Epi-MARA's approach to predicting transcription factor activities that explain dynamics in H3K27me3 levels during neuronal differentiation. Transcription factor binding sites were predicted in proximal promoters genome-wide, using a Bayesian method that explicitly models binding site evolution. Epi-MARA models measured chromatin dynamics in terms of predicted TFBSs. Mps quantifies the amount of a particular epigenetic mark M at promoter p in sample s, Npm denotes the total number of predicted binding sites for regulatory motif m in promoter p, cp indicates the basal level of the mark at promoter p, and Ams is the unknown activity of motif m in sample s, which is inferred by the method. Depicted are the normalized activity profiles of the top nine motifs (green lines, with standard errors indicated) with their respective z-values. The three time points correspond to the embryonic stem cell (ES), neuronal progenitor (NP), and terminal neuron (TN) stage. (Insets) Sequence logos of each of the motifs and the transcription factors thought to bind to them are shown.
