DNA Patterns for Nucleosome Positioning
from: Genome Analysis: Current Procedures and Applications (Edited by: Maria S. Poptsova). Caister Academic Press, U.K. (2014)
There is an abundant experimental evidence for the role of specific nucleosome positioning in gene regulation. The nucleosome positioning is determined by DNA sequence and non-sequence factors such as ATP dependent remodeling factors. The nucleosome positions differ between various cell types for the same species as well as for similar genes of the different species. A nucleosome shift by just a few base pairs can alter the entire regulation of a gene. Knowing precise nucleosome location is critical for understanding how cis-regulatory elements control genetic information. Among different factors affecting nucleosome positioning on the DNA, the DNA sequence itself is the most important, and various sequence motifs have been described as guiding nucleosome positioning in a sequence specific manner. These motifs or patterns eventually were termed nucleosome positioning sequence (NPS) patterns although this term is not necessarily universal. In this chapter, we describe various classes of such NPS patterns known from literature and possible biological implications thereof. This chapter does not embark to provide an exhaustive review of all related points of view, neither its emphasis is on new results presented here for the first time. Rather it reflects the author's point of view on general tendencies in this area of science and tries to provide a possible answer to the most difficult question in the area: why does nucleosome positioning differ between different tissues while respective DNA sequence of the involved genes is essentially identical?