Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA270631 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1721320.fastq.gz | Fastqsanger.gz | |||
| SRR1721321.fastq.gz | Fastqsanger.gz | |||
| SRR1721314.fastq.gz | Fastqsanger.gz | |||
| SRR1721315.fastq.gz | Fastqsanger.gz | |||
| SRR1721316.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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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 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.
2016-01-01 | GSE64284 | GEO
Project description:Elucidating how chromatin organization influences gene expression patterns and ultimately cell fate is fundamental to understanding development and disease. Histone variants have emerged as key regulators of genome function by creating specialized chromatin domains. The histone variant H2AZ plays an essential, but poorly understood function during early mammalian development. Genome-wide analysis reveals that H2AZ is enriched at a large class of developmentally important genes that are known targets of Polycomb-mediated repression in embryonic stem (ES) cells. H2AZ displays a highly defined spatial patterning that is remarkably similar to the Polycomb group (PcG) protein Suz12 in ES cells, but not in differentiated cell types. By using RNA interference, we demonstrate that H2AZ is a critical regulatory component at developmental genes in ES cells and show that localization of H2AZ and PcG proteins is interdependent at target promoters. Moreover, similarly to Suz12, H2AZ is required for lineage commitment. This study reveals a connection between H2AZ and PcG proteins in ES cells and suggests that these factors functionally interact to regulate chromatin states necessary for the proper execution of developmental gene expression programs.
2009-01-22 | E-TABM-556 | 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
Project description:Identification of targets of Ultrabithorax
| PRJNA89933 | ENA
Project description:ABSTRACT Polycomb group (PcG) proteins are essential for the repression of key developmental regulators during development. In Drosophila, the polycomb repressive complexes (PRC) associate with defined DNA sequences termed polycomb response elements (PREs). In mammals, however, the mechanisms underlying polycomb recruitment at targeted loci are poorly understood. We have used an in vivo approach to try and map DNA sequences of importance for the proper recruitment of polycomb proteins within the genetically well-characterized HoxD genomic locus. Here, we report that relatively small polycomb interacting sequences appear necessary and sufficient to confer polycomb recognition and targeting to ectopic loci. These elements synergize, when clustered together, to form a fully functional repressive domain. In addition, a high GC content, while not sufficient to recruit PRC2, may help its local spreading. We discuss the importance of PRC2 recruitment over Hox gene clusters, in embryonic stem cells, for their subsequent coordinated transcriptional activation during development. ChIP-chip using K27 antibodies
2015-01-27 | E-GEOD-43915 | biostudies-arrayexpress
Project description:Understanding the regulatory genome remains a significant challenge. Annotation of regulatory elements and identification of the transcription factors (TFs) targeting these elements are key steps in understanding how a given cell interprets its genetic blueprint. One goal of the modENCODE (model organism Encyclopedia of DNA Elements) project is to survey a diverse sampling of TFs, both DNA-binding and non-DNA binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also suggest the existence of a partially self-contained Polycomb regulatory network, and highlight the importance of Trithorax-like (Trl) in maintaining hotspots of DNA binding throughout development. Furthermore, the data identify over 5,800 instances in which TFs target DNA regions with demonstrated enhancer activity. Regions of high TF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. A putative regulatory network generated based on these 84 regulators reveals hundreds of co-binding events, thousands of potential regulatory interactions, and distinct regulatory strategies at developmental and housekeeping genes. These data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago.
2013-08-16 | E-GEOD-49899 | biostudies-arrayexpress
Project description:Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.
2022-05-13 | GSE196526 | GEO
Project description:Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.
2022-05-13 | GSE150906 | GEO
Project description:Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.
2022-05-13 | GSE150905 | GEO