Pluto Bioinformatics

GSE116284 (mouse): NF-B p65 dimerization and DNA-binding is important for inflammatory gene expression

Bulk RNA sequencing

Increasing evidence shows that many transcription factors execute important biologic functions independent from their DNA-binding capacity. The NF-B p65 (RELA) subunit is a central regulator of innate immunity. Here, we investigated the relative functional contribution of p65 DNA-binding and dimerization in p65-deficient human and murine cells reconstituted with single amino acid mutants preventing either DNA-binding (p65 E/I) or dimerization (p65 FL/DD). DNA-binding of p65 was required for RelB-dependent stabilization of the NF-B p100 protein. The antiapoptotic function of p65 and expression of the majority of TNF-induced genes were dependent on p65s ability to bind DNA and to dimerize. Chromatin immunoprecipitation with massively parallel DNA sequencing experiments revealed that impaired DNA-binding and dimerization strongly diminish the chromatin association of p65. However, there were also p65-independent TNF-inducible genes and a subgroup of p65 binding sites still allowed some residual chromatin association of the mutants. These sites were enriched in activator protein 1 (AP-1) binding motifs and showed increased chromatin accessibility and basal transcription. This suggests a mechanism of assisted p65 chromatin association that can be in part facilitated by chromatin priming and cooperativity with other transcription factors such as AP-1. SOURCE: Robert Liefke (robert.liefke@imt.uni-marburg.de) - Philipps University of Marburg