Mechanisms of ATP dependent chromatin remodeling

Abstract

The inter-relationship between DNA repair and ATP dependent chromatin remodeling has begun to become very apparent with recent discoveries. ATP dependent remodeling complexes mobilize nucleosomes along DNA, promote the exchange of histones, or completely displace nucleosomes from DNA. These remodeling complexes are often categorized based on the domain organization of their catalytic subunit. The biochemical properties and structural information of several of these remodeling complexes are reviewed. The different models for how these complexes are able to mobilize nucleosomes and alter nucleosome structure are presented incorporating several recent findings. Finally the role of histone tails and their respective modifications in ATP-dependent remodeling are discussed.

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

“…7. From the parameters measured here for the isolated Snf2H ATPase and its complex with Acf1 (endogenous protein concentration 0.15-0.83 μM, average residence time 75-430 ms) we estimate that nucleosomes are sampled at a rate of 0.1-3 min −1 by a specific ISWItype complex.…”

Nucleosome Remodeling and Epigenetics

“…Snf2 family helicases commonly bind a double-stranded nucleic acid and move along one strand in a defined direction, thereby separating the two strands. Detailed mechanistic studies on a small number of selected enzymes revealed that nucleosome remodelers are also DNA translocases-that is, they move along one strand of nucleosomal DNA, yet without separating the two strands (Saha et al 2006;Gangaraju and Bartholomew 2007). Remodelers engage in other defined contacts with histones and linker DNA, at the same time, which position the ATPase domain at a strategic site within the nucleosomal DNA, 2 helical turns off the dyad axis.…”

“…Remodelers engage in other defined contacts with histones and linker DNA, at the same time, which position the ATPase domain at a strategic site within the nucleosomal DNA, 2 helical turns off the dyad axis. According to the prevailing model, this anchoring combined with the translocation of the ATPase domain on nucleosomal DNA, leads to the detachment of DNA segments from the histone octamer surface (Saha et al 2006;Gangaraju and Bartholomew 2007;Racki and Narlikar 2008;Flaus and OwenHughes 2011). Cycles of ATP binding, hydrolysis, and product release define a succession of conformation changes of the enzyme, which propel the movement of the enzyme on DNA.…”

Exploring Secrets of Nuclear Actin Involvement in the Regulation of Gene Transcription and Genome Organization

“…The histone-modifying enzymes post-translationally modify the N-terminal tails of histone proteins through acetylation, phosphorylation, ubiquitination, ADP-ribosylation and methylation (Sterner and Berger, 2000;Wang et al, 2007). On the other hand, ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to disrupt the DNAhistone contact, move nucleosomes along DNA, and remove or exchange nucleosomes (Gangaraju and Bartholomew, 2007). Actin and Arps were first identified as integral components of the BAF complex, a mammalian SWI/SNF-like chromatin remodelling complex, that is involved in T-lymphocyte activation (Zhao et al, 1998).…”