Histone-DNA contacts in structure/function relationships of nucleosomes as revealed by crosslinking.

We describe studies of histone-DNA contacts in the nucleosome using the method of covalent zero length protein-DNA crosslinking. These studies show that in intact nuclei isolated from different sources the linear sequential arrangement of histone-DNA contacts in the nucleosomal core is essentially the same. However, the relative strength of certain contacts varies and correlates with the level of chromatin activity and condensation. These altered contacts are located in the sharply bent regions of the nucleosomal DNA and are supposed to be sensitive to the structural changes that may occur during nucleosome functions. Studies of the mechanism of these alterations revealed that the difference in strength of these contacts is attributed to the different conformational state of the nucleosomal core and is caused by stretching of the nucleosomal DNA upon chromatin decondensation during its activation. Histone-terminal domains may be involved in this process through posttranslational modifications affecting chromatin condensation. The described localization of the histone H2A C-terminal domain in the nucleosome by crosslinking demonstrates the ability of this methodology to determine the location of histone-terminal domains and thereby elucidate their role in nucleosome function. Results of the described experiments suggest that chromatin decondensation may alter the nucleosomal DNA conformation and affect the histone-DNA contacts resulting in a structural transition that may play a role in rendering the nucleosome competent for transcription and/or replication.