Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA248308 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters M-bM-^@M-^S one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genesM-bM-^@M-^Y core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome. STARR-seq was performed in S2 and OSC cells using two core promoters each representing housekeeping and developmental transcription programs. Data for housekeeping promoters (hkCP) are presented in this series; Data for developmental core promoters (dCP) samples are presented in GSE40739.
2014-12-10 | E-GEOD-57876 | biostudies-arrayexpress
Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters – one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genes’ core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.
2014-12-10 | GSE57876 | GEO
Project description:Multicellular development is largely determined by transcriptional regulatory programs that orchestrate the expression of thousands of protein-coding and noncoding genes. To decipher the genomic regulatory code that specifies these programs, and to investigate globally the developmental relevance of noncoding transcription, we profiled genome-wide promoter activity throughout embryonic development in 5 Drosophila species. We show that core promoters, generally not thought to play a significant regulatory role, in fact impart broad restrictions on the developmental timing of gene expression on a genome-wide scale. We propose a hierarchical model of transcriptional regulation during development in which core promoters define broad windows of opportunity for expression, by defining a limited range of transcription factors from which they are able to receive regulatory inputs. This two-tiered mechanism globally orchestrates developmental gene expression, including noncoding transcription on a scale that defies our current understanding of ontogenesis. Indeed, noncoding transcripts are far more prevalent than ever reported before, with ~4,000 long noncoding RNAs expressed during embryogenesis. Over 1,500 are functionally conserved throughout the melanogaster subgroup, and hundreds are under strong purifying selection. Overall, this work introduces a hierarchical model for the developmental regulation of transcription, and reveals the central role of noncoding transcription in animal development.
2017-12-19 | GSE89299 | GEO
Project description:Nuclear Pores provide a scaffold for induced enhancer promoter contacts
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Project description:Developmental regulation of piRNAs during spermatogenesis in Drosophila melanogaster
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Project description:A sequence-specific core promoter binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes
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Project description:Eukaryotic genome is compartmentalized into structural and functional domains. One of the concepts of higher order organization of chromatin posits that the DNA is organized in constrained loops that behave as independent functional domains. A predominantly ribo-proteinaceous nucleoskeleton, termed as Nuclear Matrix (NuMat) is proposed to provide the structural platform for attachment of these loops. The DNA sequence located at the base of the loops are known as the Matrix Attachment Regions (MARs). NuMat relates to all nuclear processes and has been shown to be cell type specific in composition. It is a biochemically defined structure and several protocols have been used to isolate the NuMat where some of the steps have been critically evaluated. In the present study we have looked into the dynamics of MARs when the isolation process is varied and also during embryonic development of D. melanogaster. Our results show that a subset of MARs termed here as “Core-MARs” are fixed and unalterable anchor points in the Drosophila genome as they remain associated with NuMat at all developmental stages and do not depend on the isolation procedure used. Core-MARs are abundant in the pericentromeric heterochromatin. On the other hand, MARs in the euchromatin are dynamic and reflect the transcriptomic profile of the developmental stage of the host cell. New MARs are generated by nuclear stabilization (a critical step in the isolation procedure), and during development, mostly at the paused RNA polymerase II (Pol II) promoters. Paused Pol II MARs depend on RNA transcription for NuMat association. RNase A treatment leads to collapse of the NuMat and loss of paused Pol II promoter MARs. Our data reveals the role of MARs in functional compartmentalization of D. melanogaster genome and adds to the current understanding of nuclear architecture and 3D organization of a functionally dynamic nucleus.
2022-10-25 | PXD031279 | Pride
Project description:Hormone-dependent control of developmental timing through regulation of chromatin accessibility
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Project description:Genome-wide quantitative core promoter activity maps reveal a wide range of sequence-intrinsic transcription initiation strengths
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Project description:One model for how cells integrate cis-regulatory information is that housekeeping and developmental core promoters respond specifically to certain types of enhancers or chromatin features at different chromosomal locations. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled at different genomic locations. We further show that core promoter scaling is a genome-wide phenomenon by testing six core promoters at thousands of locations across the genome. While the rank order of core promoters is preserved, the scaling of expression across the genome is non-linear and depends on the genomic location and the strength of the core promoter, but not on its class, suggesting that housekeeping and developmental promoters do not make different interactions with the surrounding genomic environment. Instead, our results support a modular genome in which genomic environments containing different enhancers and chromatin features scale the activities of core promoters in an independent, but non-linear manner.
2021-05-01 | GSE173678 | GEO