In Vitro DNase I Footprinting.

The association of proteins with the DNA double helix can interfere with the accessibility of the latter to nucleases. This is particularly true when using bulky nucleases such as DNase I. The DNase I footprinting method was developed to take advantage of this fact in the study of DNA-protein interactions: it consists in comparing the pattern of fragments generated by the partial digestion of a DNA sequence in the absence of a protein to that produced by its partial digestion in the presence of said protein. Normally, when the two sets of fragments are separated side by side on a gel, the ladder of DNase I-generated fragments produced in the presence of the protein will feature blank regions (devoid of fragments, indicating protection) and/or enhanced cleavage sites (indicating increased availability to the nuclease). This technique can furthermore reveal if multiple sites for a DNA-binding protein are present on a same fragment and in such a case will also allow the comparison of their respective affinities.

Analysis of DNA Supercoiling Induced by DNA-Protein Interactions.

Certain DNA-interacting proteins induce a pronounced bending in the double helix and cause topological stresses that are compensated by the formation of supercoils in DNA. Such supercoils, when forming on a circular plasmid, give rise to a series of topoisomers that run at different speeds during electrophoresis. The number of supercoils introduced in the plasmid can provide information on the protein; it can, for example, help determine the number of nucleosomes that are assembled on the plasmid or indicate whether the DNA-bending activity of a transcription factor is important enough to cause a topological stress. Because a DNA-protein activity can lead to either an overwinding or an underwinding of the helix, supercoiling can occur in either direction. Determining whether a plasmid contains positively or negatively supercoiled DNA is possible, thanks to an agarose gel containing an intercalating agent known to positively supercoil DNA, such as chloroquine. The speed of migration of the topoisomers varies in a characteristic way in the presence and absence of the agent. Topoisomer standards can furthermore be generated to allow the easy evaluation of the number of supercoils induced in a plasmid by a DNA-protein interaction.

Targeted histone acetylation at the yeast CUP1 promoter requires the transcriptional activator, the TATA boxes, and the putative histone acetylase encoded by SPT10.

The relationship between chromatin remodeling and histone acetylation at the yeast CUP1 gene was addressed. CUP1 encodes a metallothionein required for cell growth at high copper concentrations. Induction of CUP1 with copper resulted in targeted acetylation of both H3 and H4 at the CUP1 promoter. Nucleosomes containing upstream activating sequences and sequences farther upstream were the targets for H3 acetylation. Targeted acetylation of H3 and H4 required the transcriptional activator (Ace1p) and the TATA boxes, suggesting that targeted acetylation occurs when TATA-binding protein binds to the TATA box or at a later stage in initiation. We have shown previously that induction results in nucleosome repositioning over the entire CUP1 gene, which requires Ace1p but not the TATA boxes. Therefore, the movement of nucleosomes occurring on CUP1 induction is independent of targeted acetylation. Targeted acetylation of both H3 and H4 also required the product of the SPT10 gene, which encodes a putative histone acetylase implicated in regulation at core promoters. Disruption of SPT10 was lethal at high copper concentrations and correlated with slower induction and reduced maximum levels of CUP1 mRNA. These observations constitute evidence for a novel mechanism of chromatin activation at CUP1, with a major role for the TATA box.