary for promoters with low nucleosome occupancy around TSS, as their open chromatin structure facilitates regulatory proteins binding which can subsequently recruit Pol II for transcription.
Although DNA at vitro+/vivo- promoters encodes closed nucleosome organization in vitro, the nucleosome organization becomes relatively open in vivo. We found that this drastic change in nucleosome occupancy is due to two reasons. First, the high remodeler occupancy indicates that much chromatin remodeling is involved in nucleosome positioning at vitro+/vivo- promoters. As they do not show high nucleosome delocalization which is the hallmark of nucleosome sliding, we suggest that nucleosome eviction is the main mode of chromatin remodeling at vitro+/vivo- promoters. Second, the high intrinsic DNA binding affinities at vitro+/vivo- promoters enhances the capacity of TFs to compete with nucleosomes for occupancy along DNA, probably resulting in the low nucleosome occupancy in vivo. It will be very interesting to understand how the high nucleosome sequence preferences, the high intrinsic TF-DNA binding affinities, and chromatin remodelers together determine nucleosome dynamics at vitro+/vivo- promoters.
Vitro+/vivo+ promoters are enriched with unbound motifs. Their closed nucleosome organization encoded in DNA seems to protect these cryptic sites. They employ nucleosome sliding and histone acetylation to affect the interaction of histones with DNA. As our analysis is conducted in YPD medium, it is very interesting to investigate whether this regulatory mode of nucleosome positioning is conserved in other cellular conditions. They have lower TF-promoter affinities than vitro+/vivo- and vitro-/vivo- promoters (P < 10-9, Mann-Whitney U-test; Figure ). This relatively unstable TF binding which may be due to their high nucleosome occupancy and delocalization, might limit the regulatory function of TFs.
Vitro-/vivo- promoters, which are less dependent on chromatin remodeling, have open nucleosome organization encoded in DNA. This organization might guarantee the recruitment of TFs to activate transcription. As a result, the corresponding genes of vitro-/vivo- promoters have high gene activities. Other factors override the underlying DNA sequence to form the closed nucleosome organization at vitro-/vivo+ promoters. On the other hand, they show high nucleosome delocalization. A possible explanation is that the competition between TFs and nucleosomes cause nucleosome delocalization.