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Insulator or enhancer-blocking elements are proposed to play an important role in the regulation of transcription by preventing inappropriate enhancer/promoter interaction. The zinc-finger protein CTCF is well studied in vertebrates as an enhancer blocking factor, but Drosophila CTCF has only been characterised recently. To date only one endogenous binding location for CTCF has been identified in the Drosophila genome, the Fab-8 insulator in the Abdominal-B locus in the Bithorax complex (BX-C). We carried out chromatin immunopurification coupled with genomic microarray analysis to identify CTCF binding sites within representative regions of the Drosophila genome, including the 3-Mb Adh region, the BX-C, and the Antennapedia complex. Location of in vivo CTCF binding within these regions enabled us to construct a robust CTCF binding-site consensus sequence. CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8. Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; "Fab-2," "Fab-3," and "Fab-4." With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism. Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.
Pubmed ID: 17616980 RIS Download
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Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
View all literature mentionsDatabase of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.
View all literature mentionsFunctional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 17,2023. Affymetrix is a partially commercial resource that provides DNA Analysis Arrays, Expression Analysis Arrays, Gene Regulation Analysis, and Microarrays. It also provides reagents and assays, instruments, software, and services for a fee. Information is provided for Rats, Humans, and Mice.Affymetrix is now Applied Biosystems, brand of DNA microarray products sold by Thermo Fisher Scientific that originated with an American biotechnology research and development and manufacturing company of the same name.
View all literature mentionsWeb application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. The objectives of the BBSRC IGF funding that started FlyChip were to establish a genomics infrastructure that would provide UK Drosophila researchers access to these emerging technologies, thereby maintaining the internationally recognised research profile the UK fly community enjoys. Via the IGF initiative, and with other funding, we have developed core genomics resources for the UK Drosophila community and we continue to develop these resources in a national and international context. As the facility has developed we are providing access to genomics technologies for researchers working with other organisms. Our Specific objective are: To drive the development of genomics resources and techniques and make these widely available to the broader research community. It is our aim to implement new omics techniques and make them available to the community, both through our facility and also through transfer of expertise to other UK research groups. Provide access to state-of-the-art microarray platforms for expression profiling and other genomics applications. Develop methodologies, especially in terms of quality control, normalisation, quantification and data analysis, that will be broadly applicable to the design and implementation of genomics experiments in metazoans. As a complex eukaryote with a compact genome, the Drosophila model is ideally suited to such a role. To expand the scope of the genomics resources to enable the community to encompass the use of whole genome arrays for expression profiling, transcription factor binding studies and chromatin structure studies. To develop a more cohesive interaction with members of the community who require access to genomics tools. We wish offer a flexible and interactive service for UK researchers, accommodating those who need access to reagents to perform their own genomics studies or hosting researchers within the facility for more complex studies. Utilise Drosophila as a model for establishing an effective metazoan systems biology platform. To form multidisciplinary collaborations aimed at developing new genomics techniques and informatics methods. Take a proactive role in the creation of international public genomics resources that benefit not only the UK research community, but also, through the development of international standards and resources, the world wide fly community. Overview This microarray format is no longer available. Each microarray contains 18,240 elements (or ''spots''). This array is composed of transcript-specific oligonucleotides and controls developed by the International Drosophila Array Consortium (INDAC). These controls include spikes, i.e., probes complementatary to targets in A. thaliana, spotting buffer, and probe degradation. Empty wells in the INDAC set are also printed. The spot layout is randomised to facilitate correction of systematic biases. The spots have an estimated mean diameter of 90-120 m. Gene Expression Omnibus (GEO) accession: GPL5016 Materials and Equipment FL002 microarrays were printed using the Genetix Qarray2 contact-printing instrument and 48 Genetix aQu75 split-pins on FMB PowerMatrix slides. Probe DNA was dissolved in 150 mM NaPO4. The printed oligo-set consisted of: A gene-specific Drosophila melanogaster 70mer long oligonucleotide set prepared in conjunction with INDAC (INDAC) Gene-specific Arabidopsis thaliana 70mer long oligonucleotide spike controls developed by FlyChip (protocols) and prepared in conjunction with INDAC (INDAC) 70mer probe degradation long oligonucleotide set prepared in conjunction with INDAC (INDAC) Sponsor. DH is funded by a Grand Challenges in Global Health grant to a consortium led by Austin Burt.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 17,2023. Affymetrix is a partially commercial resource that provides DNA Analysis Arrays, Expression Analysis Arrays, Gene Regulation Analysis, and Microarrays. It also provides reagents and assays, instruments, software, and services for a fee. Information is provided for Rats, Humans, and Mice.Affymetrix is now Applied Biosystems, brand of DNA microarray products sold by Thermo Fisher Scientific that originated with an American biotechnology research and development and manufacturing company of the same name.
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