Circular dichroism and thermal denaturation studies of subnucleosomes and their relationships to nucleosome structure.

Abstract

Chicken erythrocyte chromatin moderately digested with micrococcal nuclease yields several species of nucleosomes and subnucleosomes that are resolved by electrophoresis in the presence of 3 M urea. This report compares the circulr dichroism spectra, thermal denaturation, and certain other properties of chromatosomes (trimmed nucleosomes cores, and four subnucleosomes. One subnucleosome is a partial core lacking an H2a-H2b pair and 40-50 DNA base pairs(bp) from one end. The stoichiometries of the other subnucleosomes, which contain homotypic histones associated with short DNA fragments, are (H3)(H4)/70-80 bp, (H1)/60-70 bp, and (H2a)(H2b)/50-60 bp. The latter subnucleosomes originate from the ends of nucleosome cores. All properties of partial and whole nucleosome cores were nearly identical, indicating that the terminal H2a-H2b pairs do not make binding contacts with the residual core DNA or histones that are critical to the conformation of the remaining core structure. Analyses of histone contributions of the far-UV circular dichroism of subnucleosomes showed that H2a-H2b pairs and H3-H4 pairs in nucleosomes are both nearly 50% ..cap alpha.. helical and that their helix contents do not depend on the nucleosome integrity. These and other results suggest that homotypic histone pairs and the DNA they tightly bind define quasi-independent conformational subdomains within nucleosomes. H3-H4more » pairs stabilized and reduced the 275-nm circular dichroism intensity of short DNA fragments much more effectively than H2a-H2b pairs. In addition, H3-H4 pairs stabilized considerably more DNA than predicted for simple electrostatic interactions. H1 also thermally stabilized less effectively than H3-H4 pairs, and modestly increased the 275-nm CD intensity relative to protein-free DNA.« less