Interplay of TFs with Chromatin

August 28, 2008

The internal structure of the nucleus is complex. It is packed with assorted molecules all trying to work together to execute cellular function. The interplay of nuclear components such as transcription factors and nucleosomes is likely more complex than previously anticipated. A recent paper by Lam, Steger, and O’Shea beings to highlight that complexity. But first, the a little back story ….

Previous work from the O’Shea lab(Springer et. al. PLoS Biology 2003) on Pho4 indicated that the transcription factor, the major activator of the phosphate response pathway, has multiple phosphorylated states. In high phosphate conditions, Pho4 is fully phosphorylated, localized to the cytoplasm and therefore inactive. In phosphate starvation, Pho4 is completely unphosphorylated and fully active. The interesting case, however, is the intermediate state. When phosphate levels are intermediate, Pho4 is partially phosphorylated, accumulates in the nucleus and activates transcription of a subset of the phosphate-responsive genes. For example, Pho5 is a phosphate target which is activated only in the fully active (no phosphorylations) state whereas Pho84 is activated in both low and intermediate phosphorylation states. The differential affinity of Pho4 for some phosphate responsive genes was attributed to affinity differences.

A later paper by Buck and Lieb hinted at a possible mechanism behind the differential binding of Pho4. The Buck paper, studying an entirely different transcription factor (Rap1), identified differential binding in different glucose concentrations. Several nice experiments later and they propose that the mechanism of differential Rap1 binding is related to nucleosome positioning. In high glucose, nucleosomes are stabilized over potential Rap1 targets blocking them from the transcription factor whereas in low glucose the sites are accessible. Figure 6 from their Nature Genetics paper sums up the model:

Given that a great deal is known about nucleosome positioning effects at the Pho5 locus, a natural hypothesis is that chromatin may be an integral part of the affinity differences postulated by Springer et. al. This is precisely the hypothesis underlying the recent Lam et. al. paper (Nature 2008). To quote Lam, “We hypothesized that chromatin may influence gene expression by differentially regulating the accessibility of Pho4 sites int he Pho5 and Pho84 promoters.” They build a library of Pho5 promoter constructs, measure nucleosome positioning in these constructs and at other Pho genes, and demonstrate that, “the interplay of chromatin and binding-site affinity allows different promoters regulated by the same factor to interpret and respond to cellular signals uniquely.”

For may transcription factors, the motif which is recognized has been well characterized. These motifs, often represented as position-specific scoring matricies, show strong positive correlation with available protein-DNA data such as Chip-chip, Chip-seq, and classical promoter bashing. In other words, bound sites more often than not have the motif nearby. However, when viewed in the reverse direction — ie. scan a genome for a given motif, the data indicates that the transcription factors could potentially bind seemingly everywhere. Yet we know that binding is discriminant, specific, and yet not linearly related to site affinity. Including nucleosome positioning in models of transcriptional control may be a necessary component for understanding regulation.

Lam, F.H., Steger, D.J., O’Shea, E.K. (2008). Chromatin decouples promoter threshold from dynamic range. Nature, 453(7192), 246-250. DOI: 10.1038/nature06867

Buck, M.J., Lieb, J.D. (2006). A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nature Genetics, 38(12), 1446-1451. DOI: 10.1038/ng1917

Springer, M., Wykoff, D.D., Miller, N., O’Shea, E.K. (2003). Partially Phosphorylated Pho4 Activates Transcription of a Subset of Phosphate-Responsive Genes. PLoS Biology, 1(2), e8. DOI: 10.1371/journal.pbio.0000028


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