Evolution of insect hindwing morphology: A comparative genomic analysis of targets of Hox protein Ultrabithorax
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ABSTRACT:
ORGANISM(S): Apis mellifera
PROVIDER: GSE71847 | GEO | 2016/08/31
SECONDARY ACCESSION(S): PRJNA292309
REPOSITORIES: GEO
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Project description:Hox proteins are transcription factors and key regulators of segmental identity along the anterior posterior axis across all bilateral animals. Despite decades of research, mechanism by which Hox proteins select their targets and specify segmental identity remains elusive. To address this question we carried out whole genome ChIP-chip experiments to identify direct targets of Hox protein Ultrabithorax (Ubx) during haltere development in Drosophila. When mis-expressed in wing segment (T2) Ubx converts its identity to that of haltere segment (T3). We used CbxHm/+ wing discs ectopically expressing Ubx in the pouch region of discs to obtain chromatin. This helped us focus on targets of Ubx involved in pouch development without mixing with the targets involved in notum development. Polyclonal Ubx antibodies against N-terminal region (excluding homeodomain) were generated in our lab and used to pull down Ubx bound regions from CbxHm/+ wing discs. Mock DNA (No antibody) was used as control. Test Vs. Mock experiment. CbxHm/+ discs for Chromatin source. Biological replicates: 3 [Agilent two-color ChIP-on-Chip experiment,Organism: Drosophila melanogaster ,Drosophila Whole Genome ChIP-on-Chip Set 244K Microarray 1 of 2 (AMADID: 014816 and 014817)]
2011-12-22 | E-GEOD-28778 | biostudies-arrayexpress
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:Hox proteins are transcription factors and key regulators of segmental identity along the anterior posterior axis across all bilateral animals. Despite decades of research, mechanism by which Hox proteins select their targets and specify segmental identity remains elusive. To address this question we carried out whole genome ChIP-chip experiments to identify direct targets of Hox protein Ultrabithorax (Ubx) during haltere development in Drosophila. When mis-expressed in wing segment (T2) Ubx converts its identity to that of haltere segment (T3). We used CbxHm/+ wing discs ectopically expressing Ubx in the pouch region of discs to obtain chromatin. This helped us focus on targets of Ubx involved in pouch development without mixing with the targets involved in notum development. Polyclonal Ubx antibodies against N-terminal region (excluding homeodomain) were generated in our lab and used to pull down Ubx bound regions from CbxHm/+ wing discs. Mock DNA (No antibody) was used as control.
2011-12-22 | GSE28778 | GEO
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.
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Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis. We have employed ChIP followed by illumina sequencing to identify the targets of Ubx in developing hind and fore wing buds of Bombyx larvae. This is a first next generation sequencing study in Lepidoptera in an attempt to understand wing development. Chromatin Immunoprecipitation (ChIP) was used to identify genome wide targets bound by Ubx in Bombyx larval wing buds. The experiment to enrich Ubx bound regions was carried out using a Bombyx N terminal-Ubx specific poylclonal antibody raised in Rabbit and purified against a Protein A column to obtain IgG fraction. An Immunoprecipitation (IP) with Normal Rabbit IgG was used as a negative control to eliminate the regions that pertained to non specific binding to an Immunogloubulin. The normalization of both ChIP and IgG was done against sequenced input chromatin. Two replicates of single end 36 bp reads were sequenced using Ilumina for all the three conditions and for both fore and hind wing tissue samples.The peaks common to both the replicates were considered after applying a FDR cutoff.The fore wing target set was used for comparison with the hind wing targets.
2016-07-27 | E-GEOD-71990 | 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.
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Project description:We investigated the transcriptional profile in Drosophila wing and haltere imaginal discs to identify differentialy expressed genes between the two tissues.
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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.
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Project description:Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis. We have employed ChIP followed by illumina sequencing to identify the targets of Ubx in developing hind and fore wing buds of Bombyx larvae. This is a first next generation sequencing study in Lepidoptera in an attempt to understand wing development.
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