Chromatin Remodeling Enzymes

The ability to remodel nucleosomes is vital for accurate and regulated transcription and efficient DNA replication. Nucleosome remodeling is defined as an enzymatic activity capable of altering the position or stability of the nucleosome. The flagship of the ATP-dependent, enzyme complexes that remodel chromatin is the SWI/SNF complex. The SWI/SNF class of chromatin remodeling complexes is named for the genetic screens used to identify sucrose non-fermenting (Snf) or mating-type switching defective (Swi) mutants. The SWI/SNF chromatin remodeling complexes contain an enzymatic ATPase protein subunit, which on its own is capable of remodeling chromatin in vitro (Cote et al., 1994). In yeast this protein is called Snf2/Swi2 and in humans there are two homologous proteins: Brgl and Brm. Each of these proteins contains a structural motif called a bromodomain, which binds to acetylated lysines. Acetylation of histones by HATs promotes recruitment of SWI/SNF remodeling complexes through bromodomain interaction and stabilizes template binding by SWI/SNF (Hassan et al., 2002). Chromatin remodeling by the stabilized SWI/SNF complex can then facilitate binding of additional factors required for activation.

The second class of chromatin remodeling enzymes is defined by the presence of the ATPase protein ISWI. This protein was discovered due to its homology to SWI/SNF and named imitation switch (ISWI). The ISWI protein subunit is present in at least three different complexes in Drosophila (Tsukiyama and Wu, 1995). Each was purified biochemically, based on the complex's ability to promote restriction enzyme accessibility of a mononucleosomal template. NURF (nucleosome remodeling factor) contains four proteins, which disrupt nucleosomes at specific sites in the genome, whereas another complex CHRAC (chromatin-accessibility complex), appears to affect chromatin condensation globally (Badenhorst et al., 2002; Fyodorov et al., 2004; Varga-Weisz et al., 1997). In addition to remodeling activity, the third complex, ACF (ATP-utilizing chromatin assembly and remodeling factor), functions in nucleosome assembly and spacing and is used for assembly of chromatin in vitro (Fyodorov and Kadonaga, 2002). Two other classes of chromatin remodelers are the CHD class, including mammalian Mi-2, which interacts with both HDACs and methylated DNA binding proteins, and the INO-8O class, which has been implicated in DNA repair (Saito and Ishikawa, 2002; van Attikum et al., 2004).

The mechanisms by which these protein complexes remodel chromatin are under intense investigation. Unlike "passive" nucleosome dynamics, all of these enzymes utilize the energy of ATP to catalyze a reaction with energy-of-activation barriers and transition states. Defining the transition states has been pursued through biochemical assays that demonstrate exposure of buried DNA due to movement of the nucleosome. Comparison of the ATPase subunits from both SWI/SNF complexes and ISWI complexes highlight some of the differences in the mechanisms of each remodeler. For instance, histone tails are not required for SWI/SNF to remodel but are required for ISWI activity (Guyon et al., 1999). Also, unlike ISWI, SWI/SNF is capable of exposing restriction enzyme sites within a nucleosome even when there is no neighboring DNA onto which the nucleosome could move (Aalfs et al., 2001). This may indicate that SWI/SNF operates either by disassembling the nucleosome and repositioning it elsewhere or by exposing portions of the DNA opposite to the DNA entry/exit site (Fig.5.2). Additional evidence for a chromatin remodeling mechanism other than sliding comes from experiments demonstrating exposure of DNA in the center of a tightly packed polynucleosome template. If sliding were the only remodeling mechanism then tightly packed nucleosomes could not be removed. Indeed, Brgl, the human SWI/SNF ATPase, generates DNA loops without sliding away the histone octamer (Fan et al., 2003).

Functionally, SWI/SNF and ISWI-containing complexes regulate different sets of genes and are involved in many other processes (Fyodorov and Kadonaga, 2001). Efficient incorporation of nucleosomes onto newly replicated DNA can be mediated by the SWI/SNF complex member, Inil, and the ISWI-containing complex, CHRAC/ACF (Alexiadis et al., 1998); both chromatin remodelers stimulate initiation of viral DNA replication in vitro (Lee et al., 1999). DNA repair proteins also require access to the DNA template, and the chromatin remodeler IN080 is recruited to phosphorylated histone H2A.X found at double strand break sites (Morrison et al., 2004; van Attikum et al., 2004). The human SWI/SNF complex ATPase, Brgl, has also been implicated as a tumor suppressor with a role in cell cycle control. Cyclin E/cdk2 phosphorylates the protein during the Gi-phase of the cell cycle and Rb requires SWI/SNF to induce cell cycle arrest (Zhang et al., 2000). Additionally, mutations in the SWI/SNF complex member Inil are found in many rhabdoid tumors and some chronic myeloid leukemia (Versteege etal., 1998).

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