Chromatin remodeling mechanisms

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. 

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... 

MECHANICS OF NUCLEOSOME REMODELLING BY ATP-DEPENDENT CHROMATIN REMODELLING FACTORS... 

Eisen JA, Sweder KS, Hanawalt PC (1995) Evolution of the SNF2 family of proteins subfamilies with distinct sequences and functions. Nucleic Acids Res 23 2715-2723 Falbo KB, Shen X (2006) Chromatin remodeling in DNA replication. J Cell Biochem 97 684-689 Fazzio TG, Gelbart ME, Tsukiyama T (2005) Two distinct mechanisms of chromatin interaction by the Isw2 chromatin remodeling complex in vivo. Mol Cell Biol 25 9165-9174... 

Kumar A, Choi KH, Renthal W, Tsankova NM, Theobald DE, Truong HT, Russo SJ, Laplant Q, Sasaki TS, Whistler KN, Neve RL, Self DW, Nestler EJ (2005) Chromatin remodeling is a key mechanism underlying cocaine-induced plasticity in striatum. Neuron 48 303-314... 

Knowledge of the detailed mechanism underlying circadian rhythms continues to be refined as new experiments reveal novel facets of the oscillatory machinery. Thus, a link has recently been established between chromatin structure and the circadian oscillatory mechanism. The CLOCK protein indeed functions as a histone acetyltransferase [116]. This enzyme activity is required for oscillations so that histone modification and the associated chromatin remodeling are implicated in the origin of circadian rhythmicity. 

Enzymatically active PARP molecules have also been found involved in transcription in undamaged cells. Recent research on Drosophila has demonstrated that active puff loci are rich in PARPl and ADPR polymers, this being the necessary condition to induce chromatin decondensation and gene expression [159]. Mechanism of PARPl-mediated puffing and chromatin remodeling reinforces the idea previously suggested by Althaus to explain the role played by PARPl in DNA repair [160]. 

Whitehouse, I., Flaus, A., Havas, K., and Owen-Hughes, T. (2000) Mechanisms for ATP-dependent chromatin remodeling. Biochem. Soc. Trans. 28, 376-379. 

Wang, W. (2003) The SWI/SNF family of ATP-dependent chromatin remodelers similar mechanisms for diverse functions. Curr. Top. Microbiol. Immunol. 274, 143-169. 

Wallberg, A.E., Neely, K.E., Hassan, A.H., Gustafsson, J.A., Workman, J.L., and Wright, A.P. (2000) Recruitment of the SWI-SNF chromatin remodeling complex as a mechanism of gene activation by the glucocorticoid receptor taul activation domain. Mol. Cell. Biol. 20, 2004-2013. 

The detailed mechanisms for transcription-associated structural changes in chromatin, called chromatin remodeling, are now coming to light, including identification of a variety of enzymes directly implicated in the process. These include enzymes that covalently modify the core histones of the nucleosome and others that use the chemical energy of ATP to remodel nucleosomes on the DNA (Table 28-2). 

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