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The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner

Frank Sleutels1*, Widia Soochit1, Marek Bartkuhn2, Helen Heath1, Sven Dienstbach2, Philipp Bergmaier2, Vedran Franke3, Manuel Rosa-Garrido45, Suzanne van de Nobelen1, Lisa Caesar1, Michael van der Reijden1, Jan Christian Bryne3, Wilfred van IJcken6, J Anton Grootegoed7, M Dolores Delgado4, Boris Lenhard3, Rainer Renkawitz2, Frank Grosveld189 and Niels Galjart189*

Author Affiliations

1 Department of Cell Biology Erasmus Medical Center, Rotterdam, The Netherlands

2 Institut für Genetik, Justus-Liebig-Universität, Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany

3 Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008, Bergen, Norway

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

5 Cell Cycle, Stem Cell Fate and Cancer Laboratory, Fundación Marqués de Valdecilla (IFIMAV), Santander, Spain

6 Center for Biomics Erasmus Medical Center, Rotterdam, The Netherlands

7 Department of Reproduction and Development Erasmus Medical Center, Rotterdam, The Netherlands

8 Cancer Genomics Center, NGI, Rotterdam, The Netherlands

9 Center for Biomedical Genetics, Rotterdam, The Netherlands

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Epigenetics & Chromatin 2012, 5:8  doi:10.1186/1756-8935-5-8

Published: 18 June 2012

Abstract

Background

CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. In conjunction with cohesin, it organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the testis-specific paralog of CTCF, is less clear.

Results

Using immunohistochemistry on testis sections and fluorescence-based microscopy on intact live seminiferous tubules, we show that CTCFL is only transiently present during spermatogenesis, prior to the onset of meiosis, when the protein co-localizes in nuclei with ubiquitously expressed CTCF. CTCFL distribution overlaps completely with that of Stra8, a retinoic acid-inducible protein essential for the propagation of meiosis. We find that absence of CTCFL in mice causes sub-fertility because of a partially penetrant testicular atrophy. CTCFL deficiency affects the expression of a number of testis-specific genes, including Gal3st1 and Prss50. Combined, these data indicate that CTCFL has a unique role in spermatogenesis. Genome-wide RNA expression studies in ES cells expressing a V5- and GFP-tagged form of CTCFL show that genes that are downregulated in CTCFL-deficient testis are upregulated in ES cells. These data indicate that CTCFL is a male germ cell gene regulator. Furthermore, genome-wide DNA-binding analysis shows that CTCFL binds a consensus sequence that is very similar to that of CTCF. However, only ~3,700 out of the ~5,700 CTCFL- and ~31,000 CTCF-binding sites overlap. CTCFL binds promoters with loosely assembled nucleosomes, whereas CTCF favors consensus sites surrounded by phased nucleosomes. Finally, an ES cell-based rescue assay shows that CTCFL is functionally different from CTCF.

Conclusions

Our data suggest that nucleosome composition specifies the genome-wide binding of CTCFL and CTCF. We propose that the transient expression of CTCFL in spermatogonia and preleptotene spermatocytes serves to occupy a subset of promoters and maintain the expression of male germ cell genes.

Keywords:
CTCF; CTCFL; Gametogenesis; Genome-wide binding; Nucleosome