Chapter 3 - Manipulating Chromatin Structure to Study the Interaction of Transcription Factors with Nucleosomes In Vitro and In Vivo

Abstract

The packaging of DNA into nucleosomes in eukaryotic cells raises the question of how proteins, such as transcription factors, gain access to their sites in chromatin. A central difficulty is obtaining templates that are homogeneous with respect to having a transcription factor-binding site within a nucleosome; this dilemma has been resolved by manipulating chromatin structure, either by removing templates having non-nucleosomal sites or by using nucleosome-positioning signals to make “designer chromatin.” Experimental results are presented, which indicate a hierarchy with respect to transcription factors and chromatin. Parameters, which may govern whether a transacting factor will be occluded from its site by histones or will successfully compete against the histones for its binding site, include the strength and stability with which a factor binds to its site, and the type of DNA-binding domain which it uses.