A novel nucleosome assembly procedure (with a little help from pectin)

Compaction kinetics on single DNAs: purified nucleosome reconstitution systems versus crude extract

Kinetics of compaction on single DNA molecules are studied by fluorescence videomicroscopy in the presence of 1), Xenopus egg extracts and 2), purified nucleosome reconstitution systems using a combination of histones with either the histone chaperone Nucleosome Assembly Protein (NAP-1) or negatively charged macromolecules such as polyglutamic acid and RNA. The comparison shows that the compaction rates can differ by a factor of up to 1000 for the same amount of histones, depending on the system used and on the presence of histone tails, which can be subjected to post-translational modifications. Reactions with purified reconstitution systems follow a slow and sequential mechanism, compatible with the deposition of one (H3-H4)(2) tetramer followed by two (H2A-H2B) dimers. Addition of the histone chaperone NAP-1 increases both the rate of the reaction and the packing ratio of the final product. These stimulatory effects cannot be obtained with polyglutamic acid or RNA, suggesting that yNAP-1 impact on the reaction cannot simply be explained in terms of charge screening. Faster compaction kinetics and higher packing ratios are reproducibly reached with extracts, indicating a role of additional components present in this system. Data are discussed and models proposed to account for the kinetics obtained in our single-molecule assay.

Assembly, remodeling, and histone binding capabilities of yeast nucleosome assembly protein 1

Recombinant yeast nucleosome assembly protein (yNAP-1) facilitates the formation of uniformly spaced nucleosomes from high molecular weight DNA and core histone octamers. No additional factors or metabolites are required. The repeat length of the chromatin produced is about 146 base pairs. To obtain the most distinct nucleosomal ladders, the core histones must preexist as an octamer complex. yNAP-1 forms complexes with core histones as judged by native gel electrophoresis, chemical cross-linking, limited histone proteolysis, and affinity blotting. A discrete complex was observed with a probable ratio of yNAP-1 to histone octamer of 4:1. Chromatin produced by salt dialysis does not contain uniformly spaced nucleosomes, but subsequent incubation with yNAP-1 creates uniform spacing. Trypsin-treated core octamers that lack amino termini, although capable of forming core particles with core-length DNA by salt dialysis, are not assembled by yNAP-1 into uniformly spaced nucleosomes on high molecular weight DNA. Proteolytic removal of the amino termini of the core histones precludes complex formation between a histone octamer and yNAP-1. Affinity blotting also demonstrates that yNAP-1 binds linker histones and high mobility group (HMG)-1/HMG-2 but not HMG-14. Competition experiments with poly-L-arginine, poly-L-lysine, and protamine reveal that yNAP-1 binds to core and linker histones more tightly despite the much higher positive charge densities of the former molecules. Naturally occurring acetylated histone H4 species show no evidence for differential yNAP-1 binding. yNAP-1 is not bound tightly to the resulting chromatin after deposition and thus could act catalytically.

Human TFIIIA alone is sufficient to prevent nucleosomal repression of a homologous 5S gene

Plasmid DNA harbouring the human 5S rRNA gene was assembled into nucleosomes using either Xenopus S150 extracts or purified core histones in the presence of pectin. In both cases reconstitution of nucleosomes led to a complete repression of transcription. This repression could be efficiently counteracted by preincubating the template DNA with highly purified hTFIIIA which allowed the protein to bind to the ICR of the 5S gene. By using an efficient and well-defined in vitro reconstitution system based on isolated core histones in the presence of pectin, which is devoid of endogenous transcription factors, we demonstrate here for the first time that human TFIIIA alone is sufficient to prevent nucleosomal repression of h5S gene transcription and that additional pol III transcription factors are not required to achieve this effect. Additionally, we investigated the binding of hTFIIIA to a mononucleosome reconstituted on the human 5S gene. DNAse I footprinting experiments reveal that the entire ICR of the human 5S gene is covered by the nucleosome, thereby precluding the subsequent binding of human TFIIIA to the promoter of the 5S gene.