Dissection of Chromosome Structure with Trypsin and Nucleases

Exhaustive digestion of chromatin with trypsin leads to the cleavage of only 20-30 amino acids from each of histones III (f3), IV (f2a1), IIb2 (f2b), and IIb1 (f2a1), the remainder of these chains being resistant. This resistance is not altered by removing the histones from the DNA with 2 M NaCl, but is dramatically reduced in 6 M urea. Histones III, IV, IIb2, and possibly IIb1 are cleaved at their N-termini. Histones I and V and the nonhistone proteins are the first to be attacked by trypsin and have no detectable trypsin-resistant fragments. The arginine rich histones, III and IV, are then cleaved as a pair, followed by most of IIb2 and IIb1, also as a pair. This data is consistent with a model in which basic N-terminal "arms" extend from a trypsin-resistant histone complex. The structural arrangement of these arms relative to the trypsin-resistant histone complex may define the spatial coordinates of DNA binding sites and, consequently, the folding of the DNA fiber in the chromosome. Accompanying the tryptic digestion of the N-terminals of histones III, IV, IIb2, and possibly IIb1, is an increased sensitivity of chromatin to staphylococcal nuclease. As analyzed by electrophoresis, untrypsinized chromatin is digested into eight discrete limit-digest fragments by nuclease. Trypsinization results in the nuclease digestion of some, but not all, of these DNA bands. Together with the information on the way trypsin cleaves histones in chromatin, the analysis of the resistant DNA suggests that histone N-terminals are associated with some DNA bands and histone C-terminals with other DNA bands. We propose that histones fold the chromosome by crosslinking the DNA corresponding to these bands.