Telomeres of Drosophila melanogaster contain arrays of the retrotransposon-like elements

The Suppressor of the Hairy wing [Su(Hw)] binding region within the gypsy retrotransposon is the best known chromatin insulator in Drosophila melanogaster. According to previous data, two copies of the gypsy insulator inserted between an enhancer and a promoter neutralize each other's actions, which is indicative of an interaction between the protein complexes bound to the insulators. We have investigated the role of pairing between the gypsy insulators located on homologous chromosomes in trans interaction between yellow enhancers and a promoter. It has been shown that trans activation of the yellow promoter strongly depends on the site of the transposon insertion, which is evidence for a role of surrounding chromatin in homologous pairing. The presence of the gypsy insulators in both homologous chromosomes even at a distance of 9 kb downstream from the promoter dramatically improves the trans activation of yellow. Moreover, the gypsy insulators have proved to stabilize trans activation between distantly located enhancers and a promoter. These data suggest that gypsy insulator pairing is involved in communication between loci in the Drosophila genome.The enhancer-mediated activation is the basic mechanism of gene regulation in eukaryotes. Enhancers can act over large distances to activate transcription independently of their orientation and position relative to the promoter without affecting adjacent genes (6, 11). Insulators represent a class of DNA sequences that restrain regulatory interactions within eukaryotic genomes (21,35,36,53,63,65). These elements restrict the enhancer and silencer functions, contributing to the establishment of independent gene regulation within heterochromatic and euchromatic domains.The best known insulator was identified in Drosophila melanogaster within the 5Ј untranslated region of the gypsy retrotransposon (42). It consists of 12 binding sites for the Su(Hw) protein (44,62). Recently, another protein, CP190, was shown to bind to the gypsy insulator (54). These DNA-binding proteins are important for the gypsy insulator function, as mutations in the su(Hw) and CP190 genes reverse the mutagenic effects of the gypsy retrotransposon (46, 54). Mutations in another gene, mod(mdg4), alter the phenotypes of the gypsyinduced mutations (17,18,22). Previous studies indicate that the Mod(mdg4)-67.2 protein isoform interacts with the Su(Hw) and CP190 proteins (14,25,54). The prevalent model suggests that boundary elements, or insulators, subdivide eukaryotic chromosomes into functionally and structurally autonomous domains (65). The insulators determine the limits of higher-order "looped" chromatin domains by interacting either with each other or with some nuclear structures (8,36,65). This interaction might be responsible, at least partially, for the establishment of independent chromatin domains. In this context, it is noteworthy that the gypsy insulators have been found to coalesce into a few "insulator bodies" located at the periphery of the nucleus (19), which are partially or complete...

Chromatin insulators are remarkable regulatory elements that can bring distant genomic sites together and block unscheduled enhancer-promoter communications. Insulators act via associated insulator proteins of two classes: sequence-specific DNA binding factors and "bridging" proteins. The latter are required to mediate interactions between distant insulator elements. Chromatin insulators are critical for correct expression of complex loci; however, their mode of action is poorly understood. Here, we use the Drosophila bithorax complex as a model to investigate the roles of the bridging proteins Cp190 and Mod(mdg4). The bithorax complex consists of three evolutionarily conserved homeotic genes Ubx, abd-A, and Abd-B, which specify anterior-posterior identity of the last thoracic and all abdominal segments of the fly. Looking at effects of CTCF, mod(mdg4), and Cp190 mutations on expression of the bithorax complex genes, we provide the first functional evidence that Mod(mdg4) acts in concert with the DNA binding insulator protein CTCF. We find that Mod(mdg4) and Cp190 are not redundant and may have distinct functional properties. We, for the first time, demonstrate that Cp190 is critical for correct regulation of the bithorax complex and show that Cp190 is required at an exceptionally strong Fub insulator to partition the bithorax complex into two topological domains.KEYWORDS HOX genes; chromatin; chromatin insulators; Drosophila; gene regulation T HE eukaryotic genome is folded extensively to fit inside the cell nucleus. The folding patterns vary between individual cells but certain conformations occur more frequently. In some cases, the likelihood of acquiring a particular conformation is linked to activation or repression of specific genes. Such links are especially important for complex loci in which multiple regulatory elements are positioned tens of thousands of base pairs (kb) away from their target promoters. The Drosophila bithorax complex is one of the best studied complex loci. The bithorax complex consists of three evolutionarily conserved homeotic genes Ubx, abd-A, and Abd-B that encode transcription factors and specify anterior-posterior identity of the last thoracic and all abdominal segments of the fly . Segment-specific expression of the bithorax complex genes is controlled by distal transcriptional enhancers and polycomb/trithorax response elements (PRE/TREs). The correct function of enhancers and PREs/ TREs is further orchestrated by chromatin insulator elements that modulate the topology of the bithorax complex by mechanisms that are not well understood.Chromatin insulator elements were first discovered in Drosophila and later found in vertebrates and plants. They are short (1 kb) DNA elements that can block ("insulate") transcriptional activation of a promoter by a remote enhancer when interposed between the two. In contrast to transcriptional repression, insulation leaves the promoter transcriptionally competent so it is free to engage with other enhancers as long as those are not sepa...

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Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell differentiation. Sponges (Porifera) are the oldest Metazoa that show unique plasticity and regenerative potential. Here, we characterize the ferritins of two cold-water sponges using proteomics, spectral microscopy, and bioinformatic analysis. The recently duplicated conservative HdF1a/b and atypical HdF2 genes were found in the Halisarca dujardini genome. Multiple related transcripts of HpF1 were identified in the Halichondria panicea transcriptome. Expression of HdF1a/b was much higher than that of HdF2 in all annual seasons and regulated differently during the sponge dissociation/reaggregation. The presence of the MRE and HRE motifs in the HdF1 and HdF2 promotor regions and the IRE motif in mRNAs of HdF1 and HpF indicates that sponge ferritins expression depends on the cellular iron and oxygen levels. The gel electrophoresis combined with specific staining and mass spectrometry confirmed the presence of ferric ions and ferritins in multi-subunit complexes. The 3D modeling predicts the iron-binding capacity of HdF1 and HpF1 at the ferroxidase center and the absence of iron-binding in atypical HdF2. Interestingly, atypical ferritins lacking iron-binding capacity were found in genomes of many invertebrate species. Their function deserves further research.