Abstract
BackgroundCTCF 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.ResultsUsing 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.ConclusionsOur 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.
Highlights
CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types
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
The localization of the CTCFL-positive cells in the basal compartment of the seminiferous tubules indicates that these cells are spermatogonia or preleptotene spermatocytes, as only upon progression in meiotic prophase do spermatocytes become disconnected from the basal lamina and move through the Sertoli cell barrier into the adluminal compartment of the seminiferous tubules
Summary
CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. Three-dimensional folding of the eukaryotic genome occurs in a highly organized manner so as to compact chromatin while allowing temporal and spatial expression of genes. The genome contains regulatory elements, such as promoters, enhancers, locus control regions, insulators and enhancer blockers, that can orchestrate chromatin folding and gene activity over short and long distances, both in cis and in trans [1]. CTCF is a key coordinator of three-dimensional chromatin structure, allowing loop formation and specific chromatin compositions [2,3]. The importance of CTCF in chromatin organization is emphasized by its evolutionary conservation, its ubiquitous expression, and its essential role in virtually all cells and tissues examined [4,5]. CTCF has been termed the “master weaver” of the genome [3]
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