Roles of the Histone H2A-H2B Dimers and the (H3-H4)2Tetramer in Nucleosome Remodeling by the SWI-SNF Complex

Abstract

SWI-SNF is an ATP-dependent chromatin remodeling complex required for expression of a number of yeast genes. Previous studies have suggested that SWI-SNF action may remove or rearrange the histone H2A-H2B dimers or induce a novel alteration in the histone octamer. Here, we have directly tested these and other models by quantifying the remodeling activity of SWI-SNF on arrays of (H3-H4) 2 tetramers, on nucleosomal arrays reconstituted with disulfide-linked histone H3, and on arrays reconstituted with histone H3 derivatives sitespecifically modified at residue 110 with the fluorescent probe acetylethylenediamine-(1,5)-naphthol sulfonate. We find that SWI-SNF can remodel (H3-H4) 2 tetramers, although tetramers are poor substrates for SWI-SNF remodeling compared with nucleosomal arrays. SWI-SNF can also remodel nucleosomal arrays that harbor disulfide-linked (H3-H4) 2 tetramers, indicating that SWI-SNF action does not involve an obligatory disruption of the tetramer. Finally, we find that although the fluorescence emission intensity of acetylethylenediamine-(1,5)-naphthol sulfonate-modified histone H3 is sensitive to octamer structure, SWI-SNF action does not alter fluorescence emission intensity. These data suggest that perturbation of the histone octamer is not a requirement or a consequence of ATP-dependent nucleosome remodeling by SWI-SNF.The assembly of eukaryotic DNA into folded nucleosomal arrays has drastic consequences for many nuclear processes that require access to the DNA sequence, including RNA transcription, DNA replication, recombination, and repair. The nucleosome, which consists of 147 bp 1 of DNA wrapped nearly twice around an octamer of histones H2A, H2B, H3, and H4, can occlude DNA sequences both in vivo and in vitro. The nucleosome is not a static structure but appears to be a dynamic and flexible assembly. For instance, moderate concentrations of NaCl can lead to several distinct changes in nucleosome conformation (1-4). In addition, nucleosomes isolated from transcriptionally active chromatin appear to be depleted of histone H2A-H2B dimers (discussed in Ref. 5) and contain histone octamers the interiors of which are more accessible to enzymatic and chemical modifications (6 -8). Nucleosomes from transcriptionally active chromatin can also be visualized microscopically as extended, largely unfolded structures (9, 10). These and other studies have led to the view that regulatory factors might antagonize the repressive effects of chromatin by disrupting the structure or conformation of the histone octamer (discussed in Ref. 11).Two types of highly conserved chromatin remodeling enzymes have been implicated as regulators of the repressive nature of chromatin structure (12, 13). Several members of the SWI2/SNF2 family of DNA-stimulated ATPases use the energy of ATP hydrolysis to disrupt nucleosome structure, which can lead to an enhanced mobility of nucleosomes (14 -16, 64). The second type consists of the nuclear histone acetyltransferases that covalently modify lysine residues within the flexibl...

Nuclear Factor 1 Synergizes with Progesterone Receptor on the Mouse Mammary Tumor Virus Promoter Wrapped around a Histone H3/H4 Tetramer by Facilitating Access to the Central Hormone-responsive Elements

“…Therefore, it seems that SWI/SNF promotes ATP-dependent remodeling of octamer particles into tetramers but does not use tetramer particles as substrate. The idea that histones H2A and H2B are necessary for SWI/SNFmediated remodeling is consistent with a previous report showing that arrays of histone tetramers are poor substrate for SWI/ SNF remodeling (38). Consistent with this idea, the acidic N terminus of the Swi3p subunit of yeast SWI/SNF was identified as a novel H2A-H2B-binding domain required for ATPdependent H2A/H2B dimer displacement (39).…”

The INO80 ATP-Dependent Chromatin Remodeling Complex Is a Nucleosome Spacing Factor

“…The presence of the H2A-H2B dimer is required for INO80 remodeling. Yeast SWI/SNF has been shown to mobilize an array of H3-H4 tetrasomes, although they are poorer remodeling substrates than nucleosomal arrays (5). The presence of H2A-H2B dimer within the nucleosome was found to be required for INO80 remodeling, but not for binding using tetrasomes assembled on the 601 positioning sequence with 70 bp of extranucleosomal DNA.…”

hSWI/SNF-Catalyzed Nucleosome Sliding Does Not Occur Solely via a Twist-Diffusion Mechanism

“…Nucleosomes were assembled onto the 215-bp Xenopus 5S DNA fragment by a salt-dialysis procedure. Chemical and nuclease mapping experiments have shown that ϳ80% of the nucleosomes are positioned near the 5Ј end of this fragment after reconstitution (4,22,34) (Fig. 1A).…”

“…However, the mechanism by which SWI/SNF chromatin remodeling complexes utilize the energy of ATP hydrolysis to perturb histone-DNA interactions is not well defined (6,7,14,19,24). Remodeling occurs without large changes in either the conformation or the configuration of the core histone octamer (2,4). However, electron energy loss microscopy and atomic force microscopy of remodeled nucleosome arrays indicate that approximately 40 bp of DNA-histone contacts are destabilized at either edge in a remodeled nucleosome (2,31).…”