Few previous studies have attempted to build qualitative or quantitative models of transcription genome-wide from TF levels because of the paucity of documented TF-binding regions and the lack of coordination around a single cell line. We thus examined the predictive capacity of TF-binding signals for the expression levels of promoters (Figure 2B). In contrast to the profiles of histone modifications, most TFs show enriched binding signals in a narrow DNA region near the TSS, with relatively higher binding signals in promoters with higher CpG content. Most of this correlation could be recapitulated by looking at the aggregate binding of TFs without specific TF terms. Together, these correlation models suggest both that a limited set of chromatin marks are sufficient to “explain” transcription and that a variety of TFs might have broad roles in general transcription levels across many genes. It is important to note that this is an inherently observational study of correlation patterns, and is consistent with a variety of mechanistic models with different causal links between the chromatin, TF and RNA assays. However it does indicate that there is enough information present at the promoter regions of genes to explain the majority of variation in RNA expression.
