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CTCF regulates the local epigenetic state of ribosomal DNA repeats

Suzanne van de Nobelen16, Manuel Rosa-Garrido2, Joerg Leers3, Helen Heath17, Widia Soochit1, Linda Joosen1, Iris Jonkers4, Jeroen Demmers5, Michael van der Reijden1, Verónica Torrano2, Frank Grosveld1, M Dolores Delgado2, Rainer Renkawitz3, Niels Galjart1* and Frank Sleutels1*

Author Affiliations

1 Department of Cell Biology and Genetics, Erasmus MC, The Netherlands

2 Department of Molecular Biology, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC, Universidad de Cantabria-CSIC-IDICAN, Santander, Spain

3 Institute for Genetics, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 58-62, D-35392 Giessen, Germany

4 Department of Reproduction and Development, Erasmus MC, The Netherlands

5 Proteomics Center, Erasmus MC, The Netherlands

6 Department of Epigenetics, Max-Planck Institute of Immunobiology, Freiburg, Germany

7 Institute of Cell and Molecular Science, Centre for Gastroenterology, London, UK

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Epigenetics & Chromatin 2010, 3:19  doi:10.1186/1756-8935-3-19

Published: 8 November 2010



CCCTC binding factor (CTCF) is a highly conserved zinc finger protein, which is involved in chromatin organization, local histone modifications, and RNA polymerase II-mediated gene transcription. CTCF may act by binding tightly to DNA and recruiting other proteins to mediate its various functions in the nucleus. To further explore the role of this essential factor, we used a mass spectrometry-based approach to screen for novel CTCF-interacting partners.


Using biotinylated CTCF as bait, we identified upstream binding factor (UBF) and multiple other components of the RNA polymerase I complex as potential CTCF-interacting partners. Interestingly, CTCFL, the testis-specific paralog of CTCF, also binds UBF. The interaction between CTCF(L) and UBF is direct, and requires the zinc finger domain of CTCF(L) and the high mobility group (HMG)-box 1 and dimerization domain of UBF. Because UBF is involved in RNA polymerase I-mediated ribosomal (r)RNA transcription, we analyzed CTCF binding to the rDNA repeat. We found that CTCF bound to a site upstream of the rDNA spacer promoter and preferred non-methylated over methylated rDNA. DNA binding by CTCF in turn stimulated binding of UBF. Absence of CTCF in cultured cells resulted in decreased association of UBF with rDNA and in nucleolar fusion. Furthermore, lack of CTCF led to reduced binding of RNA polymerase I and variant histone H2A.Z near the rDNA spacer promoter, a loss of specific histone modifications, and diminished transcription of non-coding RNA from the spacer promoter.


UBF is the first common interaction partner of CTCF and CTCFL, suggesting a role for these proteins in chromatin organization of the rDNA repeats. We propose that CTCF affects RNA polymerase I-mediated events globally by controlling nucleolar number, and locally by regulating chromatin at the rDNA spacer promoter, similar to RNA polymerase II promoters. CTCF may load UBF onto rDNA, thereby forming part of a network that maintains rDNA genes poised for transcription.