The Dynamic Nucleosome: Multiple Aspects of Positioning the +1 Nucleosome

Abstract

Genome wide nucleosome positioning maps revealed the presence of global nucleosome patterns, where nucleosomes seem to be uniformly spaced at the 5’ and 3’ ends of genes. Yet, nucleosomes are highly dynamic, as they transiently dissociate histones, wrap and unwrap themselves in a process called nucleosome breathing or move up and down on the DNA. The +1 nucleosome is the first nucleosome downstream from the nucleosome free region. Many believe that understanding the factors that position the +1 nucleosome is the key to understanding transcriptional control by nucleosome positioning. The proposal is an attempt to identify the factors that regulate the positioning of the +1 nucleosome. We present two main projects: 1. Identify the combinatorial effect of ATP dependent chromatin remodelers in the positioning of the +1 nucleosome 2. Delineate the mechanisms that link the stability of the +1 nucleosome to its positioning. ATP dependent chromatin remodelers are known to treat the +1 nucleosome differently from the other histones. The first project will identify the role of individual ATP dependent chromatin remodelers in the precise positioning of the +1 nucleosome. To this end, we propose a ChIP-exo-MS/MS method that would allow us to combine mass spectrometry based proteomics, while following a single nucleosome position over time. The second project will allow integration of these results into a model that seeks to identify factors that link the stability of the +1 nucleosome and its positioning.