Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA97603 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Cellular memory is maintained at the Drosophila homeotic gene clusters by cis-regulatory elements who mechanism of action is unknown. We have examined chromatin dynamics in the Drosophila genome by measuring histone turnover levels at high resolution. Surprisingly, homeotic gene clusters display characteristic histone turnover profiles with conspicuous peaks at boundaries of cis-regulatory domains superimposed over regions of very low turnover. Peaks of histone turnover precisely correspond to nuclease hypersensitive sites for epigenetic silencing proteins. Our results suggest that epigenetic regulation is facilitated by histone turnover, which maintains continuous accessibility ov cis-regulatory DNA. Keywords: Chromatin affinity-purification on microarray
2007-03-01 | GSE6234 | GEO
Project description:The bithorax complex (BX-C) in the fruit fly, Drosophila melanogaster, is a cluster of homeotic genes that determines the identities the body segments. Expression of these genes is governed by cis-regulatory domains, one for each parasegment, which are arranged on the chromosome in the order of the parasegments they affect. Stable repression of these domains depends on the functions of the Polycomb Group, including its ability to methylate lysine 27 of histone H3. To learn whether PcG proteins generate parasegment-specific chromatin signatures, we have used transgenes to mark and isolate nuclei from single parasegments. These nuclei were profiled for histone modifications and chromatin proteins. The H3K27me3 profiles across the BX-C in successive parasegments show a striking “stairstep” pattern that reveals sharp boundaries of the BX-C regulatory domains. The borders of H3K27me3 modification domains are sharp, and align precisely with binding sites for the CCCTC-binding protein (CTCF). H3K27ac is broadly enriched across active domains, in a pattern complementary to K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely localized H3K27 modification as a central determinant of segment identity. Nuclei from single parasegments of the Drosophila embryo were isolated and ChIP-seq performed for H3K27me3, CTCF, H3K27ac, H3K4me3, Ph, Pol2, Pc, and Suz12. For each sample, two biological replicates were performed.
2014-08-14 | E-GEOD-55257 | biostudies-arrayexpress
Project description:The mechanisms responsible for the establishment of physical domains in metazoan chromosomes are poorly understood. Here we find that physical domains in Drosophila chromosomes are demarcated at regions of active transcription and high gene density that are enriched for transcription factors and specific combinations of insulator proteins. Physical domains contain different types of chromatin defined by the presence of specific proteins and epigenetic marks, with active chromatin preferentially located at the borders and silenced chromatin in the interior. Domain boundaries participate in long-range interactions that may contribute to the clustering of regions of active or silenced chromatin in the nucleus. Analysis of transgenes suggests that chromatin is more accessible and permissive to transcription at the borders than inside domains, independent of the presence of active or silencing histone modifications. These results suggest that the higher-order physical organization of chromatin may impose an additional level of regulation over classical epigenetic marks.
2012-10-04 | GSE38468 | GEO
Project description:The mechanisms responsible for the establishment of physical domains in metazoan chromosomes are poorly understood. Here we find that physical domains in Drosophila chromosomes are demarcated at regions of active transcription and high gene density that are enriched for transcription factors and specific combinations of insulator proteins. Physical domains contain different types of chromatin defined by the presence of specific proteins and epigenetic marks, with active chromatin preferentially located at the borders and silenced chromatin in the interior. Domain boundaries participate in long-range interactions that may contribute to the clustering of regions of active or silenced chromatin in the nucleus. Analysis of transgenes suggests that chromatin is more accessible and permissive to transcription at the borders than inside domains, independent of the presence of active or silencing histone modifications. These results suggest that the higher-order physical organization of chromatin may impose an additional level of regulation over classical epigenetic marks. We carried out Hi-C experiment using HindIII on Kc167 cells and generate two libraries separately. One library was sequenced once more as technical replicates (TR1 and TR2), the other library was sequenced as biological replicate (BR). processed files contain the following: Column 1: chromosome ID in which the first read in a pair locates Column 2: coordinate of the first read Column 3: chromosome ID in which the second read in a pair locates Column 4: coordinate of the second read
2012-10-04 | E-GEOD-38468 | biostudies-arrayexpress
Project description:The bithorax complex (BX-C) in the fruit fly, Drosophila melanogaster, is a cluster of homeotic genes that determines the identities the body segments. Expression of these genes is governed by cis-regulatory domains, one for each parasegment, which are arranged on the chromosome in the order of the parasegments they affect. Stable repression of these domains depends on the functions of the Polycomb Group, including its ability to methylate lysine 27 of histone H3. To learn whether PcG proteins generate parasegment-specific chromatin signatures, we have used transgenes to mark and isolate nuclei from single parasegments. These nuclei were profiled for histone modifications and chromatin proteins. The H3K27me3 profiles across the BX-C in successive parasegments show a striking “stairstep” pattern that reveals sharp boundaries of the BX-C regulatory domains. The borders of H3K27me3 modification domains are sharp, and align precisely with binding sites for the CCCTC-binding protein (CTCF). H3K27ac is broadly enriched across active domains, in a pattern complementary to K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely localized H3K27 modification as a central determinant of segment identity.
2014-08-14 | GSE55257 | GEO
Project description:We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter ChIP-seq analysis of histone marks and chromatin associated factors across 4-5 Drosophila species
2014-10-20 | E-GEOD-60428 | biostudies-arrayexpress
Project description:Histone turnover mediates epigenetic processes in Drosophila S2 cells
| PRJNA95249 | ENA
Project description:We developed a system to study the DNA replication-independent turnover nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosome turnover in vivo: rapid turnover, intermediate turnover and, specifically at telomeres, slow turnover. Our data indicate that H3.3-containing nucleosomes at enhancers and promoters undergo a rapid turnover that is associated with active histone modification marks including H3K4me1, H3K4me3, H3K9ac, H3K27ac and the histone variant H2A.Z. The rate of turnover is negatively correlated with H3K27me3 at regulatory regions and with H3K36me3 at gene bodies. Examination of incorporation dynamics of histone variant H3.3
2013-10-23 | E-GEOD-51505 | biostudies-arrayexpress
Project description:Animal genomes fold into contact domains defined by enhanced internal contact frequencies with debated functions in establishing independent gene regulatory domains. A large fraction of contact domains in mammals are formed by stalling of chromosomal loop-extruding cohesin by CTCF at domain boundaries. 90% of domain boundaries in Drosophila form CTCF-independently, and other proteins were proposed to form chromosomal loops with dual functions of segregating promoters from inappropriate regulatory elements and connecting distal regulatory elements to their correct targets. Here, we genetically ablate the ubiquitous boundary-associated factor Cp190 and assess impacts on genome folding and transcriptional regulation in embryos. Our results reveal that Cp190 is a major factor required for contact domain boundary formation and gene insulation in Drosophila.
2022-05-30 | PXD027795 | Pride
Project description:The cis-regulatory code of Hox function in Drosophila
| PRJNA297176 | ENA