Probing the conformation of nucleosome linker DNA in situ with pyrimidine dimer formation

The distribution of pyrimidine dimers formed in nucleosomal DNA by irradiation of intact nuclei isolated from rat liver has been examined. Whereas pyrimidine dimer formation in the core region of the nucleosome occurred with peaks at approximately 10-nucleotide intervals as previously reported, the distribution of pyrimidine dimers through the linker region was nearly uniform. This distinction between core and linker DNA was found to be independent of linker length over a range of 38-60 nucleotides. Because there is now ample evidence that DNA curvature is the source of the peaks of pyrimidine dimer formation in the core region, the uniform distribution of pyrimidine dimers observed in the linker region indicates that linker DNA is relatively straight. This suggests that higher order chromatin structure in situ is based on a zigzag chain of nucleosomes.