DNA-Binding Mutant EAAE-ER alpha Genome-Wide Binding in the Uterus

Transcription factors (TFs) influence cell function by interpreting information contained within cis-regulatory elements in chromatin. Whereas ChIP-sequencing has been used to identify and map transcription factor-DNA interactions, it has been difficult to assign functionality to the binding sites identified. Thus, in this study we probed the transcriptional activity, DNA-binding competence and functional activity of select nuclear receptor (NR) mutants in cellular and animal model systems and used this information to define the sequence constraints of functional steroid nuclear receptor (sNR) cis-regulatory elements. Analysis of the architecture within sNR chromatin interacting sites revealed that only a small fraction of all sNR chromatin interacting events are associated with transcriptional output, and that this functionality is restricted to elements that vary from the consensus palindromic elements by one or two nucleotides. These findings define the transcriptional grammar necessary to predict functionality from linear genome sequences. Overall design: ERa binding of DBD-mutant ERa (EAAE) 2 samples; pools of 15 EAAE uteri (V or E2 treated) Please note that the precise mouse strain information is, unfortunately, not known. The original ES cells used to make the mice was a mixture of 129P2/OlaHsd and mice were subsequently bred to C57BL/6. The official strain name (B6;129P2-Esr1tm2.1Gsc/J) accounts for this mixture, but no one has determined the relative contribution of each.