Repair of ribosomal DNA (rDNA) is a very important nuclear process due to the most active transcription of ribosomal genes. Proper repair of rDNA is required for physiological biogenesis of ribosomes. Here, we analyzed the epigenetics of the DNA damage response in a nucleolar compartment, thus in the ribosomal genes studied in nonirradiated and UVA-irradiated mouse embryonic fibroblasts (MEFs). Using advanced microscopic techniques, we analyzed the distribution pattern and interactions of transcription factors UBF1/2 and histone modifications H3K9me3, H4K20me2 and H4K20me3. Interactions of these proteins were confirmed by co-immunoprecipitation. Furthermore, we used ChIP-PCR analysis to examine an abundance of UBF1/2, H3K9me3, H4K20me2 and H4K20me3 at the rDNA promotor and rDNA encoding 28S rRNA. We found that the promoter of ribosomal genes is not abundant on H4K20me2, but it is densely occupied by H4K20me3. Ribosomal genes, regulated via UBF1/2 proteins, were characterized by an interaction between UBF1/2 and H4K20me2/me3. This interaction was strengthened by UVA irradiation that additionally causes a focal accumulation of H4K20me3 in the nucleolus. No interaction has been found between UBF1/2 and H3K9me3. Interestingly, UVA irradiation decreases the levels of H3K9me3 and H4K20me3 at 28S rDNA. Altogether, the UVA light affects the epigenetic status of ribosomal genes at 28S rDNA and strengthens an interaction between UBF1/2 proteins and H4K20me2/me3. Based on these results, we conclude that the injury in the region encoding 28S rRNA is likely recognized via H4K20me3-dependent repair mechanism. Studied histone signature in this genomic region was, contrary to histone markers at the rDNA promoter, significantly affected by UVA light. This work was supported by Czech Science Foundation (grant number: 18-07384S). Work was also supported by Strategie AV21, programme Qualitas, the Center for Epigenetics (68081707).