Nucleosome positioning and gene regulation

Abstract

Recent genetic and biochemical studies have revealed critical information concerning the role of nucleosomes in eukaryotic gene regulation. Nucleosomes package DNA into a dynamic chromatin structure, and by assuming defined positions in chromatin, influence gene regulation. Nucleosomes can serve as repressors, presumably by blocking access to regulatory elements; consequently, the positions of nucleosomes relative to the location of cis-acting elements are critical. Some genes have a chromatin structure that is "preset," ready for activation, while others require "remodeling" for activation. Nucleosome positioning may be determined by multiple factors, including histone-DNA interactions, boundaries defined by DNA structure or protein binding, and higher-order chromatin Structure.

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

“…Recently, these studies have been extended genomewide through the analysis of populations of nucleosomes using high-density microarrays (for the yeast Sacchromyces cerevisiae) (Yuan et al 2005) and using the Chromatin Array technique (for human cell lines) (Weil et al 2004). These studies have shed considerable light on DNA sequence and other factors influencing nucleosome occupancy; certainly the results serve as a strong argument for pursuing a genome-wide analysis of nucleosome positioning and dynamics at an increasingly detailed level (Satchwell et al 1986;Dong et al 1990;Lu et al 1994;Travers and Muyldermans 1996;Flaus and Richmond 1998;Crawford et al 2006).…”

“…In some formalisms, two types of interdependent DNA features that determine nucleosome positioning have been described: "translational signal" and "rotational setting." A translational signal determines placement of, and a rotational setting determines orientation of DNA in relation to the histone octamer (Lu et al 1994). Numerous studies of nucleosomal positioning have been carried out for individual genomic regions, indicating that positioning can be both flexible and constrained (e.g., Lu et al 1994;Kornberg and Lorch 1999;Sekinger et al 2005).…”

“…A translational signal determines placement of, and a rotational setting determines orientation of DNA in relation to the histone octamer (Lu et al 1994). Numerous studies of nucleosomal positioning have been carried out for individual genomic regions, indicating that positioning can be both flexible and constrained (e.g., Lu et al 1994;Kornberg and Lorch 1999;Sekinger et al 2005). Recently, these studies have been extended genomewide through the analysis of populations of nucleosomes using high-density microarrays (for the yeast Sacchromyces cerevisiae) (Yuan et al 2005) and using the Chromatin Array technique (for human cell lines) (Weil et al 2004).…”

The Zinc Finger Repressor, ZBP-89, Binds to the Silencer Element of the Human Vimentin Gene and Complexes with the Transcriptional Activator, Sp1

“…More recently, mechanisms that repress gene activity have come under scrutiny, and it is now apparent that there are several different ways to silence gene activity (19 -22). One level of gene repression is achieved by the highly organized and condensed structure of chromatin itself (21,23).…”

“…In this case, the unraveling of chromatin by acetylation or methylation has been shown to affect transcription, and it has been proven that some repressors work by stimulating such processes as histone deacetylation (23,24). An example of a second class of repressors is Dr1 (25).…”