Chapter 2 - Higher-order chromatin structure and gene regulation

Abstract

It is estimated that the human body consists of several hundreds of cell types, which are nevertheless specified with a single genome. To understand how such a variety of cells is created from a common set of genes is one of the most fundamental problems in modern biology. In each type of cells, a certain subset of genes are expressed and this cell type-specific expression of genes is likely to be regulated mostly by enhancers/cis-regulatory regions, which exist in the noncoding regions of the genome at great many places. Since enhancers stimulate the expression of their target genes through so-called enhancer-promoter interactions caused by DNA looping, the combinatorial pattern of these interactions would be changed between different cell types with the changes of higher-order chromatin structures. In this article, we would like to briefly review how this notion has been explored. In its first half, we briefly overview what is known about the (higher-order) chromatin structure, while in the latter half, what is known about enhancers is reviewed, emphasizing their relationship with cell type-specific regulation and chromatin structure. In most cases, we only cited recent review articles for the description of general topics and added reports on recent findings, where available.