3,585 research outputs found
Correlation of ChIP enrichment using either anti-Su(Hw) on wild-type chromatin or anti-GFP on chromatin from Su(Hw)-GFP transgenic
No full textThe enrichment values are plotted as the arsinh transformation (approximately equivalent to the log2 scale) of the ratio of specific versus control ChIP. Correlation coefficient is 0.66. ChIP, chromatin immunoprecipitation; GFP, green fluorescent protein; Su(Hw), Suppressor of Hairy-wing.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p
Preparation of nanoporous poly(methyl silsesquioxane) films using core-shell silsesquioxane as porogen
No full textGenes with expression changes in su(Hw) mutant larvae (L3) and wing discs
No full textA cluster diagram showing changes in gene expression in a () null condition compared with changes in the heterozygous controls (fold change ≥ 1.7, ≤ 10for the mutants and approximately half the fold change at ≤ 10for the heterozygotes). The table lists those genes with greater than 1.7-fold expression change that have predicted Suppressor of Hairy-wing (Su [Hw]) binding sites within 30 kilobases (kb). The Expression column shows the absolute fold change for each gene. The Distance column indicates the distance between the gene model and Su(Hw) sites(s); for those genes with predicted sites within the gene model, the number of sites are indicated. If there is more than one site, the distance between them is given. The Location column indicates where the predicted sites lie with respect to the gene models. UTR, untranslated region.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p
Closeness of match to the Su(Hw) binding site consensus is associated with binding
No full textThe Patser value for each Patser match is plotted against the enrichment (arsinh transformation; approximately equal to logratio) of the fragment containing the matching sequence. The enrichment value is the highest mean value from the three chromatin sources. The vertical line indicates the Patser = e; for matches with < e, 63% show enrichment greater than 0.5 (1.4-fold) and 53% show enrichment greater than 0.8 (1.7-fold). Su(Hw), Suppressor of Hairy-wing.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p
Expression changes in the 3 Mb region with respect to Su(Hw) binding sites
No full textExpression changes (as absolute fold change according to the scale bar) are indicated by the bars above the gene models, with upregulated genes in orange and downregulated genes in blue. The bars mark the 5' end of each gene. The location of Su(Hw) binding sites are plotted on the three rows All sites, Cluster 1, and Cluster 2. Cluster 2 indicates the two sites within 100 base pairs of each other. Cluster 1 indicates the six pairs of sites within 1 kilobase of each other. All sites plots the locations of the remaining 83 sites in the region. The maps are plotted and rendered using the Affymetrix Integrated Genome Browser.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p
Functional properties of the Su(Hw) complex are determined by its regulatory environment and multiple interactions on the Su(Hw) protein platform
Full text linkThe Su(Hw) protein was first identified as a DNA-binding component of an insulator complex in Drosophila. Insulators are regulatory elements that can block the enhancer-promoter communication and exhibit boundary activity. Some insulator complexes contribute to the higher-order organization of chromatin in topologically associated domains that are fundamental elements of the eukaryotic genomic structure. The Su(Hw)-dependent protein complex is a unique model for studying the insulator, since its basic structural components affecting its activity are already known. However, the mechanisms involving this complex in various regulatory processes and the precise interaction between the components of the Su(Hw) insulators remain poorly understood. Our recent studies reveal the fine mechanism of formation and function of the Su(Hw) insulator. Our results provide, for the first time, an example of a high complexity of interactions between the insulator proteins that are required to form the (Su(Hw)/Mod(mdg4)-67.2/CP190) complex. All interactions between the proteins are to a greater or lesser extent redundant, which increases the reliability of the complex formation. We conclude that both association with CP190 and Mod(mdg4)-67.2 partners and the proper organization of the DNA binding site are essential for the efficient recruitment of the Su(Hw) complex to chromatin insulators. In this review, we demonstrate the role of multiple interactions between the major components of the Su(Hw) insulator complex (Su(Hw)/Mod(mdg4)-67.2/CP190) in its activity. It was shown that Su(Hw) may regulate the enhancer–promoter communication via the newly described insulator neutralization mechanism. Moreover, Su(Hw) participates in direct regulation of activity of vicinity promoters. Finally, we demonstrate the mechanism of organization of “insulator bodies” and suggest a model describing their role in proper binding of the Su(Hw) complex to chromatin
Role of Su(Hw) zinc finger 10 and interaction with CP190 and Mod(mdg4) proteins in recruiting the Su(Hw) complex to chromatin sites in <i>Drosophila</i>
No full textSu(Hw) belongs to the class of proteins that organize chromosome architecture and boundaries/insulators between regulatory domains. This protein contains a cluster of 12 zinc finger domains most of which are responsible for binding to three different modules in the consensus site. Su(Hw) forms a complex with CP190 and Mod(mdg4)-67.2 proteins that binds to well-known Drosophila insulators. To understand how Su(Hw) performs its activities and binds to specific sites in chromatin, we have examined the previously described su(Hw)f mutation that disrupts the 10th zinc finger (ZF10) responsible for Su(Hw) binding to the upstream module. The results have shown that Su(Hw)f loses the ability to interact with CP190 in the absence of DNA. In contrast, complete deletion of ZF10 does not prevent the interaction between Su(Hw)Δ10 and CP190. Having studied insulator complex formation in different mutant backgrounds, we conclude that both association with CP190 and Mod(mdg4)-67.2 partners and proper organization of DNA binding site are essential for the efficient recruitment of the Su(Hw) complex to chromatin insulators.</div
The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome
No full textSpecific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome – NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome – NL interactions.BiotechnologyApplied Science
Su(Hw) interacts with Combgap to establish long-range chromatin contacts
No full textAbstract Background Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) insulator-binding protein to genome topology remains unclear. Results In this study, we provide evidence for the existence of long-range interactions between chromatin bound Su(Hw) and Combgap, which was first characterised as Polycomb response elements binding protein. Loss of Su(Hw) binding to chromatin results in the disappearance of Su(Hw)-Combgap long-range interactions and in a decrease in spatial self-interactions among a subset of Su(Hw)-bound genome sites. Our findings suggest that Su(Hw)-Combgap long-range interactions are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators’ binding. Conclusions This study demonstrates that Su(Hw) insulator binding protein can form long-range interactions with Combgap, Polycomb response elements binding protein, and that these interactions are associated with active chromatin factors rather than with Polycomb dependent repression
Role of ZF10 in Su(Hw) for interaction between the insulator proteins.
No full textA structural schematic of Su(Hw). The borders between the Su(Hw) domains (NTAD, N-terminal acidic domain; CTAD, C-terminal acidic domain; ZF, zinc-finger domain) are indicated by numbers. Gray pentagon indicates H-to-Y substitution in the Su(Hw)f mutant; dotted line, deletion of ZF10 in the Su(Hw)Δ10 mutant. The number of plus signs indicates the relative strength of interaction in the Y2H assay (S1 Fig); the minus sign denoted an absence of interactions; an asterisk, a reduction in the Y2H signal due to the repressive effect of Su(Hw) C-terminal domain on the transcription in yeast [72]. All the results were reproduced in three independent experiments. Numbers in brackets refer to the amino acid residues that flank protein regions included in the analysis. (B) Co-immunoprecipitation between different Su(Hw) variants fused to the FLAG epitope and the insulator proteins under normal conditions. The FLAG-Su(Hw)+, FLAG-Su(Hw)f, and FLAG-Su(Hw)Δ10 were expressed in the S2 cells. The immunoprecipitated complexes were washed with buffers containing 150 mM NaCl before loading onto the SDS-PAGE for Western blot analysis. The PVDF membrane was consecutively probed with antibodies against the indicated proteins (CP190 or Mod-67.2) or FLAG epitope. Each column represents a single FLAG-immunoprecipitation experiment with the particular mutant variant. Each lane shows the result of a subsequent hybridization of each immunoprecipitate with different antibodies on the same membrane. "Input" is the input fraction (10% of the lysate used for the immunoprecipitation); "Output IP," the supernatant after the immunoprecipitation; "IP," the immunoprecipitate. The results were obtained in three independent experiments.</p
- …
