Chromatin structure interferes with excision of abnormal bases from DNA.

Cell-free extracts of human lymphoblastoid cells NL3 excised almost all uracil residues from free DNA with misincorporated dUMP, but only about half the uracil residues from nuclei, chromatin and reconstituted chromatin with dUMP-misincorporated DNA. This difference in susceptibility to uracil-DNA glycosylase of free and complexed DNAs was similar to the difference in susceptibility of free and complexed methylated DNAs to 3-methyladenine-DNA glycosylase. Methylated poly(dA-dT) was also protected by formation of complexes with calf thymus chromosomal proteins. It seems that the nucleosome structure prevents the action of DNA glycosylases. The very high sensitivity of PBS1 phage DNA, which contains uracil as a natural component, in complexes with calf thymus chromosomal proteins as well as in the free form [1] was confirmed. This high sensitivity seems ascribable to the high uracil content of PBS1 DNA. Methylated nucleosome monomers and dimers, and reconstituted nucleosome monomers containing methylated DNA of about 150 bp length, were considerably more resistant to 3-methyladenine-DNA glycosylase than chromatin reconstituted from methylated DNA of longer chain length. This may be due to the lower proportion of linker regions of free form stretches of the DNA chain in nucleosome oligomers.