Active Human Nucleolar Organizer Regions are Interspersed with Inactive rDNA Repeats in Normal and Tumor Cells

Abstract

Aim: The synthesis of rRNA is a key determinant of normal and malignant cell growth and subject to epigenetic regulation. Yet, the epigenomic features of rDNA arrays clustered in nucleolar organizer regions are largely unknown. We set out to explore for the first time how DNA methylation is distributed on individual rDNA arrays. Materials & Methods: Here we combined immunofluorescence detection of DNA modifications with fluorescence hybridization of single DNA fibers, metaphase immuno-FISH and methylation-sensitive restriction enzyme digestions followed by Southern blot. Results: We found clustering of both hypomethylated and hypermethylated repeat units and hypermethylation of noncanonical rDNA in IMR90 fibroblasts and HCT116 colorectal carcinoma cells. Surprisingly, we also found transitions between hypo- and hypermethylated rDNA repeat clusters on single DNA fibers. Conclusion: Collectively, our analyses revealed co-existence of different epialleles on individual nucleolar organizer regions and showed that epi-combing is a valuable approach to analyze epigenomic patterns of repetitive DNA.

Keywords::

• DNA methylation
• epigenetics
• epigenomics
• nucleolar organizer region
• nucleolus
• ribosomal DNA
• single-molecule analysis

Supplementary data

Acknowledgements

We thank J-P Capp (Genomic Vision) for help with epi-combing troubleshooting in the initial phase of the project, G Längst, H Tschochner, P Milkereit, J Griesenbeck, M Rehli (University of Regensburg), T Cremer, M Cremer and I Solovei (LMU Munich) for support with reagents and devices.

Financial & competing interests disclosure

Support was provided from the Deutsche Forschungsgemeinschaft SFB960 program (AN) and the Bavarian Elite Network (KZ). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

Support was provided from the Deutsche Forschungsgemeinschaft SFB960 program (AN) and the Bavarian Elite Network (KZ). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.