Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA93137 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Drosophila heterochromatin protein 1- HP11 is believed to be involved in active transcription, transcriptional gene silencing, and the formation of heterochromatin2-7. However, little is known about the function of HP1 during development. Using a Gal4-induced RNA interference system, we show that conditional depletion of HP1 in transgenic flies results in preferential lethality in male flies. Cytological analysis of mitotic chromosomes reveals that HP1 depletion causes sex-biased chromosomal defects, including telomere fusions. The global levels of specific histone modifications, particularly the hallmarks of active chromatin, are preferentially increased in males as well. Expression analysis revealed that approximately twice as many genes are specifically regulated by HP1 in males compared to females. Furthermore, HP1-regulated genes showed greater enrichment for HP1 binding in males. Taken together, these results reveal that HP1 modulates chromosomal integrity, histone modifications, and transcription in a sex-specific manner. Keywords: sex-specific, HP1, gender comparison
2005-08-05 | GSE3055 | GEO
Project description:Drosophila X chromosomes are subject to dosage compensation in males and are known to have a specialized chromatin structure in the male soma. We are interested in how specific chromatin structure change contributes to X chromosome hyperactivity and dosage compensation. We have conducted a global analysis of localize two dosage compensation complex dependent histone marks H4AcK16 and H3PS10 and one dosage compensation complex independent histone mark H3diMeK4 in the genome, especially on X chromosome by ChIP-chip approach in both male and female adult flies. We also probed general genomewide chromatin structure by deep DNA sequencing of sheared ChIP input DNA from male and female adult flies. Chromatin immunoprecipitations were performed in 5-7 day aged adult male and female flies with three histone modification antibodies. ChIP enriched DNA and input DNA was labeled by Cy3 or Cy5 dye separately and hybridized simultaneously to the Drosophila FlyGEM arrays. At least two biological replicates were performed for each antibody and sex. DNA-seq (NIDDK-Drosophila-Illumina-DNASeq) were performed on ChIP-input sheared DNA to check the general chromatin structure of different chromosome.
2010-01-11 | E-GEOD-15593 | biostudies-arrayexpress
Project description:Nucleus is a highly structured organelle and contains many functional compartments. While the structural basis for this complex spatial organization of compartments is unknown, a major component of this organization is likely to be the non-chromatin scaffolding called nuclear matrix (NuMat). Experimental evidence over the past decades indicates that most of the nuclear functions are at least transiently associated with the NuMat although the components of NuMat itself are poorly known. Here, we report NuMat proteome analysis from Drosophila melanogaster embryos and discuss its links with nuclear architecture and functions. In the NuMat proteome, we find structural proteins, chaperones related, DNA/RNA binding, chromatin remodeling and transcription factors. This complexity of NuMat proteome is an indicator of its structural and functional significance. Comparison of the 2D profile of NuMat proteome from different developmental stages of Drosophila embryos shows that less than half of the NuMat proteome is constant and rest of the proteins are stage specific dynamic components. This NuMat dynamics suggests a possible functional link between NuMat and the embryonic development. Finally, we also show that a subset of NuMat proteins remain associated with the mitotic chromosomes implicating their role in mitosis and possibly the epigenetic cellular memory. NuMat proteome analysis provides tools and opens up ways to understand nuclear organization and function.
2011-05-05 | PRD000255 | Pride
Project description:Heterochromatin protein 1 (HP1) modulates replication timing of Drosophila heterochromatin
| PRJNA119379 | ENA
Project description:Drosophila melanogaster sex transformed larval gonads
| PRJNA659550 | ENA
Project description:Chromatin structure marks cell-type and gender specific replication of the Drosophila genome
| PRJNA109923 | ENA
Project description:HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila
| PRJNA99549 | ENA
Project description:Drosophila heterochromatin protein 1- HP1 is believed to be involved in active transcription, transcriptional gene silencing, and the formation of heterochromatin2-7. However, little is known about the function of HP1 during development. Using a Gal4-induced RNA interference system, we show that conditional depletion of HP1 in transgenic flies results in preferential lethality in male flies. Cytological analysis of mitotic chromosomes reveals that HP1 depletion causes sex-biased chromosomal defects, including telomere fusions. The global levels of specific histone modifications, particularly the hallmarks of active chromatin, are preferentially increased in males as well. Expression analysis revealed that approximately twice as many genes are specifically regulated by HP1 in males compared to females. Furthermore, HP1-regulated genes showed greater enrichment for HP1 binding in males. Taken together, these results reveal that HP1 modulates chromosomal integrity, histone modifications, and transcription in a sex-specific manner. Overall design. The extraction of total RNA was performed following a standard protocol (www.erin.utoronto.ca/~w3flyma/protocol.htm). Total RNA was isolated from two independent populations of male and female 3rd-instar larva of HP1-21/act-Gal4 and, as controls, larval progenies from line HP1-21 with the genotype y w; +/+; HP1-21/+, and larva with the genotype y w; + /+; +/act-Gal4. In brief, larvaa frozen in liquid nitrogen were homogenized and then resuspended in Trizol reagent by pipetting. The precipitated RNA was washed, and then dissolved in RNase-free water. Five micrograms of total RNA from each experimental sample were reverse-transcribed using the SuperScript Choice cDNA synthesis kit from Stratagene. One microgram of double-stranded cDNA was in vitro-transcribed using the Affymetrix IVT kit and labeled by the incorporation of biotinylated-UTP. Fifteen micrograms of cRNA were then fragmented and hybridized to Affymetrix DGv2 GeneChips as per the manufacturers instructions (Affymetrix, Santa Clara CA, USA).
2007-08-01 | E-GEOD-3055 | biostudies-arrayexpress
Project description:Heterochromatin-associated interactions of Drosophila HP1 with dADD1, HIPP1, and repetitive RNAs
| PRJNA243597 | ENA
Project description:Heterochromatin protein HP1 is thought to play key role in chromatin structure and gene regulation. We performed a genome-wide mapping of HP1 target genes in the non-polytenic Drosophila Kc cells by using DamID. This approach is based on the ability of a chromatin protein fused to Escherichia coli DNA adenine methyltransferase (Dam) to methylate the native binding site of the chromatin protein. Dam-fusion proteins are expressed at very low levels to avoid mistargeting. Subsequently, methylated DNA fragments are isolated, labeled (using Cy3 or Cy5) and hybridized to a microarray. Methylated DNA fragments from cells transfected with Dam alone served as reference. Genomic binding sites of the protein can then be identified based on the targeted methylation pattern. For detailed background information on DamID, see: van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-8 (2001); van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8 (2000). We performed three independent replicates. We used for this study a cDNA array developed by the GeneCore facility in EMBL (Heidelberg, Germany), covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.
2007-07-05 | E-MEXP-864 | biostudies-arrayexpress