| Abstract
| - The Xenopus borealis somatic 5S ribosomal RNA gene was used as a model system to determinethe mutual effects of nucleosome folding and formation of ultraviolet (UV) photoproducts (primarilycis−syn cyclobutane pyrimidine dimers, or CPDs) in chromatin. We analyzed the preferred rotationaland translational settings of 5S rDNA on the histone octamer surface after induction of up to 0.8 CPD/nucleosome core (2.5 kJ/m2 UV dose). DNase I and hydroxyl radical footprints indicate that UV damageat these levels does not affect the average rotational setting of the 5S rDNA molecules. Moreover, acombination of nuclease trimming and restriction enzyme digestion indicates the preferred translationalpositions of the histone octamer are not affected by this level of UV damage. We also did not observedifferences in the UV damage patterns of irradiated 5S rDNA before or after nucleosome formation,indicating there is little difference in the inhibition of nucleosome folding by specific CPD sites in the 5SrRNA gene. Conversely, nucleosome folding significantly restricts CPD formation at all sites in the threehelical turns of the nontranscribed strand located in the dyad axis region of the nucleosome, where DNAis bound exclusively by the histone H3−H4 tetramer. Finally, modulation of the CPD distribution in a 14nt long pyrimidine tract correlates with its rotational setting on the histone surface, when the strong sequencebias for CPD formation in this tract is minimized by normalization. These results help establish the mutualroles of histone binding and UV photoproducts on their formation in chromatin.
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