Mapping of linear histone regions exposed at the surface of the nucleosome in solution

Abstract

Antibodies directed against defined regions of histone molecules represent one of the most specific probes for studying the topography and conformational changes of nucleosomes and chromatin. We have developed an assay involving a series of monoclonal and polyclonal antibody probes specifically reacting with a complete set of 40 overlapping synthetic peptides (6 to 28 residues long) covering the whole sequence of the four core histones H2A, H2B, H3 and H4. In this assay, mono-, di- and trinucleosomes, as well as a long chain of chromatin containing 20 to 35 nucleosomes, were used in solution as competitors of the antibody reaction. At least 11 surface-oriented linear regions were characterized on the mononucleosome; namely, the N-terminal domains of H2A (residues 1 to 20), H2B (residues 1 to 25) and H3 (residues 1 to 30), the C-terminal domains of H2A (residues 116 to 129) and H4 (residues 85 to 102), and six domains located in internal segments in the primary structures of core histones (33 to 49 H2A, 65 to 85 H2A, 60 to 78 H2B, 50 to 70 H3, 111 to 130 H3 and 42 to 59 H4). Only a few changes in the nucleosome topography were observed when free oligo- and polynucleosome structure were comparatively studied.