Chapter 4 - Mechanisms and Consequences of Transcription Factor Binding to Nucleosomes

Abstract

Biochemical analysis of the proteins involved in transcription by RNA polymerase II has revealed two classes of transcription factors. These include the general initiation factors, which are required in addition to RNA polymerase II for accurate initiation, and regulatory factors, which bind upstream promoter and/or enhancer elements and activate transcription initiation. Biochemical studies of the interactions of regulatory transcription factors with nucleosome cores have illustrated several parameters that restrict the binding of individual transcription factors to nucleosomal DNA. These include a differential intrinsic affinity of different factors for their recognition sites on nucleosomes, the location of the binding sites within the nucleosome core, and inhibition from the core histone amino termini. However, nucleosome-mediated repression of factor binding can be overcome by the facilitated binding of multiple factors, relief of inhibition from the core histone amino termini (that is, by histone acetylation), and through the function of accessory proteins that stimulate factor binding. The binding of regulatory factors to nucleosomes results in the formation of factor/nucleosome ternary complexes that contain bound factors, core histones, and DNA.