Deletion of the histone H4 N-terminal residues 4-23 decreases activation of the GAL1 promoter as much as 20-fold, while deletion of histone H3 N-terminal residues 4-15 hyperactivates GAL1 approximately 3-fold. In an attempt to understand the mechanisms by which these two different events take place, we have examined the effects of the H4 and H3 lesions on GAL1 chromatin structure. The bacterial dam methylase, which methylates adenine residues of GATC sequences, was used as an in vivo probe for chromatin structure and both indirect end-labeling and ligation mediated PCR (LMPCR) analysis of micrococcal nuclease digestions were used to analyze chromatin in isolated nuclei. We show that while deletions of the H4 and H3 N-termini have similar effects on dam methylase access in the GAL1 coding region, the H4 N-terminal deletion uniquely alters dam access at a region near the TATA element. This change is independent of the transcriptional state of GAL1. In addition, LMPCR analysis of micrococcal nuclease digests of yeast nuclei demonstrate that H4 N-terminal deletion has unique effects on nuclease accessibility in the nucleosomal region upstream of the TATA element. Our results are consistent with the H4 N-terminus mediating activation of GAL1 through its effect on the proximal promoter region near the TATA box. These data also suggest that the H3 N-terminus affects GAL1 hyperactivation through a different promoter element than that affected by H4.