Partners in Long Distance Interactions

The genome of higher eukaryotes consists of DNA, which in case of the human genome measures 2m in length and is divided over 46 chromosomes. These long DNA molecules are packed in a nucleus that measures about 10μm in diameter. In order to fit the complete DNA into such a small volume, DNA is folded and compacted by proteins in a structure called chromatin. During mitosis, is even further compacted into condensed chromosomes (Kornberg, 1974). All the information needed for the formation and proper function of an organism is stored in these structures and it is reasonable to expect that this overcrowded situation is organized in a very specific manner, with controlled three-dimensional contacts within the nucleus. The need for controlled chromatin contacts is also suggested by the fact that gene regulation is a tightly regulated process. Different levels of control must be involved in regulating proper spatio-temporal expression of genes throughout the process of cellular differentiation. These processes are coordinated by interactions of an “army” of general, cell-type and stage specific proteins that bind to chromatin and DNA. Several techniques allow the identification and study of chromatin regions that interact with each other. These include functional genetic analysis, microscopic analysis after DNA or RNA fluorescent in situ hybridization (FISH) in combination with 3D microscopy, as well as biochemical methods, such as chromosome conformation capture (3C) and the more sophisticated variation thereof (4C). The combination of these methods reveals a network of contacts in the nucleus. These interactions are mediated by insulators and other regulatory sequences, including enhancers and promoters, which mediate/promote certain functional three-dimensional interactions while preventing other enhancer-promoter contacts. In this chapter, I will introduce several factors: Ldb1, Delangin, Cohesin and CTCF which have important role long-range interactions

Critical Role for the Transcription Regulator CCCTC-Binding Factor in the Control of Th2 Cytokine Expression

Differentiation of naive CD4(+) cells into Th2 cells is accompanied by chromatin remodeling at the Th2 cytokine focus 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 Ctef 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-gamma 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 I (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 GATAX and SATB1-dependent regulation of Th2 cytokine gene expression. The Journal of Immunology, 2009, 182: 999-1010

Critical Role for the Transcription Regulator CCCTC-Binding Factor in the Control of Th2 Cytokine Expression

Differentiation of naive CD4(+) cells into Th2 cells is accompanied by chromatin remodeling at the Th2 cytokine focus 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 Ctef 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-gamma 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 I (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 GATAX and SATB1-dependent regulation of Th2 cytokine gene expression. The Journal of Immunology, 2009, 182: 999-1010

Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance

Saccharomyces cerevisiae Scc2 binds Scc4 to form an essential complex that loads cohesin onto chromosomes. The prevalence of Scc2 orthologs in eukaryotes emphasizes a conserved role in regulating sister chromatid cohesion, but homologs of Scc4 have not hitherto been identified outside certain fungi. Some metazoan orthologs of Scc2 were initially identified as developmental gene regulators, such as Drosophila Nipped-B, a regulator of cut and Ultrabithorax, and delangin, a protein mutant in Cornelia de Lange syndrome. We show that delangin and Nipped-B bind previously unstudied human and fly orthologs of Caenorhabditis elegans MAU-2, a non-axis-specific guidance factor for migrating cells and axons. PSI-BLAST shows that Scc4 is evolutionarily related to metazoan MAU-2 sequences, with the greatest homology evident in a short N-terminal domain, and protein-protein interaction studies map the site of interaction between delangin and human MAU-2 to the N-terminal regions of both proteins. Short interfering RNA knockdown of human MAU-2 in HeLa cells resulted in precocious sister chromatid separation and in impaired loading of cohesin onto chromatin, indicating that it is functionally related to Scc4, and RNAi analyses show that MAU-2 regulates chromosome segregation in C. elegans embryos. Using antisense morpholino oligonucleotides to knock down Xenopus tropicalis delangin or MAU-2 in early embryos produced similar patterns of retarded growth and developmental defects. Our data show that sister chromatid cohesion in metazoans involves the formation of a complex similar to the Scc2-Scc4 interaction in the budding yeast. The very high degree of sequence conservation between Scc4 homologs in complex metazoans is consistent with increased selection pressure to conserve additional essential functions, such as regulation of cell and axon migration during development