Domains chromatin

The native form of chromatin in cells assumes a higher order stmcture called the 30-nm filament, which adopts a solenoidal stmcture where the 10-nm filament is arranged in a left-handed cod (Fig. 5). The negative supercoiling of the DNA is manifested by writhing the hehcal axis around the nucleosomes. Chromatin stmcture is an example of toroidal winding whereas eukaryotic chromosomes are linear, the chromatin stmctures, attached to a nuclear matrix, define separate closed-circular topological domains. 

The multiple sites that serve as origins for DNA replication in eukaryotes are poorly defined except in a few animal viruses and in yeast. However, it is clear that initiation is regulated both spatially and temporaUy, since clusters of adjacent sites initiate rephcation synchronously. There are suggestions that functional domains of chromatin replicate as intact units, implying that the origins of rephcation are specificaUy located with respect to transcription units. 

Chromatin remodeling, transcription factor modification by various enzyme activities, and the communication between the nuclear receptors and the basal transcription apparatus are accomplished by protein-protein interactions with one or more of a class of coregulator molecules. The number of these coregulator molecules now exceeds 100, not counting species variations and splice variants. The first of these to be described was the CREB-binding protein, CBP. CBP, through an amino terminal domain, binds to phosphorylated serine 137 of CREB and mediates transactivation in response to cAMP. It thus is described as a coactivator. CBP and... 

High mobility group (HMG) proteins are a family of small nonhistone chromatin-associated proteins which recognize structural distortions in DNA (11, 74, 75). Several NMR structures of HMG domains have been determined (76-78). High mobility group 1 (HMG1) box A... 

CHROMO Chromatin organization modifier domain E(MFP) 4(5) 23(29) 1AP0... 

However, the packing of DNA into nucleosome-like structures is not unique to eukarya similar structures appear in archaea (reviewed in Reeve et al., 1997). Additionally, histones and minichromosome maintenance proteins (MCM) are widespread among eukarya and archaea and absent in prokarya, and the eukaryotic chromo domain has a structure that is highly reminiscent of archaeal histones that are involved in formation of archaeal chromatin (Ball et al., 1997). Consequently, it is possible that chromatin remodeling in eukaryotes is an elaboration of a similar cellular mechanism in archaea. 

Linker histones (HI, H5 and others) are also major components of metaphase chromosome, and occupy 5.8% of the total protein amount (Uchiyama et al, 2005). They play an important role in the formation of the 30 nm fiber (see also section 2.3). These linker histones carry more lysine residues ( 30% of the total amino acids) than the core histones and have a core domain in the middle part that binds to a nucleosome. The linker histones could be easily extracted from the chromatin with 0.5 M NaCl, whereas the core histone octamers need more than 0.8 M NaCl to dissociate from nucleosomes. 

Thoma F, Roller T (1977) Influence of histone HI on chromatin structure. Cell 12 101-107 Thoma F, Roller T, Klug A (1979) Involvement of histone HI in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol 83 403 27 Turner BM, Birley AJ, Lavender J (1992) Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell 69 375-384... 

Udvardy A, Maine E, Schedl P (1985) The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains. J Mol Biol 185 341-358... 

Helicases catalyze the processive separation of duplex DNA into single strands. Despite sharing similarity to helicases, none of the chromatin remodelling factors, with the exception of the INO80 complex, have been shown to catalyze the separation of DNA strands (Shen et al, 2000). Instead, they can translocate on double-stranded (ds) DNA in an ATP-hydrolysis dependent manner and are characterized by their ability to generate superhelical torsional strain in DNA (Havas et al, 2000 Saha et al, 2002 Whitehouse et al, 2003). The crystal structure of Rad54, a member of the SWI/SNF family has been solved for both S. solfataricus and zebrafish which helps to understand the mechanism of the SWI/SNF ATPase domain in remodelling processes (Durr et al, 2005 Thoma et al, 2005). It reveals... 

Thoma NH, Czyzewski BK, Alexeev AA, Mazin AV, Kowalczykowski SC, Pavletich NP (2005) Structure of the SW12/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat Struct Mol Biol 12 350-356... 

Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y (2006) Histone demethylation by a family of JmjC domain-containing proteins. Nature 439 811-816 van Holde K, Yager T (2003) Models for chromatin remodeling a critical comparison. Biochem Cell Biol 81 169-172... 

---