CTCF binding profiles in Drosophila melanogaster 3rd instar larva T1 and T3 leg discs
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE62234 | GEO | 2014/10/11
SECONDARY ACCESSION(S): PRJNA263558
REPOSITORIES: GEO
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Project description:Although the majority of genomic binding sites for the insulator protein CTCF are constitutively occupied, a subset show variable occupancy. Such variable sites provide an opportunity to assess context-specific CTCF functions in gene regulation. Here we have identified a variably occupied CTCF site in the Ultrabithorax (Ubx) gene in Drosophila. This site is occupied in tissues where Ubx is active (third thoracic imaginal leg disc) but is not bound in tissues where the Ubx gene is repressed (first thoracic imaginal leg disc). Comparison of CTCF binding in T1 leg disc vs T3 leg disc in from 3rd instar larva
2014-10-11 | E-GEOD-62234 | biostudies-arrayexpress
Project description:The Hox genes are responsible for generating morphological diversity along the anterior-posterior axis during animal development. The Drosophila Hox gene Ultrabithorax (Ubx), for example, is required for specifying the identity of the third thoracic (T3) segment of the adult, which includes the dorsal haltere, an appendage required for flight, and the ventral T3 leg. Ubx mutants show homeotic transformations of the T3 leg towards the identity of the T2 leg and the haltere towards the wing. All Hox genes, including Ubx, encode homeodomain containing transcription factors, raising the question of what target genes Ubx regulates to generate these adult structures. To address this question, we carried out whole genome ChIP-chip studies to identify all of the Ubx bound regions in the haltere and T3 leg imaginal discs, which are the precursors to these adult structures. In addition, we used ChIP-chip to identify the sites bound by the Hox cofactor, Homothorax (Hth). This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This dataset was generated in collaboration with Richard S. Mann at Columbia University. It contains ChIP-chip data on Affymetrix Drosophila Tiling 2.0R arrays for multiple transcription factor antibodies in multiple Drosophila tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Haltere or leg imaginal discs ChIPped for Ubx or Hth vs. input DNA from corresponding imaginal discs. For each combination of tissue and antibody, ChIP experiments have been performed and hybridized on Affymetrix Drosophila Tiling 2.0R arrays. At least 3 biological replicates for the ChIP sample have been hybridized.
2011-01-21 | E-GEOD-26793 | biostudies-arrayexpress
Project description:We profiled the chromatin accessibility, transcription factor binding, and gene expression in the homologous wing and haltere imaginal disc of Drosophila melanogaster, which are distinguished by the expression of the Hox protein Ultrabithorax (Ubx). Through the analysis of chromatin changes, we show Ubx has widespread effects on the chromatin landscape to specify cell identity.
2021-05-18 | GSE166714 | GEO
Project description:The Hox genes are responsible for generating morphological diversity along the anterior-posterior axis during animal development. The Drosophila Hox gene Ultrabithorax (Ubx), for example, is required for specifying the identity of the third thoracic (T3) segment of the adult, which includes the dorsal haltere, an appendage required for flight, and the ventral T3 leg. Ubx mutants show homeotic transformations of the T3 leg towards the identity of the T2 leg and the haltere towards the wing. All Hox genes, including Ubx, encode homeodomain containing transcription factors, raising the question of what target genes Ubx regulates to generate these adult structures. To address this question, we carried out whole genome ChIP-chip studies to identify all of the Ubx bound regions in the haltere and T3 leg imaginal discs, which are the precursors to these adult structures. In addition, we used ChIP-chip to identify the sites bound by the Hox cofactor, Homothorax (Hth). This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This dataset was generated in collaboration with Richard S. Mann at Columbia University. It contains ChIP-chip data on Affymetrix Drosophila Tiling 2.0R arrays for multiple transcription factor antibodies in multiple Drosophila tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2011-01-21 | GSE26793 | GEO
Project description:We have developed SpyChIP, a method that depends on covalent isopeptide bond formation, to identify sites of cell type-specific transcription factor (TF) occupancy in native physiological contexts without tissue dissociation or nuclei sorting. Using SpyChIP, we characterized the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two non-overlapping domains of the Drosophila haltere imaginal disc, revealing extensive region-specific Ubx-DNA binding events. The application of cell type-specific covalent bond formation to ChIP sets the stage for carrying out many other cell type-specific analyses and genetic manipulations in vivo that were previously unachievable.
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Project description:Adult leg muscle precursors are associated to leg imaginal disc, here we provide bulk RNA sequecing of FACS sorted myoblasts from dissected imaginal leg discs at beginning of pupation.
2024-06-28 | GSE245192 | GEO
Project description:Hox proteins have been proposed to act at multiple levels within regulatory hierarchies and to directly control the expression of a plethora of target genes. However, for any specific Hox protein or tissue, very few direct in vivo-regulated target genes have been identified. Here, we have identified target genes of the Hox protein Ultrabithorax (UBX), which modifies the genetic regulatory network of the wing to generate the haltere, a modified hindwing. We used whole-genome microarrays and custom arrays including all predicted transcription factors and signaling molecules in the D. melanogaster genome to identify differentially expressed genes in wing and haltere imaginal discs. To elucidate the regulation of selected genes in more detail, we isolated cis-regulatory elements (CREs) for genes that were specifically expressed in either the wing disc or haltere disc. We demonstrate that UBX binds directly to sites in one element, and these sites are critical for activation in the haltere disc. These results indicate that haltere and metathoracic segment morphology is not achieved merely by turning off the wing and mesothoracic development programs, but rather specific genes must also be activated to form these structures. The evolution of haltere morphology involved changes in UBX-regulated target genes, both positive and negative, throughout the wing genetic regulatory network. Keywords: tissue comparison
2006-11-23 | GSE6307 | GEO
Project description:We aim to identify the genes that encode for putatives smORF peptides in imaginal leg disc at larval and pupal stages
2023-10-09 | GSE225561 | GEO
Project description:Hox homeodomain transcription factors are key regulators of animal development. They specify the identity of segments along the anterior-posterior body axis in metazoans by controlling the expression of diverse downstream targets, including transcription factors and signaling pathway components. The Drosophila melanogaster Hox factor Ultrabithorax (Ubx) directs the development of thoracic and abdominal segments and appendages, and loss of Ubx function can lead for example to the transformation of third thoracic segment appendages (e.g. halters) into second thoracic segment appendages (e.g. wings), resulting in a characteristic four-wing phenotype. Here we present a Drosophila melanogaster strain with a V5-epitope tagged Ubx allele, which we employed to obtain a high quality genome-wide map of Ubx binding sites using ChIP-seq. We confirm the sensitivity of the V5 ChIP-seq by recovering 7/8 of well-studied Ubx-dependent cis-regulatory regions. Moreover, we show that Ubx binding is predictive of enhancer activity as suggested by comparison with a genome-scale resource of in vivo tested enhancer candidates. We observed densely clustered Ubx binding sites at 12 extended genomic loci that included ANTP-C, BX-C, Polycomb complex genes, and other regulators and the clustered binding sites were frequently active enhancers. Furthermore, Ubx binding was detected at known Polycomb response elements (PREs) and was associated with significant enrichments of Pc and Pho ChIP signals in contrast to binding sites of other developmental TFs. Together, our results show that Ubx targets developmental regulators via strongly clustered binding sites and allow us to hypothesize that regulation by Ubx might involve Polycomb group proteins to maintain specific regulatory states in cooperative or mutually exclusive fashion, an attractive model that combines two groups of proteins with prominent gene regulatory roles during animal development. Ubx was endogenously tagged with V5 epitope in Drosophila melanogaster (Ubx-V5). ChIP-seq was performed with chromatin from 0-16 hrs wild type and Ubx-V5 embryos. The samples were subjected to single-end sequencing in two replicates.
2016-07-03 | E-GEOD-64284 | biostudies-arrayexpress
Project description:Hox genes encode a family of transcription factors that are key developmental regulators with a highly conserved role in specifying segmental diversity along the metazoan body axis. Although they have been shown to regulate a wide variety of downstream processes, direct transcriptional targets have been difficult to identify and this has been a major obstacle to our understanding of Hox gene function. Here we report the use of a YFP-tagged Drosophila protein-trap line together with chromatin immunoprecipitation and microarray analysis to identify genome-wide binding sites for the Hox protein Ultrabithorax (Ubx). We find 1,147 genes bound by Ubx in chromatin from the haltere imaginal disc, a prominent site of Ubx function where it specifies haltere versus wing development. The functional relevance of these genes is supported by their overlap with genes showing differential expression between wing and haltere imaginal discs. The Ubx-bound genes are highly enriched in genes involved in developmental processes. They contain both high-level regulatory genes as well as genes involved in more basic cell functions supporting the idea that Hox genes regulate many levels of developmental pathways. Several signalling pathways are highly enriched and within these pathways Ubx target genes occur at multiple level from ligands to transcriptional effectors. We also performed genome-wide analysis of the binding sites for the Hox cofactor Homothorax (Hth), revealing a striking similarity in the binding profiles of Hth and Ubx. We suggest that these binding profiles may be strongly influenced by chromatin accessibility and we provide evidence of a clear link between Ubx/Hth binding and the chromatin state at genes regulated by Polycomb silencing. The role of chromatin accessibility has important implications for Hox gene function and for genomic target selection by transcription factors in general.
2011-04-14 | GSE23864 | GEO