The Interaction of NF-κB Transcription Factor with Centromeric Chromatin

Abstract

Centromeric chromatin is a subset of chromatin structure and governs chromosome segregation. The centromere is composed of both CENP-A nucleosomes (CENP-Anuc) and H3 nucleosomes (H3nuc) and is enriched with alpha-satellite (a-sat) DNA repeats. These CENP-Anuc have a different structure than H3nuc, decreasing the base pairs (bp) of wrapped DNA from 147 bp for H3nuc to 121 bp for CENP-Anuc. All these factors can contribute to centromere function. We investigated the interaction of H3nuc and CENP-Anuc with NF-kB, a crucial transcription factor in regulating immune response and inflammation. We utilized Atomic Force Microscopy (AFM) to characterize complexes of both types of nucleosomes with NF-kB. We found that NF-kB unravels H3nuc, removing more than 20 bp of DNA, and that NF-kB binds to the nucleosomal core. Similar results were obtained for the truncated variant of NF-kB comprised only of the Rel Homology domain and missing the transcription activation domain (TAD), suggesting the RelA TAD is not critical in unraveling H3nuc. By contrast, NF-kB did not bind to or unravel CENP-Anuc. These findings with different affinities for two types of nucleosomes to NF-kB may have implications for understanding the mechanisms of gene expression in bulk and centromere chromatin.