Transcription factor access to their sites in chromatin

Abstract

We have recently discovered a novel mechanism for exposing transcription factor binding sites in chromatin in the yeast S. cerevisiae (Floer, M. et al., 2010 Cell, 141, 407). The mechanism involves trapping of a nucleosome at a specific position and partial unwrapping of the nucleosomal DNA ends, which leads to the incorporation of a segment of DNA around 30 bp shorter than that associated with an ordinary nucleosome. At the UASg, the regulatory region in the GAL locus of yeast, such a structure is created by the so‐called nucleosome remodeler RSC, which recognizes specific sites in the UASg. Formation of the structure facilitates binding of the activator Gal4 and expression of the associated genes. Nucleosomes that are part of structures such as the one at the UASg have been missed in previous studies due to an assumed size of 147 bp for a DNA fragment associated with a nucleosome. But we find that many similar structures are found in the yeast genome, and are often associated with sites for transcription factor binding. This suggests that partial unwrapping of a nucleosome may be a common mechanism for exposing transcription factor binding sites in yeast. Using the methods we have developed we are now analyzing how transcription factors of higher eukaryotes access their sites in chromatin, taking the pro‐inflammatory genes of mouse macrophages as a paradigm for gene induction in response to environmental stimuli. The goal of these studies is to understand how chromatin contributes to lineage specific activation and repression of genes.