CTCF (CCCTC-binding factor) binds sites around the mouse ␤-globin locus that spatially cluster in the erythroid cell nucleus. We show that both conditional deletion of CTCF and targeted disruption of a DNA-binding site destabilize these long-range interactions and cause local loss of histone acetylation and gain of histone methylation, apparently without affecting transcription at the locus. Our data demonstrate that CTCF is directly involved in chromatin architecture and regulates local balance between active and repressive chromatin marks. We postulate that throughout the genome, relative position and stability of CTCF-mediated loops determine their effect on enhancer-promoter interactions, with gene insulation as one possible outcome. Chromatin insulators are DNA sequences that confer autonomous expression on genes by protecting them against inadvertent signals coming from neighboring chromatin. CTCF (CCCTC-binding factor) is the prototype vertebrate protein exhibiting insulator activity that can act as an enhancer blocker or as a barrier against repressive forces from nearby heterochromatin in vitro (Defossez and Gilson 2002; RecillasTarga et al. 2002). In vivo, CTCF binds to the imprinting control region of the H19/insulin-like growth factor (Igf2) locus, where it acts as a methylation-sensitive enhancer blocker (Bell and Felsenfeld 2000;Hark et al. 2000). Moreover, CTCF-binding sites have been foundand its insulator activity has been anticipated-at the imprinting center that determines choice of X inactivation (Chao et al. 2002), at boundaries of domains that escape X inactivation (Filippova et al. 2005), and at sites flanking CTG/CAG repeats at the DM1 locus (Filippova et al. 2001). CTCF was first defined as an insulator protein when it was found to be required for the enhancerblocking activity of a hypersensitive site 5Ј of the chicken ␤-globin locus (5ЈHS4) (Bell et al. 1999). A similar CTCF-dependent insulator site was subsequently found at the 3Ј end of the locus and both sites coincide with erythroid-specific transitions in DNase I sensitivity of chromatin (Saitoh et al. 2000). Such observations suggested that CTCF partitions the genome in physically distinct domains of gene expression. The molecular mechanism underlying CTCF's insulating activity is still unknown.CTCF-binding sites also flank the human and mouse ␤-globin locus (Fig. 1A), which contains a number of developmentally regulated, erythroid-specific ␤-globin genes and an upstream locus control region (LCR) required for high ␤-globin expression levels. In mice, three CTCF-binding sites have been identified upstream (HS-85, HS-62, and HS5) and one downstream (3ЈHS1) of the locus (Farrell et al. 2002;Bulger et al. 2003). Previously, we applied chromosome conformation capture (3C) technology (Dekker et al. 2002) to study long-range DNA interactions between these and other sites in the ␤-globin locus. In erythroid cells, the CTCF-binding sites (including HS-85; see below) were found to participate in spatial interactions between the LCR and th...

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The transcription/repair factor TFIIH operates as a DNA helix opener in RNA polymerase II (RNAP2) transcription and nucleotide excision repair. To study TFIIH in vivo, we generated cell lines expressing functional GFP-tagged TFIIH. TFIIH was homogeneously distributed throughout the nucleus with nucleolar accumulations. We provide in vivo evidence for involvement of TFIIH in RNA polymerase I (RNAP1) transcription. Photobleaching revealed that TFIIH moves freely and gets engaged in RNAP1 and RNAP2 transcription for approximately 25 and approximately 6 s, respectively. TFIIH readily switches between transcription and repair sites (where it is immobilized for approximately 4 min) without large-scale alterations in composition. Our findings support a model of diffusion and random collision of individual components that permits a quick and versatile response to changing conditions.

The 11-zinc finger protein CCCTC-binding factor (CTCF) is a highly conserved protein, involved in imprinting, longrange chromatin interactions and transcription. To investigate its function in vivo, we generated mice with a conditional Ctcf knockout allele. Consistent with a previous report, we find that ubiquitous ablation of the Ctcf gene results in early embryonic lethality. Tissue-specific inactivation of CTCF in thymocytes specifically hampers the differentiation of ab T cells and causes accumulation of late double-negative and immature single-positive cells in the thymus of mice. These cells are normally large and actively cycling, and contain elevated amounts of CTCF. In Ctcf knockout animals, however, these cells are small and blocked in the cell cycle due to increased expression of the cyclin-CDK inhibitors p21 and p27. Taken together, our results show that CTCF is required in a dose-dependent manner and is involved in cell cycle progression of ab T cells in the thymus. We propose that CTCF positively regulates cell growth in rapidly dividing thymocytes so that appropriate number of cells are generated before positive and negative selection in the thymus.

Homologous recombination is a versatile DNA damage repair pathway requiring Rad51 and Rad54. Here we show that a mammalian Rad54 paralog, Rad54B, displays physical and functional interactions with Rad51 and DNA that are similar to those of Rad54. While ablation of Rad54 in mouse embryonic stem (ES) cells leads to a mild reduction in homologous recombination efficiency, the absence of Rad54B has little effect. However, the absence of both Rad54 and Rad54B dramatically reduces homologous recombination efficiency. Furthermore, we show that Rad54B protects ES cells from ionizing radiation and the interstrand DNA cross-linking agent mitomycin C. Interestingly, at the ES cell level the paralogs do not display an additive or synergic interaction with respect to mitomycin C sensitivity, yet animals lacking both Rad54 and Rad54B are dramatically sensitized to mitomycin C compared to either single mutant. This suggests that the paralogs possibly function in a tissue-specific manner. Finally, we show that Rad54, but not Rad54B, is needed for a normal distribution of Rad51 on meiotic chromosomes. Thus, even though the paralogs have similar biochemical properties, genetic analysis in mice uncovered their nonoverlapping roles.DNA double-strand breaks (DSBs) are among a plethora of lesions that threaten the integrity of the genome. If not properly processed, DSBs can lead to cell cycle arrest or illegitimate DNA rearrangements such as translocations, inversions, or deletions. These rearrangements can contribute to cell dysfunction, cell death, or carcinogenesis (22). DSBs can arise through the action of exogenous DNA-damaging agents, but they also arise from endogenous sources, such as oxidative DNA damage and as a consequence of DNA replication (10,22). Homologous recombination is a major DNA repair pathway by which DSBs are repaired. Homologous recombination is generally a precise way of resolving DSBs, because it uses homologous sequence, usually provided on the sister chromatid, as a repair template (54).Homologous recombination is a complex process requiring a number of proteins of the RAD52 epistasis group, including Rad51 and Rad54. Rad51 is the key player in this process because it is critical for homology recognition and performs strand exchange between recombining DNA molecules. A pivotal intermediate in these reactions is the Rad51 nucleoprotein filament. This forms when Rad51 polymerizes on singlestranded DNA that results from DNA damage processing (54). Rad54 is an important accessory factor for Rad51 (56). A number of biochemical characteristics of Rad54 have been well defined for different species ranging from yeasts to humans (8,18,24,31,37,38,42,47,48,53,55,59). Rad54 is a doublestranded-DNA-dependent ATPase that can translocate on DNA, thereby affecting DNA topology. Biochemically, Rad54 has been implicated in participation in multiple steps of homologous recombination. It can stabilize the Rad51 nucleoprotein filament in an early stage of recombination (30). At a subsequent stage it can promote chromatin rem...

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.

BackgroundCCCTC 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.ResultsUsing 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.ConclusionsUBF 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.

Differentiation of naive CD4+ cells into Th2 cells is accompanied by chromatin remodeling at the Th2 cytokine locus allowing the expression of the IL-4, IL-5, and IL-13 genes. In this report, we investigated the role in Th2 differentiation of the transcription regulator CCCTC-binding factor (CTCF). Chromatin immunoprecipitation analysis revealed multiple CTCF binding sites in the Th2 cytokine locus. Conditional deletion of the Ctcf gene in double-positive thymocytes allowed development of peripheral T cells, but their activation and proliferation upon anti-CD3/anti-CD28 stimulation in vitro was severely impaired. Nevertheless, when TCR signaling was circumvented with phorbol ester and ionomycin, we observed proliferation of CTCF-deficient T cells, enabling the analysis of Th2 differentiation in vitro. We found that in CTCF-deficient Th2 polarization cultures, transcription of IL-4, IL-5, and IL-13 was strongly reduced. By contrast, CTCF deficiency had a moderate effect on IFN-γ production in Th1 cultures and IL-17 production in Th17 cultures was unaffected. Consistent with a Th2 cytokine defect, CTCF-deficient mice had very low levels of IgG1 and IgE in their serum, but IgG2c was close to normal. In CTCF-deficient Th2 cultures, cells were polarized toward the Th2 lineage, as substantiated by induction of the key transcriptional regulators GATA3 and special AT-rich binding protein 1 (SATB1) and down-regulation of T-bet. Also, STAT4 expression was low, indicating that in the absence of CTCF, GATA3 still operated as a negative regulator of STAT4. Taken together, these findings show that CTCF is essential for GATA3- and SATB1-dependent regulation of Th2 cytokine gene expression.