Looped domains, chromatin

The chapter is organized as follows. Section II is devoted to materials and methods. In Section III, we show [34, 35] that the GC content displays rather regular nonlinear oscillations with two main periods of 110 20 kbp and 400 50 kbp, which are well-recognized characteristic scales of chromatin loops and loop domains involved in the hierarchical folding of chromatin fibers. 

C. Demeret, Y. Vassetzky, and M. Mechali, Chromatin remodelling and DNA replication From nucleosomes to loop domains. Oncogene 20, 3086-3093 (2001). 

Figure 27-5 (A, B) Two possible models of the 30-nm chromatin fiber.55 (A) Thoma et al.85 (B) Woodcock et al.6i 87 The fully compacted structure is seen at the top of each figure. The bottom parts of the figures illustrate proposed intermediate steps in the ionic strength-induced compaction. (C) Possible organization of the DNA within a metaphase chromosome. Six nucleosomes form each turn of a solenoid in the 30-nm filament as in (A). The 30-nm filament forms 30 kb-loop domains of DNA and some of these attach at the base to the nuclear matrix that contains topoisomerase II. About ten of the loops form a helical radial array of 250-nm diameter around the core of the chromosome. Further winding of this helix into a tight coil 700 nm in diameter, as at the top in (C), forms a metaphase chromatid. From Manuelidis91.

Fig. 1. Hierarchy of chromatin folding in the nucleus, during interphase, chromosomes are spread in a diffuse form and the nucleoli appear as dense structures. During metaphase chromosomes which consist of condensed sections of chromatin are formed. Chromatin in interphase nuclei and in the condensed sections of chromosomes contains looped domains which are formed by the 30 nm chromatin fibre. In vitro it is possible to further unfold the 30 nm fibre to a 3-D zig-zag structure revealing the nucleosomes that consist of histone HI, the core particle and the linker DNA...

In an undamaged cell poly(ADP-ribose) polymerase could be associated with chromatin and lamina. Indeed, Gradwohl et al. (20) have demonstrated that poly(ADP-ribose) polymerase can form looped structures in DNA in vitro. This observation suggests that the enzyme may be associated with DNA looped structures in chromatin in the absence of strand breaks (Fig. 4). Furthermore, the enzyme bound to the lamina may be associated with the base of chromatin looped domains in close contact with lamina (21). Upon DNA damage, the enzyme might redistribute according... 

U. K. Laemmli, E. Kas, L. Poljak, and Y. Adachi, Scaffold-associated regions Cis-acting determinants of chromatin structural loops and functional domains. Curr. Opirt Genet. Dev. 2, 275-285 (1992). 

---