Partners in Long Distance Interactions

The genome of higher eukaryotes consists of DNA, which in case of the human genome measures 2m in length and is divided over 46 chromosomes. These long DNA molecules are packed in a nucleus that measures about 10μm in diameter. In order to fit the complete DNA into such a small volume, DNA is folded and compacted by proteins in a structure called chromatin. During mitosis, is even further compacted into condensed chromosomes (Kornberg, 1974). All the information needed for the formation and proper function of an organism is stored in these structures and it is reasonable to expect that this overcrowded situation is organized in a very specific manner, with controlled three-dimensional contacts within the nucleus. The need for controlled chromatin contacts is also suggested by the fact that gene regulation is a tightly regulated process. Different levels of control must be involved in regulating proper spatio-temporal expression of genes throughout the process of cellular differentiation. These processes are coordinated by interactions of an “army” of general, cell-type and stage specific proteins that bind to chromatin and DNA. Several techniques allow the identification and study of chromatin regions that interact with each other. These include functional genetic analysis, microscopic analysis after DNA or RNA fluorescent in situ hybridization (FISH) in combination with 3D microscopy, as well as biochemical methods, such as chromosome conformation capture (3C) and the more sophisticated variation thereof (4C). The combination of these methods reveals a network of contacts in the nucleus. These interactions are mediated by insulators and other regulatory sequences, including enhancers and promoters, which mediate/promote certain functional three-dimensional interactions while preventing other enhancer-promoter contacts. In this chapter, I will introduce several factors: Ldb1, Delangin, Cohesin and CTCF which have important role long-range interactions.